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DeSantis AH, Buss K, Coker KM, Pasternak BA, Chi J, Patterson JS, Gu H, Jurutka PW, Sandrin TR. Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD). Biomolecules 2025; 15:746. [PMID: 40427639 DOI: 10.3390/biom15050746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2025] [Revised: 05/16/2025] [Accepted: 05/17/2025] [Indexed: 05/29/2025] Open
Abstract
Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.
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Affiliation(s)
- Anita H DeSantis
- School of Mathematical and Natural Sciences, Arizona State University, 4701 W. Thunderbird Rd, Glendale, AZ 85306, USA
| | - Kristina Buss
- Biosciences Core, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85281, USA
| | - Keaton M Coker
- School of Mathematical and Natural Sciences, Arizona State University, 4701 W. Thunderbird Rd, Glendale, AZ 85306, USA
| | - Brad A Pasternak
- Phoenix Children's Hospital, 1919 E. Thomas Rd, Phoenix, AZ 85016, USA
| | - Jinhua Chi
- College of Health Solutions, Health North Building, Arizona State University, 550 N. 3rd St, Suite 501, Phoenix, AZ 85004, USA
| | - Jeffrey S Patterson
- College of Health Solutions, Health North Building, Arizona State University, 550 N. 3rd St, Suite 501, Phoenix, AZ 85004, USA
| | - Haiwei Gu
- College of Health Solutions, Health North Building, Arizona State University, 550 N. 3rd St, Suite 501, Phoenix, AZ 85004, USA
| | - Peter W Jurutka
- School of Mathematical and Natural Sciences, Arizona State University, 4701 W. Thunderbird Rd, Glendale, AZ 85306, USA
- College of Medicine, University of Arizona, 475 N. 5th St, Phoenix, AZ 85004, USA
| | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, 4701 W. Thunderbird Rd, Glendale, AZ 85306, USA
- Center for Health through Microbiomes, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85281, USA
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Pretorius L, Coetzee JA, Santos APD, Smith C. Modulating autism spectrum disorder pathophysiology using a trace amine-focused approach: targeting the gut. Mol Med 2025; 31:198. [PMID: 40394473 DOI: 10.1186/s10020-025-01232-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Accepted: 04/25/2025] [Indexed: 05/22/2025] Open
Abstract
Autism spectrum disorder (ASD) affects approximately 1% of the population directly, but also a much higher proportion (family and caregivers) indirectly. Although ASD is characterized by high prevalence of anxiety and poor gastrointestinal health, current treatment strategies are mainly focused on neurological symptomatic treatment, with little to no attention to gut health. Furthermore, many psychiatric drugs used for management of secondary neurological symptoms, are known to exacerbate gut health issues and neurological dysregulation across the gut-brain axis.Trace amines are neurotransmitter-like substances synthesized endogenously in the human brain - in trace amounts - but also in high abundance by the microbiome. Emerging evidence suggests dysregulation of the trace amine system in ASD. Since trace aminergic signalling is central to regulatory system homeostasis, we hypothesize targeting this system in the ASD context. Given the various sources of trace amines, we suggest that normalization of functional dysbiosis in terms of trace aminergic signalling - rather than microbial compositional dysbiosis - should be a focus in medicines development. In addition, a holistic consideration including also other factors at play in determining trace aminergic signalling outcome - such as receptor binding, enzymatic role players, etc. - is required to fully elucidate and therapeutically modify the pathophysiology of regulatory systems implicated in ASD.This review firstly provides a brief overview of trace amine dysregulation in ASD for context. Secondly, we formulate our hypothesis on how this may therapeutically address symptomology, with consideration of cellular and molecular mechanism interplay across the gut-brain axis. Finally, we provide a critical assessment of advances in therapeutics development and drug re-purposing, gaps in knowledge and priorities for medicines development going forward.
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Affiliation(s)
- L Pretorius
- Experimental Medicine Group, Dept Medicine, Stellenbosch University, Parow, South Africa
| | - J A Coetzee
- Experimental Medicine Group, Dept Medicine, Stellenbosch University, Parow, South Africa
| | - A P Dos Santos
- Experimental Medicine Group, Dept Medicine, Stellenbosch University, Parow, South Africa
| | - C Smith
- Experimental Medicine Group, Dept Medicine, Stellenbosch University, Parow, South Africa.
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Petracco G, Faimann I, Reichmann F. Inflammatory bowel disease and neuropsychiatric disorders: Mechanisms and emerging therapeutics targeting the microbiota-gut-brain axis. Pharmacol Ther 2025; 269:108831. [PMID: 40023320 DOI: 10.1016/j.pharmthera.2025.108831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 02/03/2025] [Accepted: 02/23/2025] [Indexed: 03/04/2025]
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are the two major entities of inflammatory bowel disease (IBD). These disorders are known for their relapsing disease course and severe gastrointestinal symptoms including pain, diarrhoea and bloody stool. Accumulating evidence suggests that IBD is not only restricted to the gastrointestinal tract and that disease processes are able to reach distant organs including the brain. In fact, up to 35 % of IBD patients also suffer from neuropsychiatric disorders such as generalized anxiety disorder and major depressive disorder. Emerging research in this area indicates that in many cases these neuropsychiatric disorders are a secondary condition as a consequence of the disturbed communication between the gut and the brain via the microbiota-gut-brain axis. In this review, we summarise the current knowledge on IBD-associated neuropsychiatric disorders. We examine the role of different pathways of the microbiota-gut-brain axis in the development of CNS disorders highlighting altered neural, immunological, humoral and microbial communication. Finally, we discuss emerging therapies targeting the microbiota-gut-brain axis to alleviate IBD and neuropsychiatric symptoms including faecal microbiota transplantation, psychobiotics, microbial metabolites and vagus nerve stimulation.
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Affiliation(s)
- Giulia Petracco
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Isabella Faimann
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Florian Reichmann
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria; BiotechMed-Graz, Austria.
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4
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Bellocchi C, Volkmann ER. Advancing Gastrointestinal Microbiota Research in Systemic Sclerosis: Lessons Learned from Prior Research and Opportunities to Accelerate Discovery. Rheum Dis Clin North Am 2025; 51:213-231. [PMID: 40246439 DOI: 10.1016/j.rdc.2025.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2025]
Abstract
Dysbiosis is a feature of patients with systemic sclerosis (SSc). While a causal relationship between the gastrointestinal (GI) microbiota and SSc pathogenesis has not been established, alterations in the GI microbiota are appreciated early in the SSc disease course. Moreover, recent research has illuminated specific microbial signatures that define SSc phenotypes. This review summarizes new research on the GI microbiome in SSc with a focus on technical advancements and the emerging study of the GI metabolome. This review also addresses diverse modalities for manipulating the GI microbiome with the hope of developing preventative treatment strategies to avert progression of SSc.
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Affiliation(s)
- Chiara Bellocchi
- Department of Clinical Sciences and Community Health, University of Milan, Dipartimento di Eccellenza 2023-2027, Milan, Italy; Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Via Pace 9, Milano 20122, Italy
| | - Elizabeth R Volkmann
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, USA.
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Shen M, Gao S, Zhu R, Wang W, Gao W, Tao L, Chen W, Zhu X, Yang Y, Xu T, Zhao T, Jiao N, Zhi M, Zhu L. Multimodal metagenomic analysis reveals microbial InDels as superior biomarkers for pediatric Crohn's disease. J Crohns Colitis 2025; 19:jjaf039. [PMID: 40052570 DOI: 10.1093/ecco-jcc/jjaf039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/22/2025]
Abstract
BACKGROUND AND AIMS The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model. METHODS A total of 1175 fecal metagenomic sequencing samples, predominantly from 3 cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms. RESULTS We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1357 KEGG orthology genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1256 insertions/deletions (InDels), and 3567 single nucleotide variants, with a considerable portion of these variants located in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an area under the ROC curve (AUC) of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC = 0.996) and 5 other microbiome-associated pediatric cohorts. CONCLUSIONS Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of noninvasive diagnostic tools and targeted therapies.
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Affiliation(s)
- Mengping Shen
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Sheng Gao
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Ruixin Zhu
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Wei Wang
- Department of Gastroenterology, The Sixth Affiliated Hospital, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, Sun Yat-sen University, Guangzhou, P. R. China
| | - Wenxing Gao
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Liwen Tao
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Wanning Chen
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Xinyue Zhu
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Yuwei Yang
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Tingjun Xu
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Tingting Zhao
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
- Research Institute, GloriousMed Clinical Laboratory Co, Ltd, Shanghai, P. R. China
| | - Na Jiao
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Min Zhi
- Department of Gastroenterology, The Sixth Affiliated Hospital, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, Sun Yat-sen University, Guangzhou, P. R. China
| | - Lixin Zhu
- Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, P. R. China
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Weng Q, Hu M, Peng G, Zhu J. DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts. BMC Bioinformatics 2025; 26:93. [PMID: 40148806 PMCID: PMC11951675 DOI: 10.1186/s12859-025-06110-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Accepted: 03/10/2025] [Indexed: 03/29/2025] Open
Abstract
BACKGROUND Understanding the metabolic activities of the gut microbiome is vital for deciphering its impact on human health. While direct measurement of these metabolites through metabolomics is effective, it is often expensive and time-consuming. In contrast, microbial composition data obtained through sequencing is more accessible, making it a promising resource for predicting metabolite profiles. However, current computational models frequently face challenges related to limited prediction accuracy, generalizability, and interpretability. METHOD Here, we present the Deep Mixture of Variational Gaussian Process Experts (DMoVGPE) model, designed to overcome these issues. DMoVGPE utilizes a dynamic gating mechanism, implemented through a neural network with fully connected layers and dropout for regularization, to select the most relevant Gaussian Process experts. During training, the gating network refines expert selection, dynamically adjusting their contribution based on the input features. The model also incorporates an Automatic Relevance Determination (ARD) mechanism, which assigns relevance scores to microbial features by evaluating their predictive power. Features linked to metabolite profiles are given smaller length scales to increase their influence, while irrelevant features are down-weighted through larger length scales, improving both prediction accuracy and interpretability. CONCLUSIONS Through extensive evaluations on various datasets, DMoVGPE consistently achieves higher prediction performance than existing models. Furthermore, our model reveals significant associations between specific microbial taxa and metabolites, aligning well with findings from existing studies. These results highlight DMoVGPE's potential to provide accurate predictions and to uncover biologically meaningful relationships, paving the way for its application in disease research and personalized healthcare strategies.
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Affiliation(s)
- Qinghui Weng
- The State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- The School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Mingyi Hu
- The State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- The School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Guohao Peng
- The School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jinlin Zhu
- The State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.
- The School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.
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7
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Gong X, Liu D, Liu L, Yang G, Lei Y, Li N, Chen Y, Yu H, Li X, Xiang D. Plasma bile acid profile analysis by liquid chromatography-tandem mass spectrometry and its application in healthy subjects and IBD patients. J Pharm Biomed Anal 2025; 255:116639. [PMID: 39709683 DOI: 10.1016/j.jpba.2024.116639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 12/03/2024] [Accepted: 12/14/2024] [Indexed: 12/24/2024]
Abstract
Bile acids (BAs), not only promote the absorption of fat-soluble nutrients and regulate the metabolism of multiple substances but also have a potential role as diagnostic and prognostic indicators in a variety of diseases such as cholestasis, hepatocellular carcinoma, and diabetes mellitus. Here, a rapid and sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous quantification of 50 BAs was developed and validated. Sample preparation included internal standard spiking, followed by protein precipitation, centrifugation, solvent evaporation, and reconstitution. Baseline separation of all isobaric BA species was achieved on an Ultimate XS-C18 column (5 μm, 150 mm × 4.6 mm). The method showed good linearity with high regression coefficients (>0.990) with acceptable accuracy and precision for intra-day and inter-day analyses and achieved good recovery rates for representative analytes. No apparent carryover or matrix effect was observed. The analytical method was successfully applied to the determination of the plasma BA profile in healthy subjects and patients with inflammatory bowel disease (IBD). The routine instrumentation, low sample volume, simple pretreatment, wide range of BAs, and good separation make this LC-MS/MS method suitable for use as a BA profile assay in clinical and basic research studies. This method could be poised to identify possible BA biomarkers for non-invasive early diagnosis and therapeutic evaluation of IBD.
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Affiliation(s)
- Xuepeng Gong
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dong Liu
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lu Liu
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guangjie Yang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yongfang Lei
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - NingHong Li
- Department of Pharmacy, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330008, China
| | - Yufei Chen
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hengyi Yu
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiping Li
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dong Xiang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Sivakumar N, Krishnamoorthy A, Ryali H, Arasaradnam RP. Gut Microbial Targets in Inflammatory Bowel Disease: Current Position and Future Developments. Biomedicines 2025; 13:716. [PMID: 40149692 PMCID: PMC11940752 DOI: 10.3390/biomedicines13030716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Revised: 03/06/2025] [Accepted: 03/12/2025] [Indexed: 03/29/2025] Open
Abstract
Inflammatory bowel disease (IBD) is a debilitating condition in which surgery is often seen as a last resort. However, this is associated with morbidity and, in some cases, mortality. There are emerging therapies that seek to better modulate the immune response of hosts with IBD. Aims: The main aim of this study is to focus on novel therapies and techniques studied in the last year that are non-surgical treatments of IBD. Methods: We looked at all the research between March 2024 and February 2025 detailing treatment in IBD and focused on the gut microbiome and gene therapy. Results: Novel therapies are gaining traction in safety and popularity. The results from some animal studies show promise and, with FDA approval, some probiotic therapies show optimistic research potential for future human trials. Conclusions: The research into the diagnostics and novel therapies available on the horizon for humans is very promising. Animal studies have shown potentially transferrable and safe therapies that can target specific sites of inflammation. Modulating the inflammatory response is a powerful therapy with what is shown to be a reasonably safe profile to build further research on.
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Affiliation(s)
- Naveen Sivakumar
- Institute of Precision Diagnostics & Translational Medicine, University Hospitals Coventry & Warwickshire, Coventry CV2 2DX, UK;
| | | | - Harshita Ryali
- Southmead Hospital, North Bristol Trust, Bristol BS10 5NB, UK;
| | - Ramesh P. Arasaradnam
- Institute of Precision Diagnostics & Translational Medicine, University Hospitals Coventry & Warwickshire, Coventry CV2 2DX, UK;
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK;
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9
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Lins LC, DE-Meira JEC, Pereira CW, Crispim AC, Gischewski MDR, Lins-Neto MÁDF, Moura FA. FECAL CALPROTECTIN AND INTESTINAL METABOLITES: WHAT IS THEIR IMPORTANCE IN THE ACTIVITY AND DIFFERENTIATION OF PATIENTS WITH INFLAMMATORY BOWEL DISEASES? ARQUIVOS BRASILEIROS DE CIRURGIA DIGESTIVA : ABCD = BRAZILIAN ARCHIVES OF DIGESTIVE SURGERY 2025; 38:e1870. [PMID: 40052996 PMCID: PMC11870234 DOI: 10.1590/0102-6720202500001e1870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 09/01/2024] [Indexed: 03/10/2025]
Abstract
BACKGROUND Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), lacks a known etiology. Although clinical symptoms, imaging, and colonoscopy are common diagnostic tools, fecal calprotectin (FC) serves as a widely used biomarker to track disease activity. Metabolomics, within the omics sciences, holds promise for identifying disease progression biomarkers. This approach involves studying metabolites in biological media to uncover pathological factors. AIMS The purpose of this study was to explore fecal metabolomics in IBD patients, evaluate its potential in differentiating subtypes, and assess disease activity using FC. METHODS Cross-sectional study including IBD patients, clinical data, and FC measurements (=200 μg/g as an indicator of active disease). RESULTS Fecal metabolomics utilized chromatography mass spectrometry/solid phase microextraction with MetaboAnalyst 5.0 software for analysis. Of 52 patients (29 UC, 23 CD), 36 (69.2%) exhibited inflammatory activity. We identified 56 fecal metabolites, with hexadecanoic acid, squalene, and octadecanoic acid notably distinguishing CD from UC. For UC, octadecanoic and hexadecanoic acids correlated with disease activity, whereas octadecanoic acid was most relevant in CD. CONCLUSIONS These findings highlight the potential of metabolomics as a noninvasive complement for evaluating IBD, aiding diagnosis, and assessing disease activity.
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Affiliation(s)
- Lucas Correia Lins
- Universidade Federal de Alagoas, Postgraduate Program in Medical Sciences - Maceió (AL), Brazil
| | | | | | - Alessandre Carmo Crispim
- Universidade Federal de Alagoas, Postgraduate Program in Chemistry and Biotechnology - Maceió (AL), Brazil
| | | | | | - Fabiana Andréa Moura
- Universidade Federal de Alagoas, Postgraduate Program in Medical Sciences - Maceió (AL), Brazil
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10
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Qiao Y, He C, Xia Y, Ocansey DKW, Mao F. Intestinal mucus barrier: A potential therapeutic target for IBD. Autoimmun Rev 2025; 24:103717. [PMID: 39662652 DOI: 10.1016/j.autrev.2024.103717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 12/03/2024] [Accepted: 12/04/2024] [Indexed: 12/13/2024]
Abstract
Intestinal mucus, a viscoelastic medium with mucin2 (MUC2) as its main component, covers the surface of intestinal epithelial cells and protects the intestine from invasion, forming the first barrier of the intestinal tract. Unlike the small intestine, where the mucus layer is a single layer, the colonic mucus layer can be divided into a sterile inner layer and an outer layer with bacterial colonization. Many of the substances in the mucus layer have beneficial effects on the intestinal epithelium, but the mucus layer is often affected by a variety of factors, mainly microbiological, dietary, and immunological. Inflammatory bowel disease (IBD) is a disease of increasing morbidity worldwide, with a complex etiology and a high relapse rate. In recent years, the mucus barrier in IBD has received increasing attention and is considered a key factor in the pathogenesis of IBD. Loss of goblet cells (GCs) and changes in the composition and properties of the mucus layer material are commonly found in the colon of IBD patients. Damage to the mucus layer may make it easier for microorganisms to access the intestinal epithelium and cause inflammation. There are currently a number of herbs and other therapies that can be used to treat IBD and repair the damaged mucus barrier. This review highlights the important role of the mucus layer in IBD and the therapies that target the mucus layer in IBD.
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Affiliation(s)
- Yaru Qiao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Changer He
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang 212399, Jiangsu, PR China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; Department of Medical Laboratory Science, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast CC0959347, Ghana
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China.
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11
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Ma Y, Yang H, Wang X, Huang Y, Li Y, Pan G. Bile acids as signaling molecules in inflammatory bowel disease: Implications for treatment strategies. JOURNAL OF ETHNOPHARMACOLOGY 2025; 337:118968. [PMID: 39427739 DOI: 10.1016/j.jep.2024.118968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 09/21/2024] [Accepted: 10/17/2024] [Indexed: 10/22/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Inflammatory bowel disease (IBD) is a globally increasing disease. Despite continuous efforts, the clinical application of treatment drugs has not achieved satisfactory success and faces limitations such as adverse drug reactions. Numerous investigations have found that the pathogenesis of IBD is connected with disturbances in bile acid circulation and metabolism. Traditional Chinese medicine targeting bile acids (BAs) has shown significant therapeutic effects and advantages in treating inflammatory bowel disease. AIM OF THIS REVIEW IThis article reviews the role of bile acids and their receptors in IBD, as well as research progress on IBD therapeutic drugs based on bile acids. It explores bile acid metabolism and its interaction with the intestinal microbiota, summarizes clinical drugs for treating IBD including single herbal medicine, traditional herbal prescriptions, and analyzes the mechanisms of action in treating IBD. MATERIALS AND METHODS IThe electronic databases such as PubMed, Web of Science, and China National Knowledge Infrastructure (CNKI) have been utilized to retrieve relevant literature up to January 2024, using keywords "bile acid", "bile acid receptor", "inflammatory bowel disease", "intestinal microbiota" and "targeted drugs". RESULTS IImbalance in bile acid levels can lead to intestinal inflammation, while IBD can disrupt the balance of microbes, result in alterations in the bile acid pool's composition and amount. This change can damage of intestinal mucosa healing ability. Bile acids are vital for keeping the gut barrier function intact, regulating gene expression, managing metabolic equilibrium, and influencing the properties and roles of the gut's microbial community. Consequently, focusing on bile acids could offer a potential treatment strategy for IBD. CONCLUSION IIBD can induce intestinal homeostasis imbalance and changes in BA pool, leading to fluctuations in levels of relevant metabolic enzymes, transporters, and nuclear receptors. Therefore, by regulating the balance of BA and key signaling molecules of bile acids, we can treat IBD. Traditional Chinese medicine has great potential and promising prospects in treating IBD. We should focus on the characteristics and advantages of Chinese medicine, promote the development and clinical application of innovative Chinese medicine, and ultimately make Chinese medicine targeting bile acids the mainstream treatment for IBD.
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Affiliation(s)
- Yueyue Ma
- Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China
| | - Haoze Yang
- Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China
| | - Xiaoming Wang
- Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China
| | - Yuhong Huang
- Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300250, PR China
| | - Yuhong Li
- Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, Jing Hai District, Tianjin, 301617, PR China.
| | - Guixiang Pan
- Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300250, PR China.
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12
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Britton GJ, Mogno I, Chen-Liaw A, Plitt T, Helmus D, Bongers G, Brough I, Colmenero P, Lam LH, Bullers SJ, Penkava F, Reyes-Mercedes P, Braun J, Jacobs JP, Desch AN, Gevers D, Simmons S, Filer A, Taylor PC, Bowness P, Huttenhower C, Littman D, Dubinsky MC, Raza K, Tankou SK, Faith JJ. Inflammatory disease microbiomes share a functional pathogenicity predicted by C-reactive protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.14.633015. [PMID: 39868147 PMCID: PMC11761010 DOI: 10.1101/2025.01.14.633015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
We examine disease-specific and cross-disease functions of the human gut microbiome by colonizing germ-free mice, at risk for inflammatory arthritis, colitis, or neuroinflammation, with over 100 human fecal microbiomes from subjects with rheumatoid arthritis, ankylosing spondylitis, multiple sclerosis, ulcerative colitis, Crohn's disease, or colorectal cancer. We find common inflammatory phenotypes driven by microbiomes from individuals with intestinal inflammation or inflammatory arthritis, as well as distinct functions specific to microbiomes from multiple sclerosis patients. Inflammatory disease in mice colonized with human microbiomes correlated with systemic inflammation, measured by C-reactive protein, in the human donors. These cross-disease patterns of human microbiome pathogenicity mirror features of the inflammatory diseases, including therapeutic targets and the presence or absence of systemic inflammation, suggesting shared and disease-specific mechanisms by which the microbiome is shaped and drives pathogenic inflammatory responses.
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Affiliation(s)
- Graham J. Britton
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - Ilaria Mogno
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - Alice Chen-Liaw
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - Tamar Plitt
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - Drew Helmus
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - India Brough
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7FY, UK
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7LD, UK
| | - Paula Colmenero
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7FY, UK
| | - Lilian H. Lam
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7FY, UK
| | - Samuel J. Bullers
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7FY, UK
| | - Frank Penkava
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7FY, UK
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7LD, UK
| | - Pamela Reyes-Mercedes
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan Braun
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars Sinai Medical Center; Los Angeles, CA 90048, USA
| | - Jonathan P. Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA; Los Angeles, CA 90095, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System; Los Angeles, CA 90073, USA
- Goodman-Luskin Microbiome Center, David Geffen School of Medicine at UCLA; Los Angeles, CA 90095, USA
| | - A. Nicole Desch
- Janssen Research and Development, LLC; Spring House, PA 19002, USA
| | - Dirk Gevers
- Janssen Research and Development, LLC; Spring House, PA 19002, USA
| | - Sheri Simmons
- Janssen Research and Development, LLC; Spring House, PA 19002, USA
| | - Andrew Filer
- Department of Inflammation and Ageing, College of Medicine and Health, University of Birmingham; Birmingham, B15 2TT, UK
| | - Peter C. Taylor
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7LD, UK
| | - Paul Bowness
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford; Oxford, OX3 7LD, UK
| | - Curtis Huttenhower
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University; Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA 02115, USA
| | - Dan Littman
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
- Perlmutter Cancer Center, New York University Langone Health; New York, NY 10016, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Marla C. Dubinsky
- Division of Pediatric Gastroenterology, Icahn School of Medicine; New York, NY, 10029
| | - Karim Raza
- Department of Inflammation and Ageing, College of Medicine and Health, University of Birmingham; Birmingham, B15 2TT, UK
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, University of Birmingham; Birmingham, B15 2TT, UK
- Department of Rheumatology, Sandwell & West Birmingham NHS Trust; West Bromwich, B71 4HJ, UK
| | - Stephanie K. Tankou
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Department of Immunology & Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - Jeremiah J. Faith
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
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13
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Govender P, Ghai M. Population-specific differences in the human microbiome: Factors defining the diversity. Gene 2025; 933:148923. [PMID: 39244168 DOI: 10.1016/j.gene.2024.148923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/15/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
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14
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Duan D, Wang M, Han J, Li M, Wang Z, Zhou S, Xin W, Li X. Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications. Front Microbiol 2025; 15:1509117. [PMID: 39831120 PMCID: PMC11739165 DOI: 10.3389/fmicb.2024.1509117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 12/13/2024] [Indexed: 01/22/2025] Open
Abstract
The gut microbiota actually shares the host's physical space and affects the host's physiological functions and health indicators through a complex network of interactions with the host. However, its role as a determinant of host health and disease is often underestimated. With the emergence of new technologies including next-generation sequencing (NGS) and advanced techniques such as microbial community sequencing, people have begun to explore the interaction mechanisms between microorganisms and hosts at various omics levels such as genomics, transcriptomics, metabolomics, and proteomics. With the enrichment of multi-omics integrated analysis methods based on the microbiome, an increasing number of complex statistical analysis methods have also been proposed. In this review, we summarized the multi-omics research analysis methods currently used to study the interaction between the microbiome and the host. We analyzed the advantages and limitations of various methods and briefly introduced their application progress.
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Affiliation(s)
- Dongdong Duan
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Mingyu Wang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
| | - Jinyi Han
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Mengyu Li
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Zhenyu Wang
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Shenping Zhou
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Wenshui Xin
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
| | - Xinjian Li
- Sanya Institute, Hainan Academy of Agricultural, Sanya, China
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, China
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15
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Olivera PA, Martinez-Lozano H, Leibovitzh H, Xue M, Neustaeter A, Espin-Garcia O, Xu W, Madsen KL, Guttman DS, Bernstein CN, Yerushalmi B, Hyams JS, Abreu MT, Marshall JK, Wrobel I, Mack DR, Jacobson K, Bitton A, Aumais G, Panacionne R, Dieleman LA, Silverberg MS, Steinhart AH, Moayyedi P, Turner D, Griffiths AM, Turpin W, Lee SH, Croitoru K. Healthy First-Degree Relatives From Multiplex Families vs Simplex Families Have Higher Subclinical Intestinal Inflammation, a Distinct Fecal Microbial Signature, and Harbor a Higher Risk of Developing Crohn's Disease. Gastroenterology 2025; 168:99-110.e2. [PMID: 39236898 DOI: 10.1053/j.gastro.2024.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 08/09/2024] [Accepted: 08/25/2024] [Indexed: 09/07/2024]
Abstract
BACKGROUND & AIMS Unaffected first-degree relatives (FDRs) from families with ≥2 affected FDRs with Crohn's disease (CD, multiplex families) have a high risk of developing CD, although the underlying mechanisms driving this risk are poorly understood. We aimed to identify differences in biomarkers between FDRs from multiplex vs simplex families and investigate the risk of future CD onset accounting for potential confounders. METHODS We assessed the Crohn's and Colitis Canada Genetic Environmental Microbial cohort of healthy FDRs of patients with CD. Genome-wide CD-polygenic risk scores, urinary fractional excretion of lactulose-to-mannitol ratio, fecal calprotectin (FCP), and fecal 16S ribosomal RNA microbiome were measured at recruitment. Associations between CD multiplex status and baseline biomarkers were determined using generalized estimating equations models. Cox models were used to assess the risk of future CD onset. RESULTS There were 4051 participants from simplex families and 334 from CD multiplex families. CD multiplex status was significantly associated with higher baseline FCP (P = .026) but not with baseline CD-polygenic risk scores or the lactulose-to-mannitol ratio. Three bacterial genera were found to be differentially abundant between both groups. CD multiplex status at recruitment was independently associated with an increased risk of developing CD (adjusted hazard ratio, 3.65; 95% confidence interval, 2.18-6.11, P < .001). CONCLUSION Within FDRs of patients with CD, participants from multiplex families had a 3-fold increased risk of CD onset, a higher FCP, and an altered bacterial composition, but not genetic burden or altered gut permeability. These results suggest that putative environmental factors might be enriched in FDRs from multiplex families.
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Affiliation(s)
- Pablo A Olivera
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Helena Martinez-Lozano
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada; Department of Digestive System Medicine, Hospital General Universitario, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Haim Leibovitzh
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Mingyue Xue
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Neustaeter
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Osvaldo Espin-Garcia
- Division of Biostatistics, University of Toronto Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Wei Xu
- Division of Biostatistics, University of Toronto Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - David S Guttman
- Department of Cell & Systems Biology and Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Charles N Bernstein
- Inflammatory Bowel Disease Clinical and Research Centre and Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut
| | - Maria T Abreu
- Division of Gastroenterology, Crohn's and Colitis Center, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - John K Marshall
- Department of Medicine, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, Canada
| | - Iwona Wrobel
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - Kevan Jacobson
- Canadian Gastro-Intestinal Epidemiology Consortium, Toronto, Ontario, Canada; British Columbia Children's Hospital, Vancouver, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alain Bitton
- Division of Gastroenterology and Hepatology, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Guy Aumais
- Department of Medicine, Montreal University, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Remo Panacionne
- Inflammatory Bowel Disease Clinic, Division of Gastroenterology and Hepatology of Gastroenterology, University of Calgary, Calgary, Alberta, Canada
| | - Levinus A Dieleman
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - A Hillary Steinhart
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Paul Moayyedi
- Department of Medicine, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, Canada
| | - Dan Turner
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, The Hebrew University of Jerusalem, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Anne M Griffiths
- Department of Gastroenterology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Sun-Ho Lee
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada.
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16
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Jacobs JP, Spencer EA, Helmus DS, Yang JC, Lagishetty V, Bongers G, Britton G, Gettler K, Reyes-Mercedes P, Hu J, Hart A, Lamousé-Smith E, Wehkamp J, Landers C, Debbas P, Torres J, Colombel JF, Cho J, Peter I, Faith J, Braun J, Dubinsky M. Age-related patterns of microbial dysbiosis in multiplex inflammatory bowel disease families. Gut 2024; 73:1953-1964. [PMID: 39122361 PMCID: PMC11560537 DOI: 10.1136/gutjnl-2024-332475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]
Abstract
OBJECTIVE IBD is characterised by dysbiosis, but it remains unclear to what extent dysbiosis develops in unaffected at-risk individuals. To address this, we investigated age-related patterns of faecal and serum markers of dysbiosis in high-risk multiplex IBD families (two or more affected first-degree relatives). DESIGN Faecal and serum samples were collected from multiplex IBD and control families (95 IBD, 292 unaffected, 51 controls). Findings were validated in independent cohorts of 616 and 1173 subjects including patients with IBD, infants born to mothers with IBD and controls. 16S rRNA gene sequencing and global untargeted metabolomics profiling of faeces and serum were performed. RESULTS Microbial and metabolomic parameters of dysbiosis progressively decreased from infancy until age 8. This microbial maturation process was slower in infants born to mothers with IBD. After age 15, dysbiosis steadily increased in unaffected relatives throughout adulthood. Dysbiosis was accompanied by marked shifts in the faecal metabolome and, to a lesser extent, the serum metabolome. Faecal and serum metabolomics dysbiosis indices were validated in an independent cohort. Dysbiosis was associated with elevated antimicrobial serologies but not with faecal calprotectin. Dysbiosis metrics differentiated IBD from non-IBD comparably to serologies, with a model combining calprotectin, faecal metabolomics dysbiosis index and serology score demonstrating highest accuracy. CONCLUSION These findings support that dysbiosis exists as a pre-disease state detectable by faecal and serum biomarkers for IBD risk prediction. Given the expansion of disease-modifying agents and non-invasive imaging, the indices developed here may facilitate earlier diagnoses and improved management in at-risk individuals.
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Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
- Goodman-Luskin Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Elizabeth A Spencer
- The Division of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Drew S Helmus
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Julianne C Yang
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Goodman-Luskin Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Gerold Bongers
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Graham Britton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kyle Gettler
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pamela Reyes-Mercedes
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amy Hart
- Janssen, Spring House, Pennsylvania, USA
| | | | | | - Carol Landers
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Philip Debbas
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Joana Torres
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Hospital da Luz, Lisboa, Portugal
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy Cho
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jeremiah Faith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jonathan Braun
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Marla Dubinsky
- The Division of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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17
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Dong TS, Peters K, Gupta A, Jacobs JP, Chang L. Prevotella Is Associated With Sex-Based Differences in Irritable Bowel Syndrome. Gastroenterology 2024; 167:1221-1224.e8. [PMID: 39004155 PMCID: PMC11845270 DOI: 10.1053/j.gastro.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024]
Affiliation(s)
- Tien S Dong
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, California; G. Oppenheimer Center for Neurobiology of Stress and Resilience, Los Angeles, California; University of California, Los Angeles Goodman-Luskin Microbiome Center, Los Angeles, California; Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Kirstin Peters
- Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Arpana Gupta
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, California; G. Oppenheimer Center for Neurobiology of Stress and Resilience, Los Angeles, California; University of California, Los Angeles Goodman-Luskin Microbiome Center, Los Angeles, California; Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, California; G. Oppenheimer Center for Neurobiology of Stress and Resilience, Los Angeles, California; University of California, Los Angeles Goodman-Luskin Microbiome Center, Los Angeles, California; Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Lin Chang
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, California; G. Oppenheimer Center for Neurobiology of Stress and Resilience, Los Angeles, California; University of California, Los Angeles Goodman-Luskin Microbiome Center, Los Angeles, California; Department of Medicine, University of California, Los Angeles, Los Angeles, California.
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18
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Anthamatten L, von Bieberstein PR, Menzi C, Zünd JN, Lacroix C, de Wouters T, Leventhal GE. Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status. MICROBIOME 2024; 12:186. [PMID: 39350289 PMCID: PMC11441152 DOI: 10.1186/s40168-024-01897-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 07/31/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND The human gut microbiome produces and consumes a variety of compounds that interact with the host and impact health. Succinate is of particular interest as it intersects with both host and microbiome metabolism. However, which gut bacteria are most responsible for the consumption of intestinal succinate is poorly understood. RESULTS We build upon an enrichment-based whole fecal sample culturing approach and identify two main bacterial taxa that are responsible for succinate consumption in the human intestinal microbiome, Phascolarctobacterium and Dialister. These two taxa have the hallmark of a functional guild and are strongly mutual exclusive across 21,459 fecal samples in 94 cohorts and can thus be used to assign a robust "succinotype" to an individual. We show that they differ with respect to their rate of succinate consumption in vitro and that this is associated with higher concentrations of fecal succinate. Finally, individuals suffering from inflammatory bowel disease (IBD) are more likely to have the Dialister succinotype compared to healthy subjects. CONCLUSIONS We identified that only two bacterial genera are the key succinate consumers in human gut microbiome, despite the fact that many more intestinal bacteria encode for the succinate pathway. This highlights the importance of phenotypic assays in functionally profiling intestinal microbiota. A stratification based on "succinotype" is to our knowledge the first function-based classification of human intestinal microbiota. The association of succinotype with IBD thus builds a bridge between microbiome function and IBD pathophysiology related to succinate homeostasis. Video Abstract.
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Affiliation(s)
- Laura Anthamatten
- PharmaBiome AG, Schlieren, Switzerland
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | | | - Janina N Zünd
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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19
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Briggs K, Tomar V, Ollberding N, Haberman Y, Bourgonje AR, Hu S, Chaaban L, Sunuwar L, Weersma RK, Denson LA, Melia JMP. Crohn's Disease-Associated Pathogenic Mutation in the Manganese Transporter ZIP8 Shifts the Ileal and Rectal Mucosal Microbiota Implicating Aberrant Bile Acid Metabolism. Inflamm Bowel Dis 2024; 30:1379-1388. [PMID: 38289995 PMCID: PMC11291615 DOI: 10.1093/ibd/izae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND A pathogenic mutation in the manganese transporter ZIP8 (A391T; rs13107325) increases the risk of Crohn's disease. ZIP8 regulates manganese homeostasis and given the shared need for metals between the host and resident microbes, there has been significant interest in alterations of the microbiome in carriers of ZIP8 A391T. Prior studies have not examined the ileal microbiome despite associations between ileal disease and ZIP8 A391T. METHODS Here, we used the Pediatric Risk Stratification Study (RISK) cohort to perform a secondary analysis of 16S ribosomal RNA gene sequencing data obtained from ileal and rectal mucosa to study associations between ZIP8 A391T carrier status and microbiota composition. RESULTS We found sequence variants mapping to Veillonella were decreased in the ileal mucosa of ZIP8 A391T carriers. Prior human studies have demonstrated the sensitivity of Veillonella to bile acid abundance. We therefore hypothesized that bile acid homeostasis is differentially regulated in carriers of ZIP8 A391T. Using a mouse model of ZIP8 A391T, we demonstrate an increase in total bile acids in the liver and stool and decreased fibroblast growth factor 15 (Fgf15) signaling, consistent with our hypothesis. We confirmed dysregulation of FGF19 in the 1000IBD cohort, finding that plasma FGF19 levels are lower in ZIP8 A391T carriers with ileocolonic Crohn's disease. CONCLUSIONS In the search for genotype-specific therapeutic paradigms for patients with Crohn's disease, these data suggest targeting the FGF19 pathway in ZIP8 A391T carriers. Aberrant bile acid metabolism may precede development of Crohn's disease and prioritize study of the interactions between manganese homeostasis, bile acid metabolism and signaling, and complicated ileal Crohn's disease.
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Affiliation(s)
- Kristi Briggs
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vartika Tomar
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas Ollberding
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yael Haberman
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, Sheba Medical Center, Tel-Hashomer, affiliated with Tel Aviv University, Tel Aviv, Israel
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Gastroenterology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Lara Chaaban
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laxmi Sunuwar
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Joanna M P Melia
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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20
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Zdanowicz K, Pietrowska K, Lebensztejn DM, Ciborowski M, Godzien J, Kretowski A, Daniluk J, Daniluk U. Evaluation of microbiome composition combined with serum untargeted metabolomic profiling in newly diagnosed children with inflammatory bowel disease. Arch Med Sci 2024; 21:416-424. [PMID: 40395900 PMCID: PMC12087318 DOI: 10.5114/aoms/190623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/29/2024] [Indexed: 05/22/2025] Open
Abstract
Introduction The relationship between the intestinal microbiota, metabolites, and development of inflammatory bowel disease (IBD) is still being investigated. We aimed to assess whether the gut microbiome and serum metabolic profile are consistent with a diagnosis of Crohn's disease (CD) or ulcerative colitis (UC) in children with newly diagnosed disease. Material and methods Bacterial abundance in fecal samples was evaluated using a 16S rRNA DNA-based test in treatment-naive children with IBD (n = 18) and healthy controls (n = 10). Metabolic fingerprinting of serum samples of the same individuals was estimated using liquid chromatography coupled with mass spectrometry. Results It was not possible to discriminate between CD and UC patients based on the gut microbiota profiles, but surprisingly, in the principal component analysis (PCA) model we observed a spontaneous separation of IBD patients into two groups, independently of IBD type. Then, serum metabolic profiles of these two microbiota-based groups of IBD patients were compared using orthogonal partial least squares discriminant analysis (OPLS-DA) modelling. Good quality models were obtained based on serum metabolomics data collected in positive and negative ion mode. In total, 12 metabolites significantly discriminating these groups were identified. Conclusions Based on microbiota profiling, a grouping of IBD patients, unrelated to the IBD type, was noted. These two groups also have specific serum metabolic profiles. Further studies are needed to assess whether IBD patients, depending on their gut microbiota and serum metabolite composition, require different treatments and whether that impacts disease outcomes.
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Affiliation(s)
- Katarzyna Zdanowicz
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition, Allergology and Pulmonology, Medical University of Bialystok, Poland
| | - Karolina Pietrowska
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Poland
| | - Dariusz M. Lebensztejn
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition, Allergology and Pulmonology, Medical University of Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Poland
| | - Joanna Godzien
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Poland
| | - Jaroslaw Daniluk
- Department of Gastroenterology and Internal Medicine, Medical University of Bialystok, Poland
| | - Urszula Daniluk
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition, Allergology and Pulmonology, Medical University of Bialystok, Poland
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21
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Chen W, Li Y, Wang W, Gao S, Hu J, Xiang B, Wu D, Jiao N, Xu T, Zhi M, Zhu L, Zhu R. Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. Cell Rep Med 2024; 5:101624. [PMID: 38942021 PMCID: PMC11293350 DOI: 10.1016/j.xcrm.2024.101624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 04/09/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]
Abstract
Prior studies indicate no correlation between the gut microbes of healthy first-degree relatives (HFDRs) of patients with Crohn's disease (CD) and the development of CD. Here, we utilize HFDRs as controls to examine the microbiota and metabolome in individuals with active (CD-A) and quiescent (CD-R) CD, thereby minimizing the influence of genetic and environmental factors. When compared to non-relative controls, the use of HFDR controls identifies fewer differential taxa. Faecalibacterium, Dorea, and Fusicatenibacter are decreased in CD-R, independent of inflammation, and correlated with fecal short-chain fatty acids (SCFAs). Validation with a large multi-center cohort confirms decreased Faecalibacterium and other SCFA-producing genera in CD-R. Classification models based on these genera distinguish CD from healthy individuals and demonstrate superior diagnostic power than models constructed with markers identified using unrelated controls. Furthermore, these markers exhibited limited discriminatory capabilities for other diseases. Finally, our results are validated across multiple cohorts, underscoring their robustness and potential for diagnostic and therapeutic applications.
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Affiliation(s)
- Wanning Chen
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Yichen Li
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China; Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Wenxia Wang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Sheng Gao
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Jun Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Bingjie Xiang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Dingfeng Wu
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Na Jiao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Tao Xu
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China
| | - Min Zhi
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China.
| | - Lixin Zhu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China.
| | - Ruixin Zhu
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China.
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22
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Koci O, Russell RK, Shaikh MG, Edwards C, Gerasimidis K, Ijaz UZ. CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets. MICROBIOME 2024; 12:117. [PMID: 38951915 PMCID: PMC11218139 DOI: 10.1186/s40168-024-01834-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 05/09/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration. RESULTS In this study, we have developed a Java-based statistical framework ( https://github.com/KociOrges/cviewer ) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships. CONCLUSIONS CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.
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Affiliation(s)
- Orges Koci
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 0SF, UK
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children & Young People, Edinburgh, EH16 4TJ, UK
| | - M Guftar Shaikh
- Department of Endocrinology, Royal Hospital for Children, Glasgow, 1345 Govan Rd., Glasgow, G51 4T, UK
| | - Christine Edwards
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 0SF, UK
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 0SF, UK
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, G11 6EW, UK.
- National University of Ireland, Galway, University Road, Galway, H91 TK33, Ireland.
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, L69 7BE, UK.
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23
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Li JH, Chen Y, Ye ZH, Chen LP, Xu JX, Han J, Xie L, Xing S, Tian DA, Seidler U, Liao JZ, Xiao F. Suppression of MyD88 disturbs gut microbiota and activates the NLR pathway and hence fails to ameliorate DSS-induced colitis. PRECISION CLINICAL MEDICINE 2024; 7:pbae013. [PMID: 38946731 PMCID: PMC11212664 DOI: 10.1093/pcmedi/pbae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024] Open
Abstract
Background Myeloid differentiation factor 88 (MyD88) is the core adaptor for Toll-like receptors defending against microbial invasion and initiating a downstream immune response during microbiota-host interaction. However, the role of MyD88 in the pathogenesis of inflammatory bowel disease is controversial. This study aims to investigate the impact of MyD88 on intestinal inflammation and the underlying mechanism. Methods MyD88 knockout (MyD88-/-) mice and the MyD88 inhibitor (TJ-M2010-5) were used to investigate the impact of MyD88 on acute dextran sodium sulfate (DSS)-induced colitis. Disease activity index, colon length, histological score, and inflammatory cytokines were examined to evaluate the severity of colitis. RNA transcriptome analysis and 16S rDNA sequencing were used to detect the potential mechanism. Results In an acute DSS-colitis model, the severity of colitis was not alleviated in MyD88-/- mice and TJ-M2010-5-treated mice, despite significantly lower levels of NF-κB activation being exhibited compared to control mice. Meanwhile, 16S rDNA sequencing and RNA transcriptome analysis revealed a higher abundance of intestinal Proteobacteria and an up-regulation of the nucleotide oligomerization domain-like receptors (NLRs) signaling pathway in colitis mice following MyD88 suppression. Further blockade of the NLRs signaling pathway or elimination of gut microbiota with broad-spectrum antibiotics in DSS-induced colitis mice treated with TJ-M2010-5 ameliorated the disease severity, which was not improved solely by MyD88 inhibition. After treatment with broad-spectrum antibiotics, downregulation of the NLR signaling pathway was observed. Conclusion Our study suggests that the suppression of MyD88 might be associated with unfavorable changes in the composition of gut microbiota, leading to NLR-mediated immune activation and intestinal inflammation.
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Affiliation(s)
- Jun-hua Li
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Chen
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zheng-hao Ye
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li-ping Chen
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jia-xin Xu
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jian Han
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lin Xie
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuai Xing
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - De-an Tian
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ursula Seidler
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover 30625, Germany
| | - Jia-zhi Liao
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Fang Xiao
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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24
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Shtossel O, Finkelstein S, Louzoun Y. mi-Mic: a novel multi-layer statistical test for microbiota-disease associations. Genome Biol 2024; 25:113. [PMID: 38693546 PMCID: PMC11064322 DOI: 10.1186/s13059-024-03256-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
mi-Mic, a novel approach for microbiome differential abundance analysis, tackles the key challenges of such statistical tests: a large number of tests, sparsity, varying abundance scales, and taxonomic relationships. mi-Mic first converts microbial counts to a cladogram of means. It then applies a priori tests on the upper levels of the cladogram to detect overall relationships. Finally, it performs a Mann-Whitney test on paths that are consistently significant along the cladogram or on the leaves. mi-Mic has much higher true to false positives ratios than existing tests, as measured by a new real-to-shuffle positive score.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Shani Finkelstein
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
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25
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Belotserkovsky I, Stabryla LM, Hunter M, Allegretti J, Callahan BJ, Carlson PE, Daschner PJ, Goudarzi M, Guyard C, Jackson SA, Rao K, Servetas SL, Sokol H, Wargo JA, Novick S. Standards for fecal microbiota transplant: Tools and therapeutic advances. Biologicals 2024; 86:101758. [PMID: 38518435 DOI: 10.1016/j.biologicals.2024.101758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/04/2024] [Indexed: 03/24/2024] Open
Abstract
Fecal microbiota transplantation (FMT) has been demonstrated to be efficacious in preventing recurrent Clostridioides difficile (C. difficile) infections, and is being investigated for treatment of several other diseases including inflammatory bowel disease, cancer, obesity, liver disease, and diabetes. To speed up the translation of FMT into clinical practice as a safe and standardized therapeutic intervention, additional evidence-based technical and regulatory guidance is needed. To this end in May of 2022, the International Alliance for Biological Standardization (IABS) and the BIOASTER Microbiology Technology Institute hosted a second webinar to discuss key issues still impeding the advancement and standardization of FMT. The goal of this two-day webinar was to provide a forum for scientific experts to share and discuss data and key challenges with one another. Discussion included a focus on the evaluation of safety, efficacy, clinical trial design, reproducibility and accuracy in obtained microbiome measurements and data reporting, and the potential for standardization across these areas. It also focused on increasing the application potential and visibility of FMT beyond treating C. difficile infections.
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Affiliation(s)
| | - Lisa M Stabryla
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Monique Hunter
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jessica Allegretti
- Division of Gastroenterology, Hepatology, and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Benjamin J Callahan
- Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA; Department of Population Health and Pathobiology, North Carolina State University, Raleigh, 27607, USA
| | - Paul E Carlson
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Phillip J Daschner
- Division of Cancer Biology, National Cancer Institute, Bethesda, MD, USA
| | | | - Cyril Guyard
- BIOSTER Technological Research Institute, Lyon, France
| | - Scott A Jackson
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephanie L Servetas
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Harry Sokol
- Assistance Publique des Hôpitaux de Paris, Saint-Antoine Hospital, Gastroenterology Department, Paris, France
| | - Jennifer A Wargo
- Departments of Surgical Oncology and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Shawn Novick
- BioPhia Consulting, Inc., 7307 W. Green Lake Dr. N., Seattle, WA, 98103, USA.
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Chang C, Gupta R, Sedighian F, Louie A, Gonzalez DM, Le C, Cho JM, Park SK, Castellanos J, Ting TW, Dong TS, Arias-Jayo N, Lagishetty V, Navab M, Reddy S, Sioutas C, Hsiai T, Jacobs JP, Araujo JA. Subchronic inhalation exposure to ultrafine particulate matter alters the intestinal microbiome in various mouse models. ENVIRONMENTAL RESEARCH 2024; 248:118242. [PMID: 38242419 PMCID: PMC11737635 DOI: 10.1016/j.envres.2024.118242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
Exposure to ultrafine particles (UFPs) has been associated with multiple adverse health effects. Inhaled UFPs could reach the gastrointestinal tract and influence the composition of the gut microbiome. We have previously shown that oral ingestion of UFPs alters the gut microbiome and promotes intestinal inflammation in hyperlipidemic Ldlr-/- mice. Particulate matter (PM)2.5 inhalation studies have also demonstrated microbiome shifts in normolipidemic C57BL/6 mice. However, it is not known whether changes in microbiome precede or follow inflammatory effects in the intestinal mucosa. We hypothesized that inhaled UFPs modulate the gut microbiome prior to the development of intestinal inflammation. We studied the effects of UFP inhalation on the gut microbiome and intestinal mucosa in two hyperlipidemic mouse models (ApoE-/- mice and Ldlr-/- mice) and normolipidemic C57BL/6 mice. Mice were exposed to PM in the ultrafine-size range by inhalation for 6 h a day, 3 times a week for 10 weeks at a concentration of 300-350 μg/m3.16S rRNA gene sequencing was performed to characterize sequential changes in the fecal microbiome during exposures, and changes in the intestinal microbiome at the end. PM exposure led to progressive differentiation of the microbiota over time, associated with increased fecal microbial richness and evenness, altered microbial composition, and differentially abundant microbes by week 10 depending on the mouse model. Cross-sectional analysis of the small intestinal microbiome at week 10 showed significant changes in α-diversity, β-diversity, and abundances of individual microbial taxa in the two hyperlipidemic models. These alterations of the intestinal microbiome were not accompanied, and therefore could not be caused, by increased intestinal inflammation as determined by histological analysis of small and large intestine, cytokine gene expression, and levels of fecal lipocalin. In conclusion, 10-week inhalation exposures to UFPs induced taxonomic changes in the microbiome of various animal models in the absence of intestinal inflammation.
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Affiliation(s)
- Candace Chang
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA; Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Rajat Gupta
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Farzaneh Sedighian
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Allen Louie
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - David M Gonzalez
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Collin Le
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jae Min Cho
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Seul-Ki Park
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jocelyn Castellanos
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - To-Wei Ting
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Tien S Dong
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA; Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, Los Angeles, CA, USA
| | - Nerea Arias-Jayo
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Mohamad Navab
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Srinivasa Reddy
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Molecular & Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA
| | - Constantinos Sioutas
- University of Southern California (USC) Viterbi School of Engineering, Los Angeles, CA, USA
| | - Tzung Hsiai
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Henry Samueli School of Engineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA; Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, Los Angeles, CA, USA.
| | - Jesus A Araujo
- Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Department of Environmental Health Sciences, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
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Tong G, Qian H, Li D, Li J, Chen J, Li X, Tan Z. Intestinal Flora Imbalance Induced by Antibiotic Use in Rats. J Inflamm Res 2024; 17:1789-1804. [PMID: 38528993 PMCID: PMC10961240 DOI: 10.2147/jir.s447098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/14/2024] [Indexed: 03/27/2024] Open
Abstract
Aim This study aims to explore the effect of different doses of antibiotics on rats in order to observe alterations in their fecal microbiota, inflammatory changes in the colonic mucosa and four types of inflammatory markers in blood serum. Methods Our methodology involved separating 84 female Sprague Dawley rats into groups A-G, with each group consisting of 12 rats. We collected the rat feces for analysis, using a distinct medium for bacterial cultivation and counting colonies under a microscope. On the 11th and 15th days of the experiment, half of the rats from each group were euthanized and 5 mL of abdominal aortic blood and colon tissues were collected. Inflammations changes of colon were observed and assessed by pathological Hematoxylin Eosin (HE) staining. Enzyme-linked immune sorbent assay (ELISA) was adopted for detecting C-reactive protein (CRP), IL-6, IL1-β and TNF-α. Results Our findings revealed that the initial average weight of the rats did not differ between groups (p>0.05); but significant differences were observed between stool samples, water intake, food intake and weight (p=0.009, <0.001, 0.016 and 0.04, respectively) within two hours after the experiment. Additionally, there were notable differences among the groups in nine tested microbiota before and after weighting methods (all p<0.001). There were no difference in nine microbiota at day 1 (all p>0.05); at day 4 A/B (p=0.044), A/D (p<0.001), A/E (p=0.029); at day 8, all p<0.01, at day 11, only A/F exist significant difference (p<0.001); at day 14 only A/D has difference (p=0.045). Inflammation changes of colon were observed between groups A-G at days 11 and 15. Significant differences between all groups can be observed for CRP, IL-6, IL1-β and TNF-α (p<0.001). Conclusion This study suggests that antibiotics administration can disrupt the balance of bacteria in the rat gut ecosystem, resulting in an inflammatory response in their bloodstream and inducing inflammation changes of colon.
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Affiliation(s)
- Guojun Tong
- General Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Hai Qian
- General Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Dongli Li
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Jing Li
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Jing Chen
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Xiongfeng Li
- Orthopedic Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Zhenhua Tan
- General Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
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Jacobs JP, Sauk JS, Ahdoot AI, Liang F, Katzka W, Ryu HJ, Khandadash A, Lagishetty V, Labus JS, Naliboff BD, Mayer EA. Microbial and Metabolite Signatures of Stress Reactivity in Ulcerative Colitis Patients in Clinical Remission Predict Clinical Flare Risk. Inflamm Bowel Dis 2024; 30:336-346. [PMID: 37650887 PMCID: PMC10906354 DOI: 10.1093/ibd/izad185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Stress reactivity (SR) is associated with increased risk of flares in ulcerative colitis (UC) patients. Because both preclinical and clinical data support that stress can influence gut microbiome composition and function, we investigated whether microbiome profiles of SR exist in UC. METHODS Ninety-one UC subjects in clinical and biochemical remission were classified into high and low SR groups by questionnaires. Baseline and longitudinal characterization of the intestinal microbiome was performed by 16S rRNA gene sequencing and fecal and plasma global untargeted metabolomics. Microbe, fecal metabolite, and plasma metabolite abundances were analyzed separately to create random forest classifiers for high SR and biomarker-derived SR scores. RESULTS High SR reactivity was characterized by altered abundance of fecal microbes, primarily in the Ruminococcaceae and Lachnospiraceae families; fecal metabolites including reduced levels of monoacylglycerols (endocannabinoid-related) and bile acids; and plasma metabolites including increased 4-ethyl phenyl sulfate, 1-arachidonoylglycerol (endocannabinoid), and sphingomyelin. Classifiers generated from baseline microbe, fecal metabolite, and plasma metabolite abundance distinguished high vs low SR with area under the receiver operating characteristic curve of 0.81, 0.83, and 0.91, respectively. Stress reactivity scores derived from these classifiers were significantly associated with flare risk during 6 to 24 months of follow-up, with odds ratios of 3.8, 4.1, and 4.9. Clinical flare and intestinal inflammation did not alter fecal microbial abundances but attenuated fecal and plasma metabolite differences between high and low SR. CONCLUSIONS High SR in UC is characterized by microbial signatures that predict clinical flare risk, suggesting that the microbiome may contribute to stress-induced UC flares.
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Affiliation(s)
- Jonathan P Jacobs
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, University of California Los Angeles, Los Angeles, CA, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Jenny S Sauk
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, University of California Los Angeles, Los Angeles, CA, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Aaron I Ahdoot
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Fengting Liang
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - William Katzka
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Hyo Jin Ryu
- A.T. Still University School of Osteopathic Medicine in Arizona, Mesa, AZ, USA
| | - Ariela Khandadash
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, University of California Los Angeles, Los Angeles, CA, USA
| | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jennifer S Labus
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, University of California Los Angeles, Los Angeles, CA, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Bruce D Naliboff
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, University of California Los Angeles, Los Angeles, CA, USA
- Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Emeran A Mayer
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, University of California Los Angeles, Los Angeles, CA, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Goodman-Luskin Microbiome Center, University of California Los Angeles, Los Angeles, CA, USA
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Shtossel O, Koren O, Shai I, Rinott E, Louzoun Y. Gut microbiome-metabolome interactions predict host condition. MICROBIOME 2024; 12:24. [PMID: 38336867 PMCID: PMC10858481 DOI: 10.1186/s40168-023-01737-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 12/10/2023] [Indexed: 02/12/2024]
Abstract
BACKGROUND The effect of microbes on their human host is often mediated through changes in metabolite concentrations. As such, multiple tools have been proposed to predict metabolite concentrations from microbial taxa frequencies. Such tools typically fail to capture the dependence of the microbiome-metabolite relation on the environment. RESULTS We propose to treat the microbiome-metabolome relation as the equilibrium of a complex interaction and to relate the host condition to a latent representation of the interaction between the log concentration of the metabolome and the log frequencies of the microbiome. We develop LOCATE (Latent variables Of miCrobiome And meTabolites rElations), a machine learning tool to predict the metabolite concentration from the microbiome composition and produce a latent representation of the interaction. This representation is then used to predict the host condition. LOCATE's accuracy in predicting the metabolome is higher than all current predictors. The metabolite concentration prediction accuracy significantly decreases cross datasets, and cross conditions, especially in 16S data. LOCATE's latent representation predicts the host condition better than either the microbiome or the metabolome. This representation is strongly correlated with host demographics. A significant improvement in accuracy (0.793 vs. 0.724 average accuracy) is obtained even with a small number of metabolite samples ([Formula: see text]). CONCLUSION These results suggest that a latent representation of the microbiome-metabolome interaction leads to a better association with the host condition than any of the two separated or the simple combination of the two. Video Abstract.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ehud Rinott
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
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Vestergaard MV, Allin KH, Eriksen C, Zakerska-Banaszak O, Arasaradnam RP, Alam MT, Kristiansen K, Brix S, Jess T. Gut microbiota signatures in inflammatory bowel disease. United European Gastroenterol J 2024; 12:22-33. [PMID: 38041519 PMCID: PMC10859715 DOI: 10.1002/ueg2.12485] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/10/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence. OBJECTIVES Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients. METHODS We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms. RESULTS Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found. CONCLUSIONS Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.
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Affiliation(s)
- Marie Vibeke Vestergaard
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Kristine H Allin
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Carsten Eriksen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Ramesh P Arasaradnam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
| | - Mohammad T Alam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Karsten Kristiansen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Brix
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
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Rudbaek JJ, Agrawal M, Torres J, Mehandru S, Colombel JF, Jess T. Deciphering the different phases of preclinical inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 2024; 21:86-100. [PMID: 37950021 PMCID: PMC11148654 DOI: 10.1038/s41575-023-00854-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/12/2023]
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated inflammatory disease (IMID) of the gastrointestinal tract and includes two subtypes: Crohn's disease and ulcerative colitis. It is well-recognized that IBD is associated with a complex multifactorial aetiology that includes genetic predisposition and environmental exposures, with downstream dysregulation of systemic immune function and host-microbial interactions in the local environment in the gut. Evidence to support the notion of a multistage development of IBD is growing, as has been observed in other IMIDs such as rheumatoid arthritis and systemic lupus erythematosus. With the rising worldwide incidence of IBD, it is increasingly important to understand the complex interplay of pathological events during the different stages of disease development to enable IBD prediction and prevention strategies. In this article, we review comprehensively the current evidence pertaining to the preclinical phase of IBD, including at-risk, initiation and expansion phases. We also discuss the framework of preclinical IBD, expanding on underlying pathways in IBD development, future research directions and IBD development in the context of other IMIDs.
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Affiliation(s)
- Jonas J Rudbaek
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Section for Biomarkers, Immunology and Antibodies, Department for Congenital Disorders, Statens Serum Institut, Copenhangen, Denmark
| | - Manasi Agrawal
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Division of Gastroenterology, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Saurabh Mehandru
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark.
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark.
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Wang L, Yin X, Liu H, Wang Y, Li Z, Zhao Y, Xu H, Huang C, Diao X. Development and validation of a sensitive liquid chromatography-tandem mass spectrometry method for the assay of 12 substances in rat plasma and its application to rat pharmacokinetics of Epimedium and Psoraleae Fructus herb pair after oral administration. J Sep Sci 2024; 47:e2300786. [PMID: 38234027 DOI: 10.1002/jssc.202300786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/11/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
Epimedium (EM) and Psoraleae Fructus (PF) are a traditional herb combination often used as a fixed form to treat osteoporosis disease in the clinic. However, the intricate interactions of this pair remain unknown. In our study, we undertook a comprehensive examination of their compatibility behaviors. Concurrently, a precise and sensitive quantitation method was successfully developed and validated using liquid chromatography-tandem mass spectrometry for the determination of 12 components. This method was applied in analyzing herbal extracts and biological samples (both in the portal vein and systemic plasma), which was also used to study the pharmacokinetics of the herb pair. The results indicated that the combination of EM and PF enhanced the dissolution of chemical components from PF in extracts, but it had a negligible influence on the contents of the components from EM. On the contrary, the in vivo exposure of the lowly exposed EM flavonoids significantly increased following the combination of EM and PF, whereas the highly exposed psoralen and isopsoralen were greatly reduced. These interactions might be crucial for the synergy and toxicity reduction of the herbal pair in disease treatment, which pave the way for further exploration into the clinical application and pharmacological mechanisms of EM and PF.
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Affiliation(s)
- Linwei Wang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoying Yin
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
- Shanghai Frontiers Science Research Center for Drug ability of Cardiovascular noncoding RNA, Shanghai, China
| | - Huan Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yangyang Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhixiong Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yuxuan Zhao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Haibo Xu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Chenggang Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingxing Diao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- XenoFinder Co. Ltd, Suzhou, China
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Pandey H, Jain D, Tang DWT, Wong SH, Lal D. Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease. Intest Res 2024; 22:15-43. [PMID: 37935653 PMCID: PMC10850697 DOI: 10.5217/ir.2023.00080] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 11/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.
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Affiliation(s)
| | | | - Daryl W. T. Tang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sunny H. Wong
- Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
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Guo W, Mao B, Tang X, Zhang Q, Zhao J, Zhang H, Chen W, Cui S. Improvement of inflammatory bowel disease by lactic acid bacteria-derived metabolites: a review. Crit Rev Food Sci Nutr 2023; 65:1261-1278. [PMID: 38078699 DOI: 10.1080/10408398.2023.2291188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Lactic acid bacteria (LAB) plays a crucial role in the establishment and maintenance of host health, as well as the improvement of some diseases. One of the major modes is the secretion of metabolites that may be intermediate or end products of the LAB's metabolism. In this review, we summarized some common metabolites (particularly short-chain fatty acids [SCFAs], bacteriocin, and exopolysaccharide [EPS]) from LAB in fermented foods and the gut for the first time. The effects of LAB-derived metabolites (LABM) on inflammation, oxidative stress, the intestinal barrier, and gut microbiota in inflammatory bowel disease (IBD) model are also discussed. The discovery of LABM and identification of IBD biomarkers are mainly attributed to the development of metabolomics technologies, especially nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), and liquid chromatography tandem mass spectrometry (LC-MS). The application of these metabolomics technologies in identification of LABM and IBD biomarkers are also summarized and analyzed. Although the beneficial effects of some LABM have been explored, undiscovered metabolites and their functions still need further investigations.
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Affiliation(s)
- Weiling Guo
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xin Tang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qiuxiang Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
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35
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Wu R, Xiong R, Li Y, Chen J, Yan R. Gut microbiome, metabolome, host immunity associated with inflammatory bowel disease and intervention of fecal microbiota transplantation. J Autoimmun 2023; 141:103062. [PMID: 37246133 DOI: 10.1016/j.jaut.2023.103062] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023]
Abstract
Gut dysbiosis has been associated with inflammatory bowel disease (IBD), one of the most common gastrointestinal diseases. The microbial communities play essential roles in host physiology, with profound effects on immune homeostasis, directly or via their metabolites and/or components. There are increasing clinical trials applying fecal microbiota transplantation (FMT) with Crohn's disease (CD) and ulcerative colitis (UC). The restoration of dysbiotic gut microbiome is considered as one of the mechanisms of FMT therapy. In this work, latest advances in the alterations in gut microbiome and metabolome features in IBD patients and experimental mechanistic understanding on their contribution to the immune dysfunction were reviewed. Then, the therapeutic outcomes of FMT on IBD were summarized based on clinical remission, endoscopic remission and histological remission of 27 clinical trials retrieved from PubMed which have been registered on ClinicalTrials.gov with the results been published in the past 10 years. Although FMT is established as an effective therapy for both subtypes of IBD, the promising outcomes are not always achieved. Among the 27 studies, only 11 studies performed gut microbiome profiling, 5 reported immune response alterations and 3 carried out metabolome analysis. Generally, FMT partially restored typical changes in IBD, resulted in increased α-diversity and species richness in responders and similar but less pronounced shifts of patient microbial and metabolomics profiles toward donor profiles. Measurements of immune responses to FMT mainly focused on T cells and revealed divergent effects on pro-/anti-inflammatory functions. The very limited information and the extremely confounding factors in the designs of the FMT trials significantly hindered a reasonable conclusion on the mechanistic involvement of gut microbiota and metabolites in clinical outcomes and an analysis of the inconsistencies.
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Affiliation(s)
- Rongrong Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Rui Xiong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Yan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Junru Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
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Hong Z, Shi C, Hu X, Chen J, Li T, Zhang L, Bai Y, Dai J, Sheng J, Xie J, Tian Y. Walnut Protein Peptides Ameliorate DSS-Induced Ulcerative Colitis Damage in Mice: An in Silico Analysis and in Vivo Investigation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15604-15619. [PMID: 37815395 DOI: 10.1021/acs.jafc.3c04220] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Walnut (Juglans regia L.) is a food with food-medicine homology, whose derived protein peptides have been shown to have anti-inflammatory activity in vitro. However, the effects and mechanisms of walnut protein peptides on ulcerative colitis (UC) in vivo have not been systematically and thoroughly investigated. In this study, we applied virtual screening and network pharmacology screening of bioactive peptides to obtain three novel WPPs (SHTLP, HYNLN, and LGTYP) that may alleviate UC through TLR4-MAPK signaling. In vivo studies have shown that WPPs improve intestinal mucosal barrier dysfunction and reduce inflammation by inhibiting activation of the TLR4-MAPK pathway. In addition, WPPs restore intestinal microbial homeostasis by reducing harmful bacteria (Helicobacter and Bacteroides) and increasing the relative abundance of beneficial bacteria (Candidatus_Saccharimonas). Our study showed that the WPPs obtained by virtual screening were effective in ameliorating colitis, which has important implications for future screening of bioactive peptides from medicinal food homologues as drugs or dietary supplements.
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Affiliation(s)
- Zishan Hong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, China
| | - Chongying Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming 650201, China
| | - Xia Hu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming 650201, China
| | - Jinlian Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming 650201, China
| | - Tingting Li
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming 650201, China
| | - Li Zhang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming 650201, China
| | - Yuying Bai
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming 650201, China
| | - Jingjing Dai
- School of Tea and Coffee, Puer University, Puer 665000, China
| | - Jun Sheng
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jing Xie
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, China
| | - Yang Tian
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, China
- School of Tea and Coffee, Puer University, Puer 665000, China
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Yin R, Wang T, Dai H, Han J, Sun J, Liu N, Dong W, Zhong J, Liu H. Immunogenic molecules associated with gut bacterial cell walls: chemical structures, immune-modulating functions, and mechanisms. Protein Cell 2023; 14:776-785. [PMID: 37013853 PMCID: PMC10599643 DOI: 10.1093/procel/pwad016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/25/2023] [Indexed: 04/05/2023] Open
Abstract
Interactions between gut microbiome and host immune system are fundamental to maintaining the intestinal mucosal barrier and homeostasis. At the host-gut microbiome interface, cell wall-derived molecules from gut commensal bacteria have been reported to play a pivotal role in training and remodeling host immune responses. In this article, we review gut bacterial cell wall-derived molecules with characterized chemical structures, including peptidoglycan and lipid-related molecules that impact host health and disease processes via regulating innate and adaptive immunity. Also, we aim to discuss the structures, immune responses, and underlying mechanisms of these immunogenic molecules. Based on current advances, we propose cell wall-derived components as important sources of medicinal agents for the treatment of infection and immune diseases.
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Affiliation(s)
- Ruopeng Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanqin Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ningning Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wang Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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Unal M, Bostanci E, Ozkul C, Acici K, Asuroglu T, Guzel MS. Crohn's Disease Prediction Using Sequence Based Machine Learning Analysis of Human Microbiome. Diagnostics (Basel) 2023; 13:2835. [PMID: 37685376 PMCID: PMC10486516 DOI: 10.3390/diagnostics13172835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/24/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Human microbiota refers to the trillions of microorganisms that inhabit our bodies and have been discovered to have a substantial impact on human health and disease. By sampling the microbiota, it is possible to generate massive quantities of data for analysis using Machine Learning algorithms. In this study, we employed several modern Machine Learning techniques to predict Inflammatory Bowel Disease using raw sequence data. The dataset was obtained from NCBI preprocessed graph representations and converted into a structured form. Seven well-known Machine Learning frameworks, including Random Forest, Support Vector Machines, Extreme Gradient Boosting, Light Gradient Boosting Machine, Gaussian Naïve Bayes, Logistic Regression, and k-Nearest Neighbor, were used. Grid Search was employed for hyperparameter optimization. The performance of the Machine Learning models was evaluated using various metrics such as accuracy, precision, fscore, kappa, and area under the receiver operating characteristic curve. Additionally, Mc Nemar's test was conducted to assess the statistical significance of the experiment. The data was constructed using k-mer lengths of 3, 4 and 5. The Light Gradient Boosting Machine model overperformed over other models with 67.24%, 74.63% and 76.47% accuracy for k-mer lengths of 3, 4 and 5, respectively. The LightGBM model also demonstrated the best performance in each metric. The study showed promising results predicting disease from raw sequence data. Finally, Mc Nemar's test results found statistically significant differences between different Machine Learning approaches.
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Affiliation(s)
- Metehan Unal
- Department of Computer Engineering, Ankara University, 06830 Ankara, Turkey; (M.U.)
| | - Erkan Bostanci
- Department of Computer Engineering, Ankara University, 06830 Ankara, Turkey; (M.U.)
| | - Ceren Ozkul
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, 06230 Ankara, Turkey
| | - Koray Acici
- Department of Artificial Intelligence and Data Engineering, Ankara University, 06830 Ankara, Turkey
| | - Tunc Asuroglu
- Faculty of Medicine and Health Technology, Tampere University, 33720 Tampere, Finland
| | - Mehmet Serdar Guzel
- Department of Computer Engineering, Ankara University, 06830 Ankara, Turkey; (M.U.)
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Mujalli A, Farrash WF, Alghamdi KS, Obaid AA. Metabolite Alterations in Autoimmune Diseases: A Systematic Review of Metabolomics Studies. Metabolites 2023; 13:987. [PMID: 37755267 PMCID: PMC10537330 DOI: 10.3390/metabo13090987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Autoimmune diseases, characterized by the immune system's loss of self-tolerance, lack definitive diagnostic tests, necessitating the search for reliable biomarkers. This systematic review aims to identify common metabolite changes across multiple autoimmune diseases. Following PRISMA guidelines, we conducted a systematic literature review by searching MEDLINE, ScienceDirect, Google Scholar, PubMed, and Scopus (Elsevier) using keywords "Metabolomics", "Autoimmune diseases", and "Metabolic changes". Articles published in English up to March 2023 were included without a specific start date filter. Among 257 studies searched, 88 full-text articles met the inclusion criteria. The included articles were categorized based on analyzed biological fluids: 33 on serum, 21 on plasma, 15 on feces, 7 on urine, and 12 on other biological fluids. Each study presented different metabolites with indications of up-regulation or down-regulation when available. The current study's findings suggest that amino acid metabolism may serve as a diagnostic biomarker for autoimmune diseases, particularly in systemic lupus erythematosus (SLE), multiple sclerosis (MS), and Crohn's disease (CD). While other metabolic alterations were reported, it implies that autoimmune disorders trigger multi-metabolite changes rather than singular alterations. These shifts could be consequential outcomes of autoimmune disorders, representing a more complex interplay. Further studies are needed to validate the metabolomics findings associated with autoimmune diseases.
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Affiliation(s)
- Abdulrahman Mujalli
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 24381, Saudi Arabia; (W.F.F.); (A.A.O.)
| | - Wesam F. Farrash
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 24381, Saudi Arabia; (W.F.F.); (A.A.O.)
| | - Kawthar S. Alghamdi
- Department of Biology, College of Science, University of Hafr Al Batin, Hafar Al-Batin 39511, Saudi Arabia;
| | - Ahmad A. Obaid
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 24381, Saudi Arabia; (W.F.F.); (A.A.O.)
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Dovrolis N, Moschoviti A, Fessatou S, Karamanolis G, Kolios G, Gazouli M. Identifying Microbiome Dynamics in Pediatric IBD: More than a Family Matter. Biomedicines 2023; 11:1979. [PMID: 37509618 PMCID: PMC10377534 DOI: 10.3390/biomedicines11071979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Pediatric inflammatory bowel disease (IBD) is a chronic inflammatory intestinal disease that affects both children and adolescents. Symptoms can significantly affect a child's growth, development, and quality of life, making early diagnosis and effective management crucial. This study focuses on treatment-naïve pediatric IBD patients and their immediate families to identify the role of the microbiome in disease onset. METHODS Nine families with pediatric IBD were recruited, comprising seven drug-naïve Crohn's disease (CD) patients and two drug-naïve ulcerative colitis (UC) patients, as well as twenty-four healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing and bioinformatics analysis. RESULTS We identified patterns of dysbiosis and hallmark microbial taxa among patients who shared ethnic, habitual, and dietary traits with themselves and their families. In addition, we examined the impact of the disease on specific microbial taxa and how these could serve as potential biomarkers for early detection. CONCLUSIONS Our results suggest a potential role of maternal factors in the establishment and modulation of the early life microbiome, consistent with the current literature, which may have implications for understanding the etiology and progression of IBD.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (N.D.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Anastasia Moschoviti
- Third Department of Pediatrics, “Attikon” General University Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Haidari, Greece; (A.M.); (S.F.)
| | - Smaragdi Fessatou
- Third Department of Pediatrics, “Attikon” General University Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Haidari, Greece; (A.M.); (S.F.)
| | - George Karamanolis
- Gastroenterology Unit, Second Department of Surgery, Aretaieio Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - George Kolios
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (N.D.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Maria Gazouli
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- School of Science and Technology, Hellenic Open University, 26335 Patra, Greece
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Su X, Gao Y, Yang R. Gut microbiota derived bile acid metabolites maintain the homeostasis of gut and systemic immunity. Front Immunol 2023; 14:1127743. [PMID: 37256134 PMCID: PMC10225537 DOI: 10.3389/fimmu.2023.1127743] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/07/2023] [Indexed: 06/01/2023] Open
Abstract
Bile acids (BAs) as cholesterol-derived molecules play an essential role in some physiological processes such as nutrient absorption, glucose homeostasis and regulation of energy expenditure. They are synthesized in the liver as primary BAs such as cholic acid (CA), chenodeoxycholic acid (CDCA) and conjugated forms. A variety of secondary BAs such as deoxycholic acid (DCA) and lithocholic acid (LCA) and their derivatives is synthesized in the intestine through the involvement of various microorganisms. In addition to essential physiological functions, BAs and their metabolites are also involved in the differentiation and functions of innate and adaptive immune cells such as macrophages (Macs), dendritic cells (DCs), myeloid derived suppressive cells (MDSCs), regulatory T cells (Treg), Breg cells, T helper (Th)17 cells, CD4 Th1 and Th2 cells, CD8 cells, B cells and NKT cells. Dysregulation of the BAs and their metabolites also affects development of some diseases such as inflammatory bowel diseases. We here summarize recent advances in how BAs and their metabolites maintain gut and systemic homeostasis, including the metabolism of the BAs and their derivatives, the role of BAs and their metabolites in the differentiation and function of immune cells, and the effects of BAs and their metabolites on immune-associated disorders.
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Affiliation(s)
- Xiaomin Su
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Yunhuan Gao
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Rongcun Yang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
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Kim SY, Shin SY, Park SJ, Im JP, Kim HJ, Lee KM, Kim JW, Jung SA, Lee J, Kang SB, Shin SJ, Kim ES, Kim YS, Kim TO, Kim HS, Park DI, Kim HK, Kim ES, Kim YH, Teng D, Kim JH, Kim W, Saeed M, Moon JM, Kim K, Choi CH, Choi HK. Changes in fecal metabolic and lipidomic features by anti-TNF treatment and prediction of clinical remission in patients with ulcerative colitis. Therap Adv Gastroenterol 2023; 16:17562848231168199. [PMID: 37153496 PMCID: PMC10161336 DOI: 10.1177/17562848231168199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/21/2023] [Indexed: 05/09/2023] Open
Abstract
Background Therapeutic targets for ulcerative colitis (UC) and prediction models of antitumor necrosis factor (TNF) therapy outcomes have not been fully reported. Objective Investigate the characteristic metabolite and lipid profiles of fecal samples of UC patients before and after adalimumab treatment and develop a prediction model of clinical remission following adalimumab treatment. Design Prospective, observational, multicenter study was conducted on moderate-to-severe UC patients (n = 116). Methods Fecal samples were collected from UC patients at 8 and 56 weeks of adalimumab treatment and from healthy controls (HC, n = 37). Clinical remission was assessed using the Mayo score. Metabolomic and lipidomic analyses were performed using gas chromatography mass spectrometry and nano electrospray ionization mass spectrometry, respectively. Orthogonal partial least squares discriminant analysis was performed to establish a remission prediction model. Results Fecal metabolites in UC patients markedly differed from those in HC at baseline and were changed similarly to those in HC during treatment; however, lipid profiles did not show these patterns. After treatment, the fecal characteristics of remitters (RM) were closer to those of HC than to those of non-remitters (NRM). At 8 and 56 weeks, amino acid levels in RM were lower than those in NRM and similar to those in HC. After 56 weeks, levels of 3-hydroxybutyrate, lysine, and phenethylamine decreased, and dodecanoate level increased in RM similarly to those in HC. The prediction model of long-term remission in male patients based on lipid biomarkers showed a higher performance than clinical markers. Conclusion Fecal metabolites in UC patients markedly differ from those in HC, and the levels in RM are changed similarly to those in HC after anti-TNF therapy. Moreover, 3-hydroxybutyrate, lysine, phenethylamine, and dodecanoate are suggested as potential therapeutic targets for UC. A prediction model of long-term remission based on lipid biomarkers may help implement personalized treatment.
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Affiliation(s)
- Seok-Young Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Seung Yong Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Soo Jung Park
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Pil Im
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyo Jong Kim
- Department of Gastroenterology, Kyung Hee University Hospital, Seoul, South Korea
| | - Kang-Moon Lee
- Department of Gastroenterology, The Catholic University of Korea St. Vincent’s Hospital, Suwon, South Korea
| | - Ji Won Kim
- Department of Gastroenterology, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Sung-Ae Jung
- Department of Gastroenterology, Ewha Woman’s University College of Medicine, Seoul, South Korea
| | - Jun Lee
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, South Korea
| | - Sang-Bum Kang
- Department of Gastroenterology, The Catholic University of Korea Daejeon St. Mary’s Hospital, Daejeon, South Korea
| | - Sung Jae Shin
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
| | - Eun Sun Kim
- Department of Gastroenterology, Korea University Anam Hospital, Seoul, South Korea
| | - You Sun Kim
- Department of Gastroenterology, Inje University Seoul Paik Hospital, Seoul, South Korea
| | - Tae Oh Kim
- Department of Gastroenterology, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Hyun-Soo Kim
- Department of Gastroenterology, Chonnam National University Hospital, Gwangju, South Korea
| | - Dong Il Park
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul, South Korea
| | - Hyung Kil Kim
- Department of Gastroenterology, Inha University Hospital, Incheon, South Korea
| | - Eun Soo Kim
- Department of Internal Medicine, Kyungpook National University, School of Medicine, Daegu, South Korea
| | - Young-Ho Kim
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul, South Korea
| | - Maham Saeed
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Jung Min Moon
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Kisung Kim
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Chang Hwan Choi
- Professor of Medicine, Internal Medicine, Chung-Ang University College of Medicine, 102 Heukseok-ro, Dongjak-gu, Seoul 06973, Republic of Korea
| | - Hyung-Kyoon Choi
- Professor of College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
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43
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Pretorius L, Smith C. Tyramine-induced gastrointestinal dysregulation is attenuated via estradiol associated mechanisms in a zebrafish larval model. Toxicol Appl Pharmacol 2023; 461:116399. [PMID: 36716863 DOI: 10.1016/j.taap.2023.116399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
Abstract
Development of targeted therapeutics to alleviate gastrointestinal (GI) inflammation and its debilitating consequences are required. In this context, the trace aminergic system may link together sex, diet and inflammation. Utilising a zebrafish larval model of GI inflammation, the current study aimed to investigate mechanisms by which excess amounts of trace amines (TAs) may influence GI health. In addition, we probed the potential role of 17β-estradiol (E2) and its receptors, given the known female-predominance of many GI disorders. To assess GI functionality and integrity, live imaging techniques (neutral red staining) and post-mortem immunofluorescent staining of tight junction proteins (occludin and ZO-1) were analyzed respectively. In addition, behavioural assays, as an indication of overall wellbeing, as well as whole body H2O2 and prostaglandin E2 assays were performed to inform on oxidative and inflammatory status. Excess β-phenethylamine (PEA), tryptamine (TRP) and ρ-tyramine (TYR) resulted in adverse GI and systemic effects. In this regard, clear beneficial effects of E2 to modulate the effects of PEA, TRP and TYR was evident. Moreover, agmatine displayed potential protective effects on GI epithelium and whole body oxidative status, however, potential to induce systemic inflammation suggests the importance of dosage and administration optimisation. Taken together, TYR seems like the most prominent TA to have damaging GI effects, feasibly exacerbating GI inflammation. In this context, the relative lack of E2 may provide mechanistic insights into the reported female-predominance of GI disorders. Moreover, an effective therapeutic in this context may be required to maintain GI TA load despite fluctuating E2 levels.
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Affiliation(s)
- L Pretorius
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - C Smith
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.
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44
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Jacobs JP, Lagishetty V, Hauer MC, Labus JS, Dong TS, Toma R, Vuyisich M, Naliboff BD, Lackner JM, Gupta A, Tillisch K, Mayer EA. Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes. MICROBIOME 2023; 11:5. [PMID: 36624530 PMCID: PMC9830758 DOI: 10.1186/s40168-022-01450-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes. METHODS Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368). Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety. Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. Differential features were used to construct random forests classifiers. RESULTS IBS was associated with global alterations in microbiome composition by 16S rRNA sequencing and metatranscriptomics, and in microbiome function by predicted metagenomics, metatranscriptomics, and metabolomics. After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety, IBS was associated with differential abundance of bacterial taxa such as Bacteroides dorei; metabolites including increased tyramine and decreased gentisate and hydrocinnamate; and transcripts related to fructooligosaccharide and polyol utilization. IBS further showed transcriptional upregulation of enzymes involved in fructose and glucan metabolism as well as the succinate pathway of carbohydrate fermentation. A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86). CONCLUSIONS IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates-consistent with the clinical benefit of diets restricting this energy source-that also includes multiple previously unrecognized metabolites and metabolic pathways. These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. Video Abstract.
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Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA.
| | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Megan C Hauer
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer S Labus
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Tien S Dong
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Ryan Toma
- Viome Life Sciences, Bellevue, WA, USA
| | | | - Bruce D Naliboff
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeffrey M Lackner
- Division of Behavioral Medicine, Department of Medicine, Jacobs School of Medicine, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Arpana Gupta
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kirsten Tillisch
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Integrative Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Emeran A Mayer
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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45
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Larabi AB, Masson HLP, Bäumler AJ. Bile acids as modulators of gut microbiota composition and function. Gut Microbes 2023; 15:2172671. [PMID: 36740850 PMCID: PMC9904317 DOI: 10.1080/19490976.2023.2172671] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Changes in the composition of gut-associated microbial communities are associated with many human illnesses, but the factors driving dysbiosis remain incompletely understood. One factor governing the microbiota composition in the gut is bile. Bile acids shape the microbiota composition through their antimicrobial activity and by activating host signaling pathways that maintain gut homeostasis. Although bile acids are host-derived, their functions are integrally linked to bacterial metabolism, which shapes the composition of the intestinal bile acid pool. Conditions that change the size or composition of the bile acid pool can trigger alterations in the microbiota composition that exacerbate inflammation or favor infection with opportunistic pathogens. Therefore, manipulating the composition or size of the bile acid pool might be a promising strategy to remediate dysbiosis.
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Affiliation(s)
- Anaïs B. Larabi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Hugo L. P. Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
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46
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Shtossel O, Isakov H, Turjeman S, Koren O, Louzoun Y. Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy. Gut Microbes 2023; 15:2224474. [PMID: 37345233 PMCID: PMC10288916 DOI: 10.1080/19490976.2023.2224474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/08/2023] [Indexed: 06/23/2023] Open
Abstract
The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine-learning-based biomarker development for multiple diseases and conditions. The microbiome is often analyzed using 16S rRNA gene sequencing or shotgun metagenomics. However, several properties of microbial sequence-based studies hinder machine learning (ML), including non-uniform representation, a small number of samples compared with the dimension of each sample, and sparsity of the data, with the majority of taxa present in a small subset of samples. We show here using a graph representation that the cladogram structure is as informative as the taxa frequency. We then suggest a novel method to combine information from different taxa and improve data representation for ML using microbial taxonomy. iMic (image microbiome) translates the microbiome to images through an iterative ordering scheme, and applies convolutional neural networks to the resulting image. We show that iMic has a higher precision in static microbiome gene sequence-based ML than state-of-the-art methods. iMic also facilitates the interpretation of the classifiers through an explainable artificial intelligence (AI) algorithm to iMic to detect taxa relevant to each condition. iMic is then extended to dynamic microbiome samples by translating them to movies.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Haim Isakov
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Sondra Turjeman
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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47
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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48
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Calzadilla N, Comiskey SM, Dudeja PK, Saksena S, Gill RK, Alrefai WA. Bile acids as inflammatory mediators and modulators of intestinal permeability. Front Immunol 2022; 13:1021924. [PMID: 36569849 PMCID: PMC9768584 DOI: 10.3389/fimmu.2022.1021924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Bile acids are critical for the digestion and absorption of lipids and fat-soluble vitamins; however, evidence continues to emerge supporting additional roles for bile acids as signaling molecules. After they are synthesized from cholesterol in the liver, primary bile acids are modified into secondary bile acids by gut flora contributing to a diverse pool and making the composition of bile acids highly sensitive to alterations in gut microbiota. Disturbances in bile acid homeostasis have been observed in patients with Inflammatory Bowel Diseases (IBD). In fact, a decrease in secondary bile acids was shown to occur because of IBD-associated dysbiosis. Further, the increase in luminal bile acids due to malabsorption in Crohn's ileitis and ileal resection has been implicated in the induction of diarrhea and the exacerbation of inflammation. A causal link between bile acid signaling and intestinal inflammation has been recently suggested. With respect to potential mechanisms related to bile acids and IBD, several studies have provided strong evidence for direct effects of bile acids on intestinal permeability in porcine and rodent models as well as in humans. Interestingly, different bile acids were shown to exert distinct effects on the inflammatory response and intestinal permeability that require careful consideration. Such findings revealed a potential effect for changes in the relative abundance of different bile acids on the induction of inflammation by bile acids and the development of IBD. This review summarizes current knowledge about the roles for bile acids as inflammatory mediators and modulators of intestinal permeability mainly in the context of inflammatory bowel diseases.
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Affiliation(s)
- Nathan Calzadilla
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Department of Bioengineering, University of Illinois, Chicago, IL, United States
| | - Shane M. Comiskey
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
| | - Pradeep K. Dudeja
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Research and Development, Jesse Brown VA Medical Center, Chicago, IL, United States
| | - Seema Saksena
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Research and Development, Jesse Brown VA Medical Center, Chicago, IL, United States
| | - Ravinder K. Gill
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
| | - Waddah A. Alrefai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Research and Development, Jesse Brown VA Medical Center, Chicago, IL, United States
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49
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Monma T, Iwamoto J, Ueda H, Tamamushi M, Kakizaki F, Konishi N, Yara S, Miyazaki T, Hirayama T, Ikegami T, Honda A. Evaluation of gut dysbiosis using serum and fecal bile acid profiles. World J Clin Cases 2022; 10:12484-12493. [PMID: 36579096 PMCID: PMC9791502 DOI: 10.12998/wjcc.v10.i34.12484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 12/02/2022] Open
Abstract
Dysbiosis in the intestinal microflora can affect the gut production of microbial metabolites, and toxic substances can disrupt the barrier function of the intestinal wall, leading to the development of various diseases. Decreased levels of Clostridium subcluster XIVa (XIVa) are associated with the intestinal dysbiosis found in inflammatory bowel disease (IBD) and Clostridium difficile infection (CDI). Since XIVa is a bacterial group responsible for the conversion of primary bile acids (BAs) to secondary BAs, the proportion of intestinal XIVa can be predicted by determining the ratio of deoxycholic acid (DCA)/[DCA + cholic acid (CA)] in feces orserum. For example, serum DCA/(DCA+CA) was significantly lower in IBD patients than in healthy controls, even in the remission period. These results suggest that a low proportion of intestinal XIVa in IBD patients might be a precondition for IBD onset but not a consequence of intestinal inflammation. Another report showed that a reduced serum DCA/(DCA + CA) ratio could predict susceptibility to CDI. Thus, the BA profile, particularly the ratio of secondary to primary BAs, can serve as a surrogate marker of the intestinal dysbiosis caused by decreased XIVa.
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Affiliation(s)
- Tadakuni Monma
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Junichi Iwamoto
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Hajime Ueda
- Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Makoto Tamamushi
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Fumio Kakizaki
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Naoki Konishi
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Shoichiro Yara
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Teruo Miyazaki
- Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Takeshi Hirayama
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Tadashi Ikegami
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Akira Honda
- Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
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50
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Muller E, Algavi YM, Borenstein E. The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis. NPJ Biofilms Microbiomes 2022; 8:79. [PMID: 36243731 PMCID: PMC9569371 DOI: 10.1038/s41522-022-00345-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Integrative analysis of microbiome and metabolome data obtained from human fecal samples is a promising avenue for better understanding the interplay between bacteria and metabolites in the human gut, in both health and disease. However, acquiring, processing, and unifying such datasets from multiple sources is a daunting and challenging task. Here we present a publicly available, simple-to-use, curated dataset collection of paired fecal microbiome-metabolome data from multiple cohorts. This data resource allows researchers to easily obtain multiple fully processed and integrated microbiome-metabolome datasets, facilitating the discovery of universal microbe-metabolite links, benchmark various microbiome-metabolome integration tools, and compare newly identified microbe-metabolite findings to other published datasets.
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Affiliation(s)
- Efrat Muller
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Yadid M Algavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
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