1
|
Rahaman MM, Wangchuk P, Sarker S. A systematic review on the role of gut microbiome in inflammatory bowel disease: Spotlight on virome and plant metabolites. Microb Pathog 2025; 205:107608. [PMID: 40250496 DOI: 10.1016/j.micpath.2025.107608] [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: 08/02/2024] [Revised: 04/14/2025] [Accepted: 04/16/2025] [Indexed: 04/20/2025]
Abstract
Inflammatory bowel diseases (IBD), including ulcerative colitis and Crohn's disease, arise from various factors such as dietary, genetic, immunological, and microbiological influences. The gut microbiota plays a crucial role in the development and treatment of IBD, though the exact mechanisms remain uncertain. Current research has yet to definitively establish the beneficial effects of the microbiome on IBD. Bacteria and viruses (both prokaryotic and eukaryotic) are key components of the microbiome uniquely related to IBD. Numerous studies suggest that dysbiosis of the microbiota, including bacteria, viruses, and bacteriophages, contributes to IBD pathogenesis. Conversely, some research indicates that bacteria and bacteriophages may positively impact IBD outcomes. Additionally, plant metabolites play a crucial role in alleviating IBD due to their anti-inflammatory and microbiome-modulating properties. This systematic review discusses the role of the microbiome in IBD pathogenesis and evaluates the potential connection between plant metabolites and the microbiome in the context of IBD pathophysiology.
Collapse
Affiliation(s)
- Md Mizanur Rahaman
- Biomedical Sciences and Molecular Biology, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
| | - Phurpa Wangchuk
- College of Science and Engineering, James Cook University, Nguma Bada campus, McGregor Rd, Smithfield, Cairns, QLD 4878, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Nguma Bada campus, McGregor Rd, Smithfield, Cairns, QLD, 4878, Australia
| | - Subir Sarker
- Biomedical Sciences and Molecular Biology, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia.
| |
Collapse
|
2
|
Seira Curto J, Dominguez Martinez A, Perez Collell G, Barniol Simon E, Romero Ruiz M, Franco Bordés B, Sotillo Sotillo P, Villegas Hernandez S, Fernandez MR, Sanchez de Groot N. Exogenous prion-like proteins and their potential to trigger cognitive dysfunction. Mol Syst Biol 2025:10.1038/s44320-025-00114-4. [PMID: 40425815 DOI: 10.1038/s44320-025-00114-4] [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: 05/03/2024] [Revised: 04/16/2025] [Accepted: 05/02/2025] [Indexed: 05/29/2025] Open
Abstract
The gut is exposed to a wide range of proteins, including ingested proteins and those produced by the resident microbiota. While ingested prion-like proteins can propagate across species, their implications for disease development remain largely unknown. Here, we apply a multidisciplinary approach to examine the relationship between the biophysical properties of exogenous prion-like proteins and the phenotypic consequences of ingesting them. Through computational analysis of gut bacterial proteins, we identified an enrichment of prion-like sequences in Helicobacter pylori. Based on these findings, we rationally designed a set of synthetic prion-like sequences that form amyloid fibrils, interfere with amyloid-beta-peptide aggregation, and trigger prion propagation when introduced in the yeast Sup35 model. When C. elegans were fed bacteria expressing these prion-like proteins, they lost associative memory and exhibited increased lipid oxidation. These data suggest a link between memory impairment, the conformational state of aggregates, and oxidative stress. Overall, this work supports gut microbiota as a reservoir of exogenous prion-like sequences, especially H. pylori, and the gut as an entry point for molecules capable of triggering cognitive dysfunction.
Collapse
Affiliation(s)
- Jofre Seira Curto
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Adan Dominguez Martinez
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Genis Perez Collell
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Estrella Barniol Simon
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina Romero Ruiz
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Berta Franco Bordés
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Paula Sotillo Sotillo
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sandra Villegas Hernandez
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Rosario Fernandez
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Natalia Sanchez de Groot
- Unitat de Bioquímica, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.
| |
Collapse
|
3
|
Pastuszka A, Tobor S, Łoniewski I, Wierzbicka-Woś A, Sielatycka K, Styburski D, Cembrowska-Lech D, Koszutski T, Kurowicz M, Korlacka K, Podkówka A, Lemiński A, Brodkiewicz A, Hyla-Klekot L, Skonieczna-Żydecka K. Rewriting the urinary tract paradigm: the urobiome as a gatekeeper of host defense. Mol Biol Rep 2025; 52:497. [PMID: 40407923 PMCID: PMC12102141 DOI: 10.1007/s11033-025-10609-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 05/13/2025] [Indexed: 05/26/2025]
Abstract
The urobiome, or urinary tract microbiome, has emerged as a crucial component in maintaining urinary health and defending against infections. Recent advances in next-generation sequencing (NGS) have debunked the long-held belief that the urinary tract is sterile, revealing a unique ecosystem of microorganisms. The urobiome interacts with the urothelium and mucosa-associated lymphoid tissue (MALT) to support local immunity, playing an integral role in defending the urinary tract against pathogens. Through complex communication processes like quorum sensing, the urobiome regulates microbial behavior and controls interactions with host tissues, helping to prevent pathogen colonization and infection. However, dysbiosis in the urobiome can disrupt this balance, making the urinary tract more susceptible to infections, including urinary tract infections (UTIs). Studies have highlighted specific microbial compositions associated with both healthy and disease states, suggesting that shifts in the urobiome may correlate with various urological diseases. Furthermore, microbial diversity within the urinary tract differs by factors such as age and gender, reflecting the dynamic nature of the urobiome. Future research focusing on the interplay between the urobiome, host immune defenses, and pathogenic mechanisms may lead to innovative diagnostic and therapeutic approaches. Understanding how microbial composition changes during disease states could enable targeted treatments, potentially reducing reliance on antibiotics and minimizing resistance issues. The urobiome thus represents a promising frontier in urology, with implications for enhancing urinary health and treating infections more effectively.
Collapse
Affiliation(s)
- Agnieszka Pastuszka
- Chair and Department of Descriptive and Topographic Anatomy, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Szymon Tobor
- Department of Pediatric Surgery and Urology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Igor Łoniewski
- Department of Biochemical Science, Faculty of Health Sciences, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | | | - Katarzyna Sielatycka
- Sanprobi Sp. z. o. o sp. k., Szczecin, Poland
- Institute of Biology, Faculty of Exact and Natural Sciences, University of Szczecin, Szczecin, Poland
| | | | | | - Tomasz Koszutski
- Department of Pediatric Surgery and Urology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Marek Kurowicz
- Chair and Department of Descriptive and Topographic Anatomy, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Klaudia Korlacka
- Department of Pediatric Surgery and Urology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Albert Podkówka
- Department of Biochemical Science, Faculty of Health Sciences, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Artur Lemiński
- Department of Biochemical Science, Faculty of Health Sciences, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotherapy and Management of Acute Poisoning, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Lidia Hyla-Klekot
- Department of Pediatric Surgery and Urology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Karolina Skonieczna-Żydecka
- Department of Biochemical Science, Faculty of Health Sciences, Pomeranian Medical University in Szczecin, Szczecin, Poland.
| |
Collapse
|
4
|
Chen ASY, Kim H, Nzabarushimana E, Shen J, Williams K, Gurung J, McGoldrick J, Burke KE, Yarze JC, Nguyen LH, Staller K, Chung DC, Xavier RJ, Khalili H. Association of distinct microbial and metabolic signatures with microscopic colitis. Nat Commun 2025; 16:4644. [PMID: 40410138 PMCID: PMC12102337 DOI: 10.1038/s41467-025-59566-9] [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: 12/14/2024] [Accepted: 04/25/2025] [Indexed: 05/25/2025] Open
Abstract
Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine that primarily affects older adults and presents with chronic diarrhea. The etiology is unknown and there are currently no FDA approved medications or biomarkers for treatment or monitoring of the disease. Emerging evidence have implicated the gut microbiome and metabolome disturbances in MC pathogenesis. We conduct a comprehensive analysis of gut microbial and metabolic changes in a cohort of 683 participants, including 131 patients with active MC, 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. Stool microbiome and metabolome are profiled using whole-genome shotgun metagenomic sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Compared to controls, eight microbial species including pro-inflammatory oral-typical Veillonella dispar and Haemophilus parainfluenzae, and 11 species, including anti-inflammatory Blautia glucerasea and Bacteroides stercoris are enriched and depleted in MC, respectively. Pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens, are enriched in active MC. Multi-omics analyses reveal robust associations between microbial species, metabolic pathways, and metabolites, suggesting concordant disruptions in MC. Here, we show distinct shifts in gut microbiome and metabolome in MC that can inform the development of non-invasive biomarkers and novel therapeutics.
Collapse
Affiliation(s)
- Albert Sheng-Yin Chen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanseul Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Etienne Nzabarushimana
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiaxian Shen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Katherine Williams
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jenny Gurung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica McGoldrick
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kristin E Burke
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph C Yarze
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kyle Staller
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hamed Khalili
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
5
|
Rahman Hera M, Koslicki D. Estimating similarity and distance using FracMinHash. Algorithms Mol Biol 2025; 20:8. [PMID: 40375084 DOI: 10.1186/s13015-025-00276-8] [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: 10/25/2024] [Accepted: 03/30/2025] [Indexed: 05/18/2025] Open
Abstract
MOTIVATION The increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizing k -mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash has emerged as a popular sketching technique and has been used in several useful applications. Recent studies on FracMinHash proved unbiased estimators for the containment and Jaccard indices. However, theoretical investigations for other metrics are still lacking. THEORETICAL CONTRIBUTIONS In this paper, we present a theoretical framework for estimating similarity/distance metrics by using FracMinHash sketches, when the metric is expressible in a certain form. We establish conditions under which such an estimation is sound and recommend a minimum scale factor s for accurate results. Experimental evidence supports our theoretical findings. PRACTICAL CONTRIBUTIONS We also present frac-kmc, a fast and efficient FracMinHash sketch generator program. frac-kmc is the fastest known FracMinHash sketch generator, delivering accurate and precise results for cosine similarity estimation on real data. frac-kmc is also the first parallel tool for this task, allowing for speeding up sketch generation using multiple CPU cores - an option lacking in existing serialized tools. We show that by computing FracMinHash sketches using frac-kmc, we can estimate pairwise similarity speedily and accurately on real data. frac-kmc is freely available here: https://github.com/KoslickiLab/frac-kmc/.
Collapse
Affiliation(s)
- Mahmudur Rahman Hera
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park, USA.
| | - David Koslicki
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA.
- Department of Biology, Pennsylvania State University, University Park , USA.
| |
Collapse
|
6
|
Mishra AK, Dhiman RK. Hepatic encephalopathy in cirrhosis: therapies and developments. Metab Brain Dis 2025; 40:198. [PMID: 40332628 DOI: 10.1007/s11011-025-01598-7] [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: 07/07/2024] [Accepted: 03/30/2025] [Indexed: 05/08/2025]
Abstract
Hepatic encephalopathy (HE) is a frequent decompensation in patients with cirrhosis, which significantly affects morbidity and mortality. Ammonia is a major neurotoxin implicated in the pathogenesis, progression, and severity of HE, and various organs including the gut, muscle, kidney, and brain are involved in its metabolism. Therefore, therapeutic management involves reducing ammonia production and increasing its elimination from the blood and the brain. Prevention of HE in patients at high risk of first and recurrent episodes is important for prolonging survival. Various anti-ammonia therapies with synergistic and complementary actions have been attempted for overt HE and for prophylaxis of the first and recurrent episodes of HE. In the current review, we summarize the currently used and under-development pharmacotherapies/procedure(s) for HE in cirrhosis and their mechanism of action. Primary and secondary prophylaxis with monotherapies and combination therapies are also discussed.
Collapse
Affiliation(s)
- Ajay Kumar Mishra
- Department of Hepatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India
| | - Radha Krishan Dhiman
- Department of Hepatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India.
| |
Collapse
|
7
|
Rizzuto V, Settino M, Stroffolini G, Covello G, Vanags J, Naccarato M, Montanari R, de Lossada CR, Mazzotta C, Forestiero A, Adornetto C, Rechichi M, Ricca F, Greco G, Laganovska G, Borroni D. Ocular surface microbiome: Influences of physiological, environmental, and lifestyle factors. Comput Biol Med 2025; 190:110046. [PMID: 40174504 DOI: 10.1016/j.compbiomed.2025.110046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 01/22/2025] [Accepted: 03/16/2025] [Indexed: 04/04/2025]
Abstract
PURPOSE The ocular surface (OS) microbiome is influenced by various factors and impacts on ocular health. Understanding its composition and dynamics is crucial for developing targeted interventions for ocular diseases. This study aims to identify host variables, including physiological, environmental, and lifestyle (PEL) factors, that influence the ocular microbiome composition and establish valid associations between the ocular microbiome and health outcomes. METHODS The 16S rRNA gene sequencing was performed on OS samples collected from 135 healthy individuals using eSwab. DNA was extracted, libraries prepared, and PCR products purified and analyzed. PEL confounding factors were identified, and a cross-validation strategy using various bioinformatics methods including Machine learning was used to identify features that classify microbial profiles. RESULTS Nationality, allergy, sport practice, and eyeglasses usage are significant PEL confounding factors influencing the eye microbiome. Alpha-diversity analysis revealed significant differences between Spanish and Italian subjects (p-value < 0.001), with a median Shannon index of 1.05 for Spanish subjects and 0.59 for Italian subjects. Additionally, 8 microbial genera were significantly associated with eyeglass usage. Beta-diversity analysis indicated significant differences in microbial community composition based on nationality, age, sport, and eyeglasses usage. Differential abundance analysis identified several microbial genera associated with these PEL factors. The Support Vector Machine (SVM) model for Nationality achieved an accuracy of 100%, with an AUC-ROC score of 1.0, indicating excellent performance in classifying microbial profiles. CONCLUSION This study underscores the importance of considering PEL factors when studying the ocular microbiome. Our findings highlight the complex interplay between environmental, lifestyle, and demographic factors in shaping the OS microbiome. Future research should further explore these interactions to develop personalized approaches for managing ocular health.
Collapse
Affiliation(s)
- Vincenzo Rizzuto
- Clinic of Ophthalmology, P. Stradins Clinical University Hospital, Riga, Latvia; School of Advanced Studies, Center for Neuroscience, University of Camerino, Camerino, Italy; Latvian American Eye Center (LAAC), Riga, Latvia
| | - Marzia Settino
- Department of Mathematics and Computer Science, University of Calabria, Rende, Italy; Institute of High Performance Computing and Networks-National Research Council (ICAR-CNR), Rende, Italy.
| | - Giacomo Stroffolini
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Giuseppe Covello
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, Pisa, Italy
| | - Juris Vanags
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia; Clinic of Ophthalmology, P. Stradins Clinical University Hospital, Riga, Latvia
| | - Marta Naccarato
- Clinic of Ophthalmology, P. Stradins Clinical University Hospital, Riga, Latvia; Iris Medical Center, Cosenza, Italy
| | - Roberto Montanari
- Pharmacology Institute, Heidelberg University Hospital, Heidelberg, Germany
| | - Carlos Rocha de Lossada
- Eyemetagenomics Ltd., London, United Kingdom; Ophthalmology Department, QVision, Almeria, Spain; Ophthalmology Department, Hospital Regional Universitario of Malaga, Malaga, Spain; Department of Surgery, Ophthalmology Area, University of Seville, Seville, Spain
| | - Cosimo Mazzotta
- Siena Crosslinking Center, Siena, Italy; Departmental Ophthalmology Unit, USL Toscana Sud Est, Siena, Italy; Postgraduate Ophthalmology School, University of Siena, Siena, Italy
| | - Agostino Forestiero
- Institute of High Performance Computing and Networks-National Research Council (ICAR-CNR), Rende, Italy
| | | | | | - Francesco Ricca
- Department of Mathematics and Computer Science, University of Calabria, Rende, Italy
| | - Gianluigi Greco
- Department of Mathematics and Computer Science, University of Calabria, Rende, Italy
| | - Guna Laganovska
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia; Clinic of Ophthalmology, P. Stradins Clinical University Hospital, Riga, Latvia
| | - Davide Borroni
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia; Eyemetagenomics Ltd., London, United Kingdom; Centro Oculistico Borroni, Gallarate, Italy
| |
Collapse
|
8
|
Yu S, Huang F, Huang Y, Yan F, Li Y, Xu S, Zhao Y, Zhang X, Chen R, Chen X, Zhang P. Deciphering the influence of gut and oral microbiomes on menopause for healthy aging. J Genet Genomics 2025; 52:601-614. [PMID: 39577767 DOI: 10.1016/j.jgg.2024.11.010] [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: 09/27/2024] [Revised: 11/08/2024] [Accepted: 11/14/2024] [Indexed: 11/24/2024]
Abstract
Menopause is characterized by the cessation of menstruation and a decline in reproductive function, which is an intrinsic component of the aging process. However, it has been a frequently overlooked field of women's health. The oral and gut microbiota, constituting the largest ecosystem within the human body, are important for maintaining human health and notably contribute to the healthy aging of menopausal women. Therefore, a comprehensive review elucidating the impact of the gut and oral microbiota on menopause for healthy aging is of paramount importance. This paper presents the current understanding of the microbiome during menopause, with a particular focus on alterations in the oral and gut microbiota. Our study elucidates the complex interplay between the microbiome and sex hormone levels, explores microbial crosstalk dynamics, and investigates the associations between the microbiome and diseases linked to menopause. Additionally, this review explores the potential of microbiome-targeting therapies for managing menopause-related diseases. Given that menopause can last for approximately 30 years, gaining insights into how the microbiome and menopause interact could pave the way for innovative interventions, which may result in symptomatic relief from menopause and an increase in quality of life in women.
Collapse
Affiliation(s)
- Shuting Yu
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Feiling Huang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - Yixuan Huang
- Beijing ClouDNA Technology Co., Ltd., Beijing 101407, China
| | - Fangxu Yan
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yi Li
- Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Shenglong Xu
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yan Zhao
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Xinlei Zhang
- Beijing ClouDNA Technology Co., Ltd., Beijing 101407, China
| | - Rong Chen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China.
| | - Xingming Chen
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Peng Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China.
| |
Collapse
|
9
|
Molina NM, Canha-Gouveia A, Leonés-Baños I, Sola-Leyva A, Vargas E, Ruíz-Durán S, Tenorio CM, Clavero-Gilabert A, Mändar R, Altmäe S. The complementary seminovaginal microbiome in health and disease. Reprod Biomed Online 2025; 50:104707. [PMID: 40174296 DOI: 10.1016/j.rbmo.2024.104707] [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: 07/03/2024] [Revised: 10/04/2024] [Accepted: 10/31/2024] [Indexed: 04/04/2025]
Abstract
Infertility, adverse pregnancy outcomes and genital infections are global concerns. The reproductive tract microbiome appears to play a crucial role in the physiology of both the female and male reproductive tracts. Despite the presence of thousands of microbes in body fluids shared during unprotected sexual intercourse, they have traditionally been studied separately, with greater emphasis on the female (mostly vaginal) microbiome, and the interaction between these microbiomes in a sexually active couple has been overlooked. This review introduces the concept of the 'seminovaginal microbiome' - the collective microbiota of both partners, transferred and shared during sexual interaction. By synthesizing the existing body of next-generation sequencing-based literature, this review establishes the first holistic view of how these microbiomes interact, influence reproductive health and affect assisted reproductive technique outcomes, as well as the occurrence of microbe-associated diseases such as sexually transmitted infections, prostatitis, bacterial vaginosis and candidiasis. Additionally, the microbial interplay in homosexual couples and transgender individuals is discussed.
Collapse
Affiliation(s)
- Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain
| | - Analuce Canha-Gouveia
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain; Department of Physiology, Faculty of Veterinary Medicine, University of Murcia, Campus Mare Nostrum, Murcia, Spain.
| | - Irene Leonés-Baños
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain; Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Alberto Sola-Leyva
- Celvia CC AS, Tartu, Estonia; Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Vargas
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain; Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Jaén, Spain
| | - Susana Ruíz-Durán
- Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain; Department of Obstetrics and Gynaecology, Virgen de las Nieves University Hospital, Granada, Spain
| | - Celia M Tenorio
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain
| | - Ana Clavero-Gilabert
- Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain; Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Reet Mändar
- Celvia CC AS, Tartu, Estonia; Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs. Granada, Granada, Spain; Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
10
|
Tláskal V, Hrbáček J, Hanáček V, Baránková P, Čermák P, Zachoval R, Thiago Dobbler P. Short- and mid-term temporal variability of the human urinary microbiota: a prospective observational cohort study. BMC Microbiol 2025; 25:222. [PMID: 40240922 PMCID: PMC12001408 DOI: 10.1186/s12866-025-03915-7] [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: 10/01/2024] [Accepted: 03/20/2025] [Indexed: 04/18/2025] Open
Abstract
BACKGROUND Understanding the temporal variability of the microbiome is critical for translating associations of the microbiome with health and disease into clinical practice. The aim of this study is to assess the extent of temporal variability of the human urinary microbiota. A pair of urine samples were collected from study participants at 3-40-month interval. DNA was extracted and the bacterial V4 hypervariable region of the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The alpha diversity of paired samples was analyzed using Chao1 and Shannon indices and PERMANOVA was used to test the factors influencing beta diversity. RESULTS A total of 63 participants (43 men and 20 women with a mean age of 63.0 and 57.1 years, respectively) were included in the final analysis. An average of 152 ± 128 bacterial operational taxonomic units (OTUs) were identified in each urine sample from the entire cohort. There was an average of 41 ± 32 overlapping OTUs in each sample pair, accounting for 66.3 ± 29.4% of the relative abundance. There was a clear correlation between the number of overlapping OTUs and the relative abundance covered. The difference in Chao1 index between paired samples was statistically significant; the difference in Shannon index was not. Beta diversity did not differ significantly within the paired samples. Neither age nor sex of the participants influenced the variation in community composition. With a longer interval between the collections, the relative abundance covered by the overlapping OTUs changed significantly but not the number of OTUs. CONCLUSION Our findings demonstrated that, while the relative abundance of dominant bacteria varied, repeated collections generally shared more than 60% of the bacterial community. Furthermore, we observed little variation in the alpha and beta diversity of the microbial community in human urine. These results help to understand the dynamics of human urinary microbiota and enable interpretation of future studies.
Collapse
Affiliation(s)
- Vojtěch Tláskal
- Department of Urology, Thomayer University Hospital, Prague, Czech Republic.
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
| | - Jan Hrbáček
- Department of Urology, Thomayer University Hospital, Prague, Czech Republic.
- 3rd Faculty of Medicine, Charles University, Prague, Czech Republic.
- Department of Urology, Bulovka University Hospital, Prague, Czech Republic.
| | - Vítězslav Hanáček
- Department of Urology, Thomayer University Hospital, Prague, Czech Republic
| | - Petra Baránková
- Department of Urology, Thomayer University Hospital, Prague, Czech Republic
| | - Pavel Čermák
- Department of Clinical Microbiology, Thomayer University Hospital, Prague, Czech Republic
| | - Roman Zachoval
- Department of Urology, Thomayer University Hospital, Prague, Czech Republic
- 3rd Faculty of Medicine, Charles University, Prague, Czech Republic
| | | |
Collapse
|
11
|
Mohapatra S, Panda S, Mohanty N, Mishra BP. Comparative analysis of bacterial abundance and diversity in tumour tissue of oral squamous cell carcinoma and non-tumour tissue: insights from a systematic review of 16S ribosomal RNA sequencing. BMC Oral Health 2025; 25:577. [PMID: 40241078 PMCID: PMC12001643 DOI: 10.1186/s12903-025-05941-3] [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: 10/19/2024] [Accepted: 04/03/2025] [Indexed: 04/18/2025] Open
Abstract
BACKGROUND As per the recent research findings, there is a significant difference between the bacteriome of normal tissue (NT) and tumor tissues (TT) of oral squamous cell carcinoma (OSCC). Identifying this distinct bacteriome is crucial for understanding their potential contribution to oral carcinogenesis. This systematic review (SR) aims to identify exclusive and relative bacterial abundance and bacterial diversity in TT and NT. METHODOLOGY The review was conducted following the PRISMA guidelines. PUBMED and SCOPUS databases were searched for studies in English published till 31st August 2024. The inclusion criteria focused on identifying bacteriome in NT versus TT at either species,/genus, and/or phylum level through 16 s ribosomal RNA sequencing. Quality assessment was performed using an eleven-parameter tool combining the Newcastle-Ottawa Scale and customized criteria. RESULT Evaluating the selected 13 articles, we have identified the exclusive and relative abundance of bacteriome in TT and NT at phylum, genus, and species levels. Three phyla such as Chloroflexota, Deinococcus-Thermus, and Mycoplasmatota, are found exclusively in TT. Seven genus such as Eubacterium, Campylobacter, Aeromonas, Oceanivigra, Rheinheimera, Weissella, and Catonella are exclusively found in TT. Ten species such as Micrococcus luteus, Prevotella melaninogenica, Exiguobacterium oxidotolerans, Fusobacterium naviforme, Staphylococcus aureus, Veillonella parvula, Parvimonas sp oral taxon 110, Eubacterium II G1 infirmum, Eubacterium XI G3 Brachy, Weissella viridescens are found in TT. Six genus such as Capnocytophaga, Selenomonas, Leptothrix, Desulfovibrio, Desulfoplanes, Pelospora are found exclusively in NT. Eleven species, such as Streptococcus sp. Oral taxon 071,Selenomonas sputigena, Treponema pedis, Acholeplasmatales bacterium, Capnocytophaga haemolytica, Eubacterium sp., Syntrophomonadaceae genomosp.,Treponema putidum, Mitsuokella sp., Actinomyces sp. Oral taxon 848 str. F0332, p- 2534 - 18B5-gut-group are found in NT. Seven common genera within which different species are identified in TT and NT, suggesting differences in bacterial behaviour and characteristics within the same genus. A total of 12 phyla, 35 genera, and 54 species were found to be relatively more abundant in TT compared to NT. Conversely, 7 phyla, 32 genera, and 45 species were relatively more abundant in NT than in TT. Considerable variations in diversity metrics were found between TT and NT. CONCLUSION This systematic review is the first to identify a distinct bacteriome exclusive to OSCC tumour tissue compared to normal tissue using 16S ribosomal RNA sequencing. This pioneering work lays the foundation for future studies on the oral microbiome as a potential diagnostic or therapeutic target in oral cancer management. It emphasizes the importance of exploring species-level differences for a deeper understanding of their roles in OSCC. TRIAL REGISTRATION Not applicable.
Collapse
Affiliation(s)
- Swagatika Mohapatra
- Department of Oral Pathology and Microbiology, Institute of Dental Sciences, Siksha 'O' Anusandhan University, Bhubaneswar, Odisha, India
| | - Swagatika Panda
- Department of Oral Pathology and Microbiology, Institute of Dental Sciences, Siksha 'O' Anusandhan University, Bhubaneswar, Odisha, India.
| | - Neeta Mohanty
- Department of Oral Pathology and Microbiology, Institute of Dental Sciences, Siksha 'O' Anusandhan University, Bhubaneswar, Odisha, India
| | - Bibhu Prasad Mishra
- Department of General Surgery, Maharaja Krushnachandra Gajapati Medical College and Hospital, Berhampur, Odisha, India
| |
Collapse
|
12
|
Rahim MA, Seo H, Barman I, Hossain MS, Shuvo MSH, Song HY. Insights into Autophagy in Microbiome Therapeutic Approaches for Drug-Resistant Tuberculosis. Cells 2025; 14:540. [PMID: 40214493 PMCID: PMC11989032 DOI: 10.3390/cells14070540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Revised: 03/23/2025] [Accepted: 04/02/2025] [Indexed: 04/14/2025] Open
Abstract
Tuberculosis, primarily caused by Mycobacterium tuberculosis, is an airborne lung disease and continues to pose a significant global health threat, resulting in millions of deaths annually. The current treatment for tuberculosis involves a prolonged regimen of antibiotics, which leads to complications such as recurrence, drug resistance, reinfection, and a range of side effects. This scenario underscores the urgent need for novel therapeutic strategies to combat this lethal pathogen. Over the last two decades, microbiome therapeutics have emerged as promising next-generation drug candidates, offering advantages over traditional medications. In 2022, the Food and Drug Administration approved the first microbiome therapeutic for recurrent Clostridium infections, and extensive research is underway on microbiome treatments for various challenging diseases, including metabolic disorders and cancer. Research on microbiomes concerning tuberculosis commenced roughly a decade ago, and the scope of this research has broadened considerably over the last five years, with microbiome therapeutics now viewed as viable options for managing drug-resistant tuberculosis. Nevertheless, the understanding of their mechanisms is still in its infancy. Although autophagy has been extensively studied in other diseases, research into its role in tuberculosis is just beginning, with preliminary developments in progress. Against this backdrop, this comprehensive review begins by succinctly outlining tuberculosis' characteristics and assessing existing treatments' strengths and weaknesses, followed by a detailed examination of microbiome-based therapeutic approaches for drug-resistant tuberculosis. Additionally, this review focuses on establishing a basic understanding of microbiome treatments for tuberculosis, mainly through the lens of autophagy as a mechanism of action. Ultimately, this review aims to contribute to the foundational comprehension of microbiome-based therapies for tuberculosis, thereby setting the stage for the further advancement of microbiome therapeutics for drug-resistant tuberculosis.
Collapse
Affiliation(s)
- Md Abdur Rahim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, 31, Suncheonhyang 6-gil, Dongnam-gu, Cheonan-si 31151, Republic of Korea
- Human Microbiome Medical Research Center (HM·MRC), School of Medicine, Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
| | - Hoonhee Seo
- Human Microbiome Medical Research Center (HM·MRC), School of Medicine, Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
- Probiotics Microbiome Commercialization Research Center (PMC), Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
| | - Indrajeet Barman
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, 31, Suncheonhyang 6-gil, Dongnam-gu, Cheonan-si 31151, Republic of Korea
- Human Microbiome Medical Research Center (HM·MRC), School of Medicine, Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
| | - Mohammed Solayman Hossain
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, 31, Suncheonhyang 6-gil, Dongnam-gu, Cheonan-si 31151, Republic of Korea
- Human Microbiome Medical Research Center (HM·MRC), School of Medicine, Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
| | - Md Sarower Hossen Shuvo
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, 31, Suncheonhyang 6-gil, Dongnam-gu, Cheonan-si 31151, Republic of Korea
- Human Microbiome Medical Research Center (HM·MRC), School of Medicine, Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, 31, Suncheonhyang 6-gil, Dongnam-gu, Cheonan-si 31151, Republic of Korea
- Human Microbiome Medical Research Center (HM·MRC), School of Medicine, Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
- Probiotics Microbiome Commercialization Research Center (PMC), Soonchunhyang University, 22, Soonchunhyang-ro, Sinchang-myeon, Asan-si 31538, Republic of Korea
| |
Collapse
|
13
|
Coskuner-Weber O, Alpsoy S, Yolcu O, Teber E, de Marco A, Shumka S. Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing. Comput Biol Chem 2025; 118:108444. [PMID: 40187295 DOI: 10.1016/j.compbiolchem.2025.108444] [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: 01/03/2025] [Revised: 03/15/2025] [Accepted: 03/25/2025] [Indexed: 04/07/2025]
Abstract
The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.
Collapse
Affiliation(s)
- Orkid Coskuner-Weber
- Turkish-German University, Molecular Biotechnology, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey.
| | - Semih Alpsoy
- Turkish-German University, Molecular Biotechnology, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey
| | - Ozgur Yolcu
- Turkish-German University, Molecular Biotechnology, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey
| | - Egehan Teber
- Turkish-German University, Molecular Biotechnology, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Nova Gorica 5000, Slovenia
| | - Spase Shumka
- Faculty of Biotechnology and Food, Agricultural University of Tirana, 1019 Koder Kamza, Tirana, Albania
| |
Collapse
|
14
|
Wu Y, Shi L, Jin Z, Chen W, Wang F, Wu H, Li H, Zhang C, Zhu R. A nomogram prediction model for embryo implantation outcomes based on the cervical microbiota of the infertile patients during IVF-FET. Microbiol Spectr 2025; 13:e0146224. [PMID: 40052785 PMCID: PMC11960138 DOI: 10.1128/spectrum.01462-24] [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: 06/13/2024] [Accepted: 02/07/2025] [Indexed: 04/03/2025] Open
Abstract
The microbiota of the female genital tract is crucial for reproductive health. This study aims to investigate the impact of the lower genital tract microbiota on in vitro fertilization and frozen embryo transfer (IVF-FET) outcomes. This study included 131 women aged 20-35 years who underwent their first or second IVF-FET cycle with no obvious unfavorable factors for implantation. Cervical microbiota samples were collected on the embryo transfer day and analyzed using 16S rDNA full-length sequencing. Clinical outcomes were followed up for analysis. Clinical pregnancy (CP) was achieved in 84 patients, and 47 patients experienced non-pregnancy (NP). The cervical microbiota diversity between NP and CP groups showed no significant differences, but some genera such as Halomonas (P = 0.018), Klebsiella (P = 0.039), Atopobium (P = 0.016), and Ligilactobacillus (P = 0.021) were obviously different between the two groups. Notably, there was no significant difference in the abundance of Lactobacillus between the two groups. A nomogram prediction model was developed using the random forest algorithm and logistic regression, including the classification of Halomonas, Atopobium, and Veillonella, as well as the relative abundance of Lactobacillus, to identify high-risk patients with embryo implantation failure. Both internal (area under the curve [AUC] = 0.718, 95% confidence interval [CI]: 0.628-0.807, P < 0.001) and external validation (AUC = 0.654, 95% CI: 0.553-0.755, P = 0.037) of the model performed well. In conclusion, this study established a correlation between cervical microbiota and embryo implantation failure in infertile women undergoing IVF-FET and developed a prediction model that could help in early identification of patients at high risk of implantation failure.IMPORTANCEThis study investigated the potential role of abnormal cervical microbiota in the pathology of implantation failure after in vitro fertilization and frozen embryo transfer (IVF-FET) treatment. Despite nearly half a century of advancements in assisted reproductive technology (ART), the implantation rate of high-quality embryos still hovered around 50%. Moreover, unexplained recurrent implantation failure (RIF) remains a significant challenge in ART. To our knowledge, we first discovered a prediction model for embryo implantation failure, identifying Halomonas and Veillonella as significantly adverse factors for embryo implantation. Despite some limitations, the internal and external validation of the model could bode well for its clinical application prospect. The insights gained from this study pave the way for intervention in the genital tract microbiota prior to IVF-FET, particularly in patients with RIF and RSA.
Collapse
Affiliation(s)
- Yanan Wu
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Lingyun Shi
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Zili Jin
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Wenjun Chen
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Fuxin Wang
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Huihua Wu
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Hong Li
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Ce Zhang
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Rui Zhu
- Center for Human Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| |
Collapse
|
15
|
Jyoti J, Hütt MT. Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns. Bioinformatics 2025; 41:btaf095. [PMID: 40036964 PMCID: PMC11961200 DOI: 10.1093/bioinformatics/btaf095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 02/05/2025] [Accepted: 02/26/2025] [Indexed: 03/06/2025] Open
Abstract
MOTIVATION Inferring microbial interaction networks from microbiome data is a core task of computational ecology. An avenue of research to create reliable inference methods is based on a stylized view of microbiome data, starting from the assumption that the presences and absences of microbiomes, rather than the quantitative abundances, are informative about the underlying interaction network. With this starting point, inference algorithms can be based on the notion of attractors (asymptotic states) in Boolean networks. Boolean network framework offers a computationally efficient method to tackle this problem. However, often existing algorithms operating under a Boolean network assumption, fail to provide networks that can reproduce the complete set of initial attractors (abundance patterns). Therefore, there is a need for network inference algorithms capable of reproducing the initial stable states of the system. RESULTS We study the change of attractors in Boolean threshold dynamics on signed undirected graphs under small changes in network architecture and show, how to leverage these relationships to enhance network inference algorithms. As an illustration of this algorithmic approach, we analyse microbial abundance patterns from stool samples of humans with inflammatory bowel disease (IBD), with colorectal cancer and from healthy individuals to study differences between the interaction networks of the three conditions. The method reveals strong diversity in IBD interaction networks. The networks are first partially deduced by an earlier inference method called ESABO, then we apply the new algorithm developed here, EDAME, to this result to generate a network that comes nearest to satisfying the original attractors. AVAILABILITY AND IMPLEMENTATION Implementation code is freely available at https://github.com/Jojo6297/edame.git.
Collapse
Affiliation(s)
- Jyoti Jyoti
- School of Science, Constructor University, Bremen 28759, Germany
| | | |
Collapse
|
16
|
Amar Y, Niedermeier S, Silva R, Kublik S, Schloter M, Biedermann T, Köberle M, Eberlein B. Skin microbiome dynamics in patients with polymorphic light eruption in response to ultraviolet radiation. Br J Dermatol 2025; 192:684-696. [PMID: 39576029 DOI: 10.1093/bjd/ljae464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 11/19/2024] [Accepted: 11/21/2024] [Indexed: 12/28/2024]
Abstract
BACKGROUND Polymorphic light eruption (PLE) is the most frequent photodermatosis in Europe, with an estimated prevalence of 10-20%, particularly in temperate climates. Itching or burning lesions appear only in sun-exposed areas, predominantly on the chest, arms and forearms, within a few hours following exposure. The cause of the disease remains unknown, yet studies have suggested that microbial elements in the skin may play a role in its pathogenesis. OBJECTIVES To investigate the skin microbiome of a cohort of patients with PLE upon exposure to ultraviolet radiation (UVR), to assess its role in the onset of PLE lesions. METHODS Forty-one skin swabs were collected from 11 patients with PLE at baseline and after 3 days of exposure to UVR, and from healthy control participants. The collected swabs were analysed for their microbial composition using a 16S amplicon sequencing approach. RESULTS PLE skin showed a dysbalanced microbiome at baseline, with significantly reduced microbial diversity and noticeable colonization by bacterial pathogens, including Staphylococcus aureus. Upon UVR exposure, the PLE microbiome exhibited further loss of diversity and a reduction in beneficial skin commensals. In line with this, we found that UVR exerted strong antimicrobial effects in vitro against representative skin residents. CONCLUSIONS UVR can lead to profound changes in the skin microbiome, allowing the proliferation of dysbiotic members that can release a variety of elements able to trigger PLE lesions. This is the first study to investigate the cutaneous microbiome changes in patients with PLE upon UVR exposure, offering new insights into disease pathogenesis that has so far been unexplored.
Collapse
Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Munich, Germany
| | - Rafaela Silva
- Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Center Munich, Munich, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Center Munich, Munich, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Köberle
- Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Munich, Germany
| | - Bernadette Eberlein
- Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Munich, Germany
| |
Collapse
|
17
|
Kim KS, Na HS, Oh TJ, Han H, Kim J, Hong JS, Lee HJ, Park YS, Chung J. Oral microbiome changes in subjects with obesity following bariatric surgery compared to lean counterparts. Front Microbiol 2025; 16:1553404. [PMID: 40170925 PMCID: PMC11959278 DOI: 10.3389/fmicb.2025.1553404] [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: 12/30/2024] [Accepted: 02/27/2025] [Indexed: 04/03/2025] Open
Abstract
Introduction This study aimed to compare oral microbiome profiles between obese and lean individuals without clinical periodontitis, and to assess changes in the oral microbiome of obese subjects following bariatric surgery. Methods Individuals with a body mass index (BMI) > 30 were enrolled in the obese group, whereas those with a BMI < 23 served as controls. The obese surgery group, which consented to bariatric surgery, was followed up at 1, 3, and 6 months with clinical examinations. Oral examinations were conducted and periodontal disease was classified based on probing results. Saliva, buccal and subgingival microbiome samples were analyzed for community diversity, relative bacterial abundance, and differential abundance between control (n = 24) and obese group (n = 31). To evaluate effect size and statistical power, we used micropower, a simulation-based method for Permutational Multivariate Analysis of Variance-based β-diversity comparisons. Results The obese group exhibited distinct alpha diversity (buccal: Chao1 p = 0.0002, Shannon p = 0.0003, supragingival: Shannon p < 0.0001) compared with the control group. Bray-Curtis distance analysis indicated significant disparities in microbiome composition distribution in saliva (p = 0.003), buccal (p = 0.002), and subgingival plaque samples (p = 0.001). Although the obese and normal weight groups exhibited no significant periodontal differences, the obese group showed distinct species associated with periodontal disease, especially in subgingival plaque including Filifactor alocis, Peptostreptococcaceae spp., Prevotella spp., and Treponema maltophilum. Cluster analysis of the obese surgery group indicated the emergence of microbiomes associated with a healthy state that increased over time including Streptococcus salivarious and various Veillonella spp., whereas clusters containing periodontal pathogens including Porphyromonas spp., tended to diminish. Discussion The oral microbiome at 6 months post-bariatric surgery indicates a potential shift toward a healthy periodontal state, suggesting that weight loss interventions may positively impact oral microbial communities even in the absence of clinical periodontitis.
Collapse
Affiliation(s)
- Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
| | - Tae Jung Oh
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyejung Han
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
| | - Jiyeon Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jin-Sil Hong
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Young Suk Park
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jin Chung
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, Republic of Korea
| |
Collapse
|
18
|
Papamentzelopoulou M, Pitiriga VC. Unlocking the Interactions Between the Whole-Body Microbiome and HPV Infection: A Literature Review. Pathogens 2025; 14:293. [PMID: 40137778 PMCID: PMC11945791 DOI: 10.3390/pathogens14030293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 03/12/2025] [Accepted: 03/13/2025] [Indexed: 03/29/2025] Open
Abstract
The human microbiome plays a vital role in maintaining human homeostasis, acting as a key regulator of host immunity and defense mechanisms. However, dysbiotic microbial communities may cause disruption of the symbiotic relationship between the host and the local microbiota, leading to the pathogenesis of various diseases, including viral infections and cancers. One of the most common infectious agents causing cancer is the human papilloma virus (HPV), which accounts for more than 90% of cervical cancers. In most cases, the host immune system is activated and clears HPV, whereas in some cases, the infection persists and can lead to precancerous lesions. Over the last two decades, the advent of next-generation sequencing (NGS) technology and bioinformatics has allowed a thorough and in-depth analysis of the microbial composition in various anatomical niches, allowing researchers to unveil the interactions and the underlying mechanisms through which the human microbiota could affect HPV infection establishment, persistence, and progression. Accordingly, the present narrative review aims to shed light on our understanding of the role of the human microbiome in the context of HPV infection and its progression, mainly to cervical cancer. Furthermore, we explore the mechanisms by which the composition and balance of microbial communities exert potential pathogenic or protective effects, leading to either HPV persistence and disease outcomes or clearance. Special interest is given to how the microbiome can modulate host immunity to HPV infection. Lastly, we summarize the latest findings on the therapeutic efficacy of probiotics and prebiotics in preventing and/or treating HPV infections and the potential of vaginal microbiota transplantation while highlighting the significance of personalized medicine approaches emerging from NGS-based microbiome profiling and artificial intelligence (AI) for the optimal management of HPV-related diseases.
Collapse
Affiliation(s)
- Myrto Papamentzelopoulou
- Molecular Biology Unit, 1st Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Vassiliki C. Pitiriga
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| |
Collapse
|
19
|
Chen H, Chen K. Ensemble learning based on matrix completion improves microbe-disease association prediction. Brief Bioinform 2025; 26:bbaf075. [PMID: 40037643 PMCID: PMC11879468 DOI: 10.1093/bib/bbaf075] [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: 11/08/2024] [Revised: 01/18/2025] [Accepted: 02/10/2025] [Indexed: 03/06/2025] Open
Abstract
Microbes have a profound impact on human health. Identifying disease-associated microbes would provide helpful guidance for drug development and disease treatment. Through an enormous experimental effort, limited disease-associated microbes have been determined. Accurate computational approaches are needed to predict potential microbe-disease associations for biomedical screening. In this study, we present an ensemble learning framework entitled SABMDA to improve microbe-disease association inference. We first integrate multi-source of information from both microbes and diseases, and develop two matrix completion algorithms to predict microbe-disease associations successively. Ablation tests show combining the two matrix completion algorithms can receive better prediction performance. Moreover, comprehensive experiments, including cross-validations and independent test, demonstrate that SABMDA outperforms seven recent baseline methods significantly. Finally, we apply SABMDA to three diseases to predict their associated microbes, and results show SABMDA's remarkable prediction ability in real situations.
Collapse
Affiliation(s)
- Hailin Chen
- School of Information and Software Engineering, East China Jiaotong University, No. 808, Shuanggangdong Street, Nanchang 330013, China
| | - Kuan Chen
- School of Information and Software Engineering, East China Jiaotong University, No. 808, Shuanggangdong Street, Nanchang 330013, China
| |
Collapse
|
20
|
Peng S, Meri AQ, Zhou M, Yu Y, Tian D, Zhu S. Human embryo implantation: The complex interplay between endometrial receptivity and the microbiome. J Reprod Immunol 2025; 168:104440. [PMID: 39862472 DOI: 10.1016/j.jri.2025.104440] [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: 06/11/2024] [Revised: 01/14/2025] [Accepted: 01/17/2025] [Indexed: 01/27/2025]
Abstract
The endometrial and vaginal microbiota have co-evolved with the reproductive tract and play a key role in both health and disease. However, the difference between endometrial and vaginal microbiota, as well as their association with reproductive outcomes in women undergoing frozen embryo transfer, remains unclear. 120 women who underwent in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) and whole embryo freezing were enrolled. The vaginal and uterine microbiome were sequenced during the first frozen thawed embryo transfer. Based on whether or not they were pregnant after embryo transfer, women were assigned into two groups, and the microbiome of their reproductive tract was compared. The V3-V4 regions of the 16S rRNA gene were examined in the samples using the Next Generation Sequencing method. In the vagina, the non-pregnant group had higher bacterial species richness and diversity, with significantly lower Lactobacillus levels (91.66 % & 74.50 %) and higher Gardnerella levels (3.92 % & 12.12 %) than pregnant group (P < 0.05). In the uterine cavity, the diversity of uterine microbiome between pregnant group and non-pregnant group showed no significant differences. However, dramatic decrease in Lactobacillus (37.27 % & 33.45 %) and Pseudomonas (9.80 % & 4.08 %) were observed in the non-pregnant group (P < 0.05). There may be a correlation between the composition of female reproductive tract microbiome and the reproductive outcomes of patients with frozen-thawed embryo transfer. Lactobacillus-dominated microbiome in reproductive tract is more likely to be associated with higher clinical and ongoing pregnancy rate.
Collapse
Affiliation(s)
- Shiyang Peng
- Chengdu Fifth People's Hospital, (School of Medical and Life Sciences/Affiliated Fifth People's Hospital, Chengdu University of Traditional Chinese Medicine), Chengdu, China
| | - Amu Qingsan Meri
- Chengdu Fifth People's Hospital, (School of Medical and Life Sciences/Affiliated Fifth People's Hospital, Chengdu University of Traditional Chinese Medicine), Chengdu, China
| | - Min Zhou
- Department of Reproductive medicine center of Obstetrics and Gynecology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuan Yu
- Chengdu Fifth People's Hospital, (School of Medical and Life Sciences/Affiliated Fifth People's Hospital, Chengdu University of Traditional Chinese Medicine), Chengdu, China
| | - Dongmei Tian
- Affiliated Reproductive & Women-Children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shaomi Zhu
- Chengdu Fifth People's Hospital, (School of Medical and Life Sciences/Affiliated Fifth People's Hospital, Chengdu University of Traditional Chinese Medicine), Chengdu, China.
| |
Collapse
|
21
|
Džidić Krivić A, Begagić E, Hadžić S, Bećirović A, Bećirović E, Hibić H, Tandir Lihić L, Kadić Vukas S, Bečulić H, Kasapović T, Pojskić M. Unveiling the Important Role of Gut Microbiota and Diet in Multiple Sclerosis. Brain Sci 2025; 15:253. [PMID: 40149775 PMCID: PMC11939953 DOI: 10.3390/brainsci15030253] [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: 12/27/2024] [Revised: 02/23/2025] [Accepted: 02/25/2025] [Indexed: 03/29/2025] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS), characterized by neurodegeneration, axonal damage, demyelination, and inflammation. Recently, gut dysbiosis has been linked to MS and other autoimmune conditions. Namely, gut microbiota has a vital role in regulating immune function by influencing immune cell development, cytokine production, and intestinal barrier integrity. While balanced microbiota fosters immune tolerance, dysbiosis disrupts immune regulation, damages intestinal permeability, and heightens the risk of autoimmune diseases. The critical factor in shaping the gut microbiota and modulating immune response is diet. Research shows that high-fat diets rich in saturated fats are associated with disease progression. Conversely, diets rich in fruits, yogurt, and legumes may lower the risk of MS onset and progression. Specific dietary interventions, such as the Mediterranean diet (MD) and ketogenic diet, have shown potential to reduce inflammation, support neuroprotection, and promote CNS repair. Probiotics, by restoring microbial balance, may also help mitigate immune dysfunction noted in MS. Personalized dietary strategies targeting the gut microbiota hold promise for managing MS by modulating immune responses and slowing disease progression. Optimizing nutrient intake and adopting anti-inflammatory diets could improve disease control and quality of life. Understanding gut-immune interactions is essential for developing tailored nutritional therapies for MS patients.
Collapse
Affiliation(s)
- Amina Džidić Krivić
- Department of Neurology, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina; (A.D.K.); (L.T.L.)
- Department of Physiology, School of Medicine, University of Zenica, Travnička 1, 72000 Zenica, Bosnia and Herzegovina
| | - Emir Begagić
- Department of Neurosurgery, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina; (E.B.)
- Department of Doctoral Studies, School of Medicine, University of Tuzla, 75000 Tuzla, Bosnia and Herzegovina
| | - Semir Hadžić
- Internal Medicine Clinic, University Clinical Center of Tuzla, Ulica prof. dr. Ibre Pašića, 75000 Tuzla, Bosnia and Herzegovina (E.B.)
- Department of Physiology, School of Medicine, University of Tuzla, Univerzitetska 1, 75000 Tuzla, Bosnia and Herzegovina
| | - Amir Bećirović
- Internal Medicine Clinic, University Clinical Center of Tuzla, Ulica prof. dr. Ibre Pašića, 75000 Tuzla, Bosnia and Herzegovina (E.B.)
| | - Emir Bećirović
- Internal Medicine Clinic, University Clinical Center of Tuzla, Ulica prof. dr. Ibre Pašića, 75000 Tuzla, Bosnia and Herzegovina (E.B.)
| | - Harisa Hibić
- Department of Maxillofacial Surgery, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina
| | - Lejla Tandir Lihić
- Department of Neurology, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina; (A.D.K.); (L.T.L.)
- Department of Neurology, School of Medicine, University of Zenica, Travnička 1, 72000 Zenica, Bosnia and Herzegovina
| | - Samra Kadić Vukas
- Department of Neurology, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina; (A.D.K.); (L.T.L.)
- Department of Neurology, School of Medicine, University of Zenica, Travnička 1, 72000 Zenica, Bosnia and Herzegovina
| | - Hakija Bečulić
- Department of Neurosurgery, Cantonal Hospital Zenica, Crkvice 67, 72000 Zenica, Bosnia and Herzegovina; (E.B.)
- Department of Anatomy, School of Medicine, University of Zenica, Travnička 1, 72000 Zenica, Bosnia and Herzegovina
| | - Tarik Kasapović
- Internal Medicine Clinic, University Clinical Center of Tuzla, Ulica prof. dr. Ibre Pašića, 75000 Tuzla, Bosnia and Herzegovina (E.B.)
| | - Mirza Pojskić
- Department of Neurosurgery, University Hospital Marburg, Baldingerstr., 35033 Marburg, Germany
| |
Collapse
|
22
|
Devaraja K, Aggarwal S. Dysbiosis of Oral Microbiome: A Key Player in Oral Carcinogenesis? A Critical Review. Biomedicines 2025; 13:448. [PMID: 40002861 PMCID: PMC11852717 DOI: 10.3390/biomedicines13020448] [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: 01/06/2025] [Revised: 02/08/2025] [Accepted: 02/10/2025] [Indexed: 02/27/2025] Open
Abstract
The oral cavity is known to harbor hundreds of microorganisms, belonging to various genera, constituting a peculiar flora called the oral microbiome. The change in the relative distribution of the constituents of this microbial flora, due to any reason, leads to oral dysbiosis. For centuries, oral dysbiosis has been linked to the etiopathogenesis of several medical illnesses, both locally and systemically-. However, aided by the recent advent of bio-technological capabilities, several reports have re-emerged that link oral dysbiosis to oral carcinogenesis, and numerous studies are currently exploring their association and plausible mechanisms. Some of the proposed mechanisms of oral dysbiosis-induced carcinogenesis (ODIC) include-a bacteria-induced chronic inflammatory state leading to direct cellular damage, inflammatory-cytokine-mediated promotion of cellular proliferation and invasion, release of bacterial products that are carcinogenic, and suppression of local immunity by alteration of the tumor microenvironment. However, the actual interactions between these cellular mechanisms and their role in carcinogenesis are not yet fully understood. This review provides a comprehensive overview of the various hypotheses and mechanisms implicated in the ODIC, along with the corresponding molecular aberrations. Apart from discussing the usual constituents of the oral microbiome profile, the review also summarizes the various dysbiosis profiles implicated in ODIC. The review also sheds light on the potential clinical implications of the research on oral microbiome in the prevention and management of oral cancer.
Collapse
Affiliation(s)
- K. Devaraja
- Department of Head and Neck Surgery, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Sadhna Aggarwal
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
23
|
Zhou Z, Riley R, Kautsar S, Wu W, Egan R, Hofmeyr S, Goldhaber-Gordon S, Yu M, Ho H, Liu F, Chen F, Morgan-Kiss R, Shi L, Liu H, Wang Z. GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.30.635558. [PMID: 39975405 PMCID: PMC11838515 DOI: 10.1101/2025.01.30.635558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Genome foundation models hold transformative potential for precision medicine, drug discovery, and understanding complex biological systems. However, existing models are often inefficient, constrained by suboptimal tokenization and architectural design, and biased toward reference genomes, limiting their representation of low-abundance, uncultured microbes in the rare biosphere. To address these challenges, we developed GenomeOcean, a 4-billion-parameter generative genome foundation model trained on over 600 Gbp of high-quality contigs derived from 220 TB of metagenomic datasets collected from diverse habitats across Earth's ecosystems. A key innovation of GenomeOcean is training directly on large-scale co-assemblies of metagenomic samples, enabling enhanced representation of rare microbial species and improving generalizability beyond genome-centric approaches. We implemented a byte-pair encoding (BPE) tokenization strategy for genome sequence generation, alongside architectural optimizations, achieving up to 150× faster sequence generation while maintaining high biological fidelity. GenomeOcean excels in representing microbial species and generating protein-coding genes constrained by evolutionary principles. Additionally, its fine-tuned model demonstrates the ability to discover novel biosynthetic gene clusters (BGCs) in natural genomes and perform zero-shot synthesis of biochemically plausible, complete BGCs. GenomeOcean sets a new benchmark for metagenomic research, natural product discovery, and synthetic biology, offering a robust foundation for advancing these fields.
Collapse
Affiliation(s)
| | - Robert Riley
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Satria Kautsar
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Weimin Wu
- Northwestern University, Evanston, IL, USA
| | - Rob Egan
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven Hofmeyr
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Mutian Yu
- Northwestern University, Evanston, IL, USA
| | - Harrison Ho
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California at Merced, Merced, CA, USA
| | - Fengchen Liu
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California at Berkeley, Berkeley, CA, USA
| | | | | | - Lizhen Shi
- Northwestern University, Evanston, IL, USA
| | - Han Liu
- Northwestern University, Evanston, IL, USA
| | - Zhong Wang
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California at Merced, Merced, CA, USA
| |
Collapse
|
24
|
Castellanos-Ruiz D, Ojeda-Borbolla JG, Ruiz-García OV, Peña-Corona SI, Martínez-Peña AA, Ibarra-Rubio ME, Gavilanes-Ruiz M, Mendoza-Rodríguez CA. Uterine Microbiota and Bisphenols: Novel Influencers in Reproductive Health. J Xenobiot 2025; 15:26. [PMID: 39997369 PMCID: PMC11856463 DOI: 10.3390/jox15010026] [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: 10/18/2024] [Revised: 01/10/2025] [Accepted: 01/24/2025] [Indexed: 02/26/2025] Open
Abstract
Infertility affects 8-12% of couples worldwide, and 30-75% of preclinical pregnancy losses are due to a failure during the implantation process. Exposure to endocrine disruptors, like bisphenols, among others, has been associated with the increase in infertility observed in the past decades. An increase in infertility has correlated with exposure to endocrine disruptors like bisphenols. The uterus harbors its own microbiota, and changes in this microbiota have been linked to several gynecological conditions, including reproductive failure. There are no studies on the effects of bisphenols on the uterine-microbiota composition, but some inferences can be gleaned by looking at the gut. Bisphenols can alter the gut microbiota, and the molecular mechanism by which gut microbiota regulates intestinal permeability involves Toll-like receptors (TLRs) and tight junction (TJ) proteins. TJs participate in embryo implantation in the uterus, but bisphenol exposure disrupts the expression and localization of TJ proteins. The aim of this review is to summarize the current knowledge on the microbiota of the female reproductive tract (FRT), its association with different reproductive diseases-particularly reproductive failure-the effects of bisphenols on microbiota composition and reproductive health, and the molecular mechanisms regulating uterine-microbiota interactions crucial for embryo implantation. This review also highlights existing knowledge gaps and outlines research needs for future risk assessments regarding the effects of bisphenols on reproduction.
Collapse
Affiliation(s)
- Dafne Castellanos-Ruiz
- Facultad de Química, Departamento de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico (M.E.I.-R.)
| | - J. Gerardo Ojeda-Borbolla
- Facultad de Química, Departamento de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico (M.E.I.-R.)
| | - Olga V. Ruiz-García
- Facultad de Química, Departamento de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico (M.E.I.-R.)
| | - Sheila I. Peña-Corona
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Annia A. Martínez-Peña
- División de Ciencias de la Salud, Universidad Intercontinental, A. C., Ciudad de México 14420, Mexico
| | - María Elena Ibarra-Rubio
- Facultad de Química, Departamento de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico (M.E.I.-R.)
| | - Marina Gavilanes-Ruiz
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - C. Adriana Mendoza-Rodríguez
- Facultad de Química, Departamento de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico (M.E.I.-R.)
| |
Collapse
|
25
|
Eg Gadegaard IS, Eskildsen MH, Østergaard SK, Nielsen JL, Rasmussen JT. Xanthine oxidase-lactoperoxidase system: Dose-dependent antibacterial effects and global gene expression changes in infant oral microbiota. Food Res Int 2025; 201:115596. [PMID: 39849752 DOI: 10.1016/j.foodres.2024.115596] [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: 08/29/2024] [Revised: 12/05/2024] [Accepted: 12/28/2024] [Indexed: 01/25/2025]
Abstract
Xanthine oxidase (XO) and lactoperoxidase (LPO) are highly abundant enzymes in milk. Their substrates, xanthine and thiocyanate, are found in elevated amounts in infant saliva, leading to a proposed interaction between milk and saliva referred to as the XO-LPO system. This system is suggested to generate reactive oxygen and nitrogen species with potential antibacterial effects. The antibacterial activity of the XO-LPO system was assessed on bacteria cultured from the oral cavities of five infants, where a reduction in bacterial growth rate was observed at 40 µg mL-1 of each enzyme and with complete inhibition achieved at 200 µg mL-1. Gene expression analysis showed that XO-LPO treatment led to downregulation of several reactive oxygen species-related genes, suggesting a transient bacterial stress response. The study also observed downregulation of key glycolytic enzymes, indicating that XO-LPO treatment affects bacterial metabolism at transcriptional level, suggesting a possible mechanism of action for the XO-LPO system. Collectively, these findings offer new insights into the XO-LPO system, revealing novel aspects of the interaction between lactation and microbiome influence.
Collapse
Affiliation(s)
- Ida Schnack Eg Gadegaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | | | | | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Jan Trige Rasmussen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.
| |
Collapse
|
26
|
Bensouda S, Cromack SC, Komorowski AS, HogenEsch E, Schipma MJ, Wang X, Fowler H, Pavone M, Green SJ, Bernardi LA, Bakkensen JB. Uterine pathology and microbiome among patients with endometrial polyps and fibroids. F&S SCIENCE 2025; 6:107-116. [PMID: 39710357 DOI: 10.1016/j.xfss.2024.12.002] [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: 09/14/2024] [Revised: 12/16/2024] [Accepted: 12/17/2024] [Indexed: 12/24/2024]
Abstract
OBJECTIVE To evaluate the uterine microbiome among women with endometrial polyps and submucosal fibroids and to compare results between endometrial sampling techniques. DESIGN Patients with polyps or fibroids were prospectively recruited before hysteroscopy, whereas patients undergoing retrieval for planned oocyte cryopreservation were recruited prospectively as controls. Three specimen types obtained for each patient were the distal 5 mm of an embryo catheter passed to the uterine fundus (C), endometrial tissue from an endometrial biopsy (T), and formalin-fixed paraffin-embedded (FFPE) endometrial tissue from the same endometrial biopsy. 16S ribosomal RNA gene amplicon sequencing was performed to analyze the structure of the endometrial microbiome. SUBJECTS Thirty-seven participants including 28 women with polyps and/or fibroids and 9 controls. EXPOSURE None. MAIN OUTCOME MEASURES Microbial taxonomic alpha and beta diversity; differential abundance of taxa. RESULTS Across all sample types, participants with polyps had higher microbial alpha diversity than controls (4.3 vs. 5.1, q = 0.049), and microbial communities were significantly different (pairwise Permutational Multivariate Analysis of Variance (PERMANOVA) pseudo-F = 2.1, q = 0.003). These differences were observed when examining C specimens alone (5.4 vs. 6.4, q = 0.001; pairwise PERMANOVA pseudo-F = 2.5, q = 0.003), although they did not reach significance when examining either T or FFPE specimens alone. Participants with fibroids had similar alpha diversity yet significant differences in beta diversity compared with controls in analyses combining all specimens (pairwise PERMANOVA pseudo-F = 1.475, q = 0.030); however, these differences did not achieve significance when analyzing C, T, or FFPE specimens alone. When comparing C and T specimens vs. FFPE specimens overall, alpha diversity was significantly higher (q < 0.001 and q < 0.001, respectively) and there were significant differences in beta diversity (q < 0.003 and q < 0.003, respectively). Analyses of C specimens generated a larger number of significantly differentially abundant taxa compared with other sampling methods. Although not statistically significant, relative abundance of putative pathogens was higher in participants with polyps than controls regardless of sampling technique. CONCLUSIONS Results of this exploratory study suggest that significant microbial differences exist among patients with endometrial polyps vs. healthy controls. However, results varied by sampling technique, highlighting a need to identify optimal sampling methods before validating findings in larger prospective cohort studies.
Collapse
Affiliation(s)
- Sabrine Bensouda
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Sarah C Cromack
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Allison S Komorowski
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Elena HogenEsch
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Matthew J Schipma
- NUSeq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Xinkun Wang
- NUSeq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hailie Fowler
- NUSeq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - MaryEllen Pavone
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Stefan J Green
- Department of Internal Medicine, Division of Infectious Diseases, Rush University, Chicago, Illinois
| | - Lia A Bernardi
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jennifer B Bakkensen
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| |
Collapse
|
27
|
Almutary AG, Begum MY, Kyada AK, Gupta S, Jyothi SR, Chaudhary K, Sharma S, Sinha A, Abomughaid MM, Imran M, Lakhanpal S, Babalghith AO, Abu-Seer EA, Avinash D, Alzahrani HA, Alhindi AA, Iqbal D, Kumar S, Jha NK, Alghamdi S. Inflammatory signaling pathways in Alzheimer's disease: Mechanistic insights and possible therapeutic interventions. Ageing Res Rev 2025; 104:102548. [PMID: 39419399 DOI: 10.1016/j.arr.2024.102548] [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: 01/26/2024] [Revised: 10/09/2024] [Accepted: 10/11/2024] [Indexed: 10/19/2024]
Abstract
The complex pathophysiology of Alzheimer's disease (AD) poses challenges for the development of therapies. Recently, neuroinflammation has been identified as a key pathogenic mechanism underlying AD, while inflammation has emerged as a possible target for the management and prevention of AD. Several prior studies have demonstrated that medications modulating neuroinflammation might lessen AD symptoms, mostly by controlling neuroinflammatory signaling pathways such as the NF-κB, MAPK, NLRP3, etc, and their respective signaling cascade. Moreover, targeting these inflammatory modalities with inhibitors, natural products, and metabolites has been the subject of intensive research because of their anti-inflammatory characteristics, with many studies demonstrating noteworthy pharmacological capabilities and potential clinical applications. Therefore, targeting inflammation is considered a promising strategy for treating AD. This review comprehensively elucidates the neuroinflammatory mechanisms underlying AD progression and the beneficial effects of inhibitors, natural products, and metabolites in AD treatment.
Collapse
Affiliation(s)
- Abdulmajeed G Almutary
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, P.O. Box 59911, Abu Dhabi, United Arab Emirates
| | - M Yasmin Begum
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ashish Kumar Kyada
- Marwadi University Research Center, Department of Pharmaceutical Sciences, Faculty of Health Sciences, Marwadi University, Rajkot, Gujarat 360003, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - S Renuka Jyothi
- Department of Biotechnology and Genetics, School of Sciences, JAIN (Deemed to be University), Bangalore, Karnataka, India
| | - Kamlesh Chaudhary
- Department of Neurology, National Institute of Medical Sciences, NIMS University Rajasthan, Jaipur, India
| | - Swati Sharma
- Chandigarh Pharmacy College, Chandigarh Group of Colleges, Jhanjeri, Mohali, Punjab 140307, India
| | - Aashna Sinha
- School of Applied and Life Sciences, Division of Research and Innovation, Uttaranchal University, Dehradun, Uttarakhand
| | - Mosleh Mohammad Abomughaid
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; Center for Health Research, Northern Border University, Arar, Saudi Arabia
| | - Sorabh Lakhanpal
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Ahmad O Babalghith
- Medical Genetics Department, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Eman Adnan Abu-Seer
- Department of Epidemiology and Medical Statistic, Faculty of Public Health and Health Informatics, Umm Al-Qura University, Makkah, Saudi Arabia
| | - D Avinash
- Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India
| | - Hassan A Alzahrani
- Department of Respiratory Care, Medical Cities at the Minister of Interior, MCMOl, Riyadh, Saudi Arabia
| | | | - Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
| | - Sandeep Kumar
- School of Pharmacy, Sharda University, Greater Noida, India; DST-FIST Laboratory, Sharda University, Greater Noida, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Biosciences and Technology (SBT), Galgotias University, Greater Noida, India; Centre for Research Impact & Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura 140401, Punjab, India.
| | - Saad Alghamdi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| |
Collapse
|
28
|
Li D, Luo Y, Fan H, Dong L, Zhang X, Feng Y, Tian M, Zhang S, Chen W, Zhang L, Gao J, Ma X, Wang X, Ma C, Zheng R, Hu X, Wang J, Chen F. Acrylamide drives amidase-mediated gut dysbiosis to aggravate colitis. Sci Bull (Beijing) 2025; 70:157-161. [PMID: 38909004 DOI: 10.1016/j.scib.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/18/2024] [Accepted: 06/05/2024] [Indexed: 06/24/2024]
Affiliation(s)
- Daotong Li
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Yinghua Luo
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Huimin Fan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Li Dong
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Xiaoying Zhang
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Yu Feng
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Meiling Tian
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Shuqing Zhang
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Wenjing Chen
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Lujia Zhang
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Jianwei Gao
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Xiangning Ma
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Xiaofei Wang
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Chen Ma
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Ruimao Zheng
- Department of Anatomy, Histology and Embryology, Health Science Center, Peking University, Beijing 100191, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Fang Chen
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Engineering Research Centre for Fruits and Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China.
| |
Collapse
|
29
|
Raimundo M, Rodrigues P, Esteban S, Espinosa-Martos I, Jiménez E. Ligilactobacillus salivarius PS11610 Enhances the Fertilization Success of IVF: A Preliminary Retrospective Analysis. Nutrients 2025; 17:410. [PMID: 39940268 PMCID: PMC11821006 DOI: 10.3390/nu17030410] [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: 11/25/2024] [Revised: 12/27/2024] [Accepted: 12/30/2024] [Indexed: 02/14/2025] Open
Abstract
BACKGROUND/OBJECTIVES Infertility affects couples at reproductive age, with in vitro fertilization (IVF) being the most effective treatment. Success rates of IVF are influenced by several factors, including a healthy female reproductive system microbiome, which can improve implantation rates and pregnancy outcomes. This study evaluated the impact of Ligilactobacillus salivarius PS11610 on IVF outcomes. This strain showed antimicrobial activity against pathogens related to dysbiosis, commonly observed in women undergoing assisted reproductive treatment. RESULTS The administration of L. salivarius PS11610 at a dose of 1 × 109 CFU every 12 h for at least one month before IVF procedures, particularly in the frozen embryo transfer (FET) group, appears to enhance the success rate of IVF. IVF procedures without embryo transfer showed no significant differences between the groups. However, there were statistically significant differences in the quality of embryos, specifically in category 2, which were higher in the group without L. salivarius PS11610 supplementation (p = 0.042). Similar results were seen in the IVF with embryo transfer group, where the quality of embryos in categories 2 and 3 was higher in the group without L. salivarius PS11610 (p = 0.019 and p = 0.05, respectively). IVF with FET showed notable improvements, where intake of L. salivarius PS11610 was associated with a significant increase in live birth infants (26.4% with L. salivarius PS11610 vs. 17.9% without, p = 0.034) and higher biochemical pregnancy rates (42.6% vs. 34%, p = 0.071). CONCLUSIONS Despite some differences in embryo quality, the overall positive impact on pregnancy and birth outcomes highlights L. salivarius PS11610 as a promising supplement in assisted reproductive treatments.
Collapse
Affiliation(s)
- Miguel Raimundo
- NOVA National School of Public Health, NOVA University Lisbon, 1600-560 Lisbon, Portugal
| | - Patrícia Rodrigues
- School of Psychology and Life Sciences, Lusófona University Lisbon, 1749-024 Lisbon, Portugal;
| | - Sergio Esteban
- Probisearch SLU, 28760 Tres Cantos, Spain; (S.E.); (I.E.-M.); (E.J.)
| | | | - Esther Jiménez
- Probisearch SLU, 28760 Tres Cantos, Spain; (S.E.); (I.E.-M.); (E.J.)
| |
Collapse
|
30
|
Nelson S, Parkinson EI. Synthetic-bioinformatic natural product-inspired peptides. Nat Prod Rep 2025; 42:50-66. [PMID: 39479929 PMCID: PMC11525955 DOI: 10.1039/d4np00043a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Indexed: 11/02/2024]
Abstract
Covering: 2016 to 2024Natural products, particularly cyclic peptides, are a promising source of bioactive compounds. Nonribosomal peptide synthetases (NRPSs) play a key role in biosynthesizing these compounds, which include antibiotic and anticancer agents, immunosuppressants, and others. Traditional methods of discovering natural products have limitations including cryptic biosynthetic gene clusters (BGCs), low titers, and currently unculturable organisms. This has prompted the exploration of alternative approaches. Synthetic-bioinformatic natural products (syn-BNPs) are one such alternative that utilizes bioinformatics techniques to predict nonribosomal peptides (NRPs) followed by chemical synthesis of the predicted peptides. This approach has shown promise, resulting in the discovery of a variety of bioactive compounds including peptides with antibacterial, antifungal, anticancer, and proteasome-stimulating activities. Despite the success of this approach, challenges remain especially in the accurate prediction of fatty acid incorporation, tailoring enzyme modifications, and peptide release mechanisms. Further work in these areas will enable the discovery of many bioactive peptides that are currently inaccessible.
Collapse
Affiliation(s)
- Samantha Nelson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
| | - Elizabeth I Parkinson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
- James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, USA
| |
Collapse
|
31
|
Condori-Catachura S, Ahannach S, Ticlla M, Kenfack J, Livo E, Anukam KC, Pinedo-Cancino V, Collado MC, Dominguez-Bello MG, Miller C, Vinderola G, Merten S, Donders GGG, Gehrmann T, Lebeer S. Diversity in women and their vaginal microbiota. Trends Microbiol 2025:S0966-842X(24)00328-7. [PMID: 39919958 DOI: 10.1016/j.tim.2024.12.012] [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: 11/08/2024] [Revised: 12/18/2024] [Accepted: 12/23/2024] [Indexed: 02/09/2025]
Abstract
Women's health is essential to global societal and economic wellbeing, yet health disparities remain prevalent. The vaginal microbiota plays a critical role in health, with research indicating that reduced levels of core bacteria, such as lactobacilli, are associated with conditions like bacterial vaginosis (BV) and increased infection susceptibility. Lower levels of vaginal lactobacilli are reported more frequently in women of African and Latin American descent compared with women of European and Asian descent. However, geographical and other study inclusion and analysis biases influence current research. This opinion highlights the need for a more comprehensive understanding of a 'healthy' vaginal microbiome. It underscores efforts to broaden global research on microbiome diversity in socially relevant contexts, avoiding inappropriate applications of terms such as race and ethnicity.
Collapse
Affiliation(s)
- Sandra Condori-Catachura
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sarah Ahannach
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; U-MaMi Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Monica Ticlla
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; Unit Society, Gender and Health - Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Josiane Kenfack
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; Department of Biochemistry, Faculty of Science, University of Yaounde I, Yaounde, Cameroon; Centre for Research on Emerging and Reemerging Diseases, Institute of Medical Research and Medicinal Plant Studies, Yaounde, Cameroon; The Biotechnology Center, University of Yaounde I, Yaounde, Cameroon
| | - Esemu Livo
- Centre for Research on Emerging and Reemerging Diseases, Institute of Medical Research and Medicinal Plant Studies, Yaounde, Cameroon; The Biotechnology Center, University of Yaounde I, Yaounde, Cameroon; Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon; Strengthening Health and Applied Research, Yaounde, Cameroon
| | - Kingsley C Anukam
- Department of Medical Microbiology and Public Health, Faculty of Medical Laboratory Science, Nnamdi Azikiwe University, Nigeria
| | - Viviana Pinedo-Cancino
- Laboratorio de Investigación de Productos Naturales Antiparasitarios de la Amazonía (LIPNAA), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Iquitos, Peru; Facultad de Medicina Humana, Universidad Nacional de la Amazonía Peruana (UNAP), Iquitos, Peru
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Department of Anthropology, Rutgers University, New Brunswick, NJ, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Corrie Miller
- Department of Obstetrics, Gynecology, and Women's Health, Division of Maternal Fetal Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, CONICET-UNL), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sonja Merten
- Unit Society, Gender and Health - Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Gilbert G G Donders
- Department of Obstetrics and Gynaecology, University Hospital Antwerp, Edegem, Belgium.; Regional Hospital Heilig Hart, Tienen, Belgium; Femicare Clinical Research for Women, Tienen, Belgium
| | - Thies Gehrmann
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sarah Lebeer
- Laboratory of Applied Microbiology and Biotechnology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; U-MaMi Centre of Excellence, University of Antwerp, Antwerp, Belgium.
| |
Collapse
|
32
|
Zheng ZL, Zheng QF, Wang LQ, Liu Y. Bowel preparation before colonoscopy: Consequences, mechanisms, and treatment of intestinal dysbiosis. World J Gastroenterol 2025; 31:100589. [PMID: 39811511 PMCID: PMC11684204 DOI: 10.3748/wjg.v31.i2.100589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 10/22/2024] [Accepted: 11/12/2024] [Indexed: 12/18/2024] Open
Abstract
The term "gut microbiota" primarily refers to the ecological community of various microorganisms in the gut, which constitutes the largest microbial community in the human body. Although adequate bowel preparation can improve the results of colonoscopy, it may interfere with the gut microbiota. Bowel preparation for colonoscopy can lead to transient changes in the gut microbiota, potentially affecting an individual's health, especially in vulnerable populations, such as patients with inflammatory bowel disease. However, measures such as oral probiotics may ameliorate these adverse effects. We focused on the bowel preparation-induced changes in the gut microbiota and host health status, hypothesized the factors influencing these changes, and attempted to identify measures that may reduce dysbiosis, thereby providing more information for individualized bowel preparation for colonoscopy in the future.
Collapse
Affiliation(s)
- Ze-Long Zheng
- Department of Gastroenterology (Endoscopy Center), China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin Province, China
| | - Qing-Fan Zheng
- Department of Gastroenterology (Endoscopy Center), China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin Province, China
| | - Li-Qiang Wang
- Department of Gastroenterology (Endoscopy Center), China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin Province, China
| | - Yi Liu
- Department of Gastroenterology (Endoscopy Center), China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin Province, China
| |
Collapse
|
33
|
Heckmann ND, Culler MW, Mont MA, Lieberman JR, Parvizi J. Emerging Concepts in Periprosthetic Joint Infection Research: The Human Microbiome. J Arthroplasty 2025:S0883-5403(25)00001-4. [PMID: 39798621 DOI: 10.1016/j.arth.2025.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 11/26/2024] [Accepted: 01/06/2025] [Indexed: 01/15/2025] Open
Abstract
Microorganisms, including bacteria, fungi, and viruses, that reside on and within the human body are collectively known as the human microbiome. Dysbiosis, or disruption in the microbiome, has been implicated in several disease processes, including asthma, obesity, autoimmune diseases, and numerous other conditions. While the Human Microbiome Project and the generation of descriptive studies it inspired established correlations between characteristic patterns in the composition of the microbiome and specific disease phenotypes, current research has begun to focus on elucidating the causal role of the microbiome in disease pathogenesis. Within the field of orthopaedic surgery, researchers have proposed the concept of a "gut-joint axis," whereby the intestinal microbiome influences joint health and the development of diseases, such as osteoarthritis and periprosthetic joint infection (PJI). It is theorized that intestinal dysbiosis increases gut permeability, leading to the translocation of bacteria and their metabolic products into the systemic circulation and the stimulation of proinflammatory response cascades throughout the body, including within the joints. While correlative studies have identified patterns of dysbiotic derangement associated with osteoarthritis and PJI, translational research is needed to clarify the precise mechanisms by which these changes influence disease processes. Additionally, an emerging body of literature has challenged the previously held belief that certain body sites are sterile and do not possess a microbiome, with studies identifying distinct microbial genomic signatures and a core microbiome that varies between anatomic sites. A more thorough characterization of the joint microbiome may have profound implications for our understanding of PJI pathogenesis and our ability to stratify patients based on risk. The purpose of this review was to outline our current understanding of the human microbiome to describe the gut-joint axis and its role in specific pathologies, including PJI, and to highlight the potential of microbiome-based therapeutic interventions in the field of orthopaedics.
Collapse
Affiliation(s)
- Nathanael D Heckmann
- Department of Orthopaedic Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
| | - McKenzie W Culler
- Department of Orthopaedic Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
| | - Michael A Mont
- LifeBridge Health, Sinai Hospital of Baltimore, The Rubin Institute for Advanced Orthopaedics, Baltimore, Maryland, United States
| | - Jay R Lieberman
- Department of Orthopaedic Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
| | - Javad Parvizi
- International Joint Center, Acibadem University Hospital, Istanbul, Turkey
| |
Collapse
|
34
|
Tegegne HA, Savidge TC. Leveraging human microbiomes for disease prediction and treatment. Trends Pharmacol Sci 2025; 46:32-44. [PMID: 39732609 PMCID: PMC11786253 DOI: 10.1016/j.tips.2024.11.007] [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: 09/10/2024] [Revised: 11/19/2024] [Accepted: 11/20/2024] [Indexed: 12/30/2024]
Abstract
The human microbiome consists of diverse microorganisms that inhabit various body sites. As these microbes are increasingly recognized as key determinants of health, there is significant interest in leveraging individual microbiome profiles for early disease detection, prevention, and drug efficacy prediction. However, the complexity of microbiome data, coupled with conflicting study outcomes, has hindered its integration into clinical practice. This challenge is partially due to demographic and technological biases that impede the development of reliable disease classifiers. Here, we examine recent advances in 16S rRNA and shotgun-metagenomics sequencing, along with bioinformatics tools designed to enhance microbiome data integration for precision diagnostics and personalized treatments. We also highlight progress in microbiome-based therapies and address the challenges of establishing causality to ensure robust diagnostics and effective treatments for complex diseases.
Collapse
Affiliation(s)
- Henok Ayalew Tegegne
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
| |
Collapse
|
35
|
Iwami N, Komiya S, Asada Y, Tatsumi K, Habara T, Kuramoto T, Seki M, Yoshida H, Takeuchi K, Shiotani M, Mukaida T, Odawara Y, Mio Y, Kamiya H. "Shortening time to pregnancy in infertile women by personalizing treatment of microbial imbalance through Emma & Alice: A multicenter prospective study". Reprod Med Biol 2025; 24:e12634. [PMID: 39896099 PMCID: PMC11786016 DOI: 10.1002/rmb2.12634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 01/16/2025] [Indexed: 02/04/2025] Open
Abstract
Purpose To evaluate the impact of Endometrial Microbiome Metagenomic Analysis and Analysis of Infectious Chronic Endometritis (EMMA & ALICE) on pregnancy outcomes following recommended treatments in women with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL). Methods This prospective, multicenter cohort study included 527 women under 42 years old with RIF or RPL across 14 IVF centers in Japan. Endometrial samples were analyzed using EMMA & ALICE, and patients received antibiotics, probiotics, or no treatment based on test results. Pregnancy outcomes were assessed using Kaplan-Meier survival analysis and multivariate generalized linear models. Results Amongst participants, 43.4% had a normal Lactobacillus-dominated microbiota, 20.9% had dysbiosis, and 35.7% had mild dysbiosis or ultralow biomass. Kaplan-Meier analysis revealed significantly higher ongoing pregnancy rates in the dysbiosis group treated with antibiotics and probiotics compared to other groups (p = 0.031). Post-treatment, ongoing pregnancy rates in the dysbiosis and mild dysbiosis groups were comparable to the normal group. Conclusions EMMA & ALICE-guided antimicrobial and probiotic treatments improved pregnancy outcomes, enabling the dysbiosis group to achieve pregnancy earlier than the normal group. Addressing uterine dysbiosis may reduce the time to pregnancy in patients with RIF and RPL. Trial registration University Hospital Medical Information Network (UMIN), UMIN000036917.
Collapse
Affiliation(s)
| | | | - Yoshimasa Asada
- Asada Ladies Clinic (Nagoya Station Clinic)NagoyaJapan
- Asada Ladies Clinic (Kachigawa Clinic)KasugaiJapan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Duman H, Karav S. Fiber and the gut microbiome and its impact on inflammation. NUTRITION IN THE CONTROL OF INFLAMMATION 2025:51-76. [DOI: 10.1016/b978-0-443-18979-1.00004-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
|
37
|
Ferreira MR, Carratto TMT, Frontanilla TS, Bonadio RS, Jain M, de Oliveira SF, Castelli EC, Mendes-Junior CT. Advances in forensic genetics: Exploring the potential of long read sequencing. Forensic Sci Int Genet 2025; 74:103156. [PMID: 39427416 DOI: 10.1016/j.fsigen.2024.103156] [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: 05/03/2024] [Revised: 10/04/2024] [Accepted: 10/06/2024] [Indexed: 10/22/2024]
Abstract
DNA-based technologies have been used in forensic practice since the mid-1980s. While PCR-based STR genotyping using Capillary Electrophoresis remains the gold standard for generating DNA profiles in routine casework worldwide, the research community is continually seeking alternative methods capable of providing additional information to enhance discrimination power or contribute with new investigative leads. Oxford Nanopore Technologies (ONT) and PacBio third-generation sequencing have revolutionized the field, offering real-time capabilities, single-molecule resolution, and long-read sequencing (LRS). ONT, the pioneer of nanopore sequencing, uses biological nanopores to analyze nucleic acids in real-time. Its devices have revolutionized sequencing and may represent an interesting alternative for forensic research and routine casework, given that it offers unparalleled flexibility in a portable size: it enables sequencing approaches that range widely from PCR-amplified short target regions (e.g., CODIS STRs) to PCR-free whole transcriptome or even ultra-long whole genome sequencing. Despite its higher error rate compared to Illumina sequencing, it can significantly improve accuracy in read alignment against a reference genome or de novo genome assembly. This is achieved by generating long contiguous sequences that correctly assemble repetitive sections and regions with structural variation. Moreover, it allows real-time determination of DNA methylation status from native DNA without the need for bisulfite conversion. LRS enables the analysis of thousands of markers at once, providing phasing information and eliminating the need for multiple assays. This maximizes the information retrieved from a single invaluable sample. In this review, we explore the potential use of LRS in different forensic genetics approaches.
Collapse
Affiliation(s)
- Marcel Rodrigues Ferreira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit - Unipex, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Thássia Mayra Telles Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-901, Brazil
| | - Tamara Soledad Frontanilla
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Raphael Severino Bonadio
- Depto Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA, United States
| | | | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit - Unipex, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil; Pathology Department, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-901, Brazil.
| |
Collapse
|
38
|
Jeyaraman N, Jeyaraman M, Dhanpal P, Ramasubramanian S, Ragavanandam L, Muthu S, Santos GS, da Fonseca LF, Lana JF. Gut microbiome and orthopaedic health: Bridging the divide between digestion and bone integrity. World J Orthop 2024; 15:1135-1145. [PMID: 39744736 PMCID: PMC11686522 DOI: 10.5312/wjo.v15.i12.1135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 10/12/2024] [Accepted: 11/13/2024] [Indexed: 12/17/2024] Open
Abstract
The gut microbiome, a complex ecosystem of microorganisms in the digestive tract, has emerged as a critical factor in human health, influencing metabolic, immune, and neurological functions. This review explores the connection between the gut microbiome and orthopedic health, examining how gut microbes impact bone density, joint integrity, and skeletal health. It highlights mechanisms linking gut dysbiosis to inflammation in conditions such as rheumatoid arthritis and osteoarthritis, suggesting microbiome modulation as a potential therapeutic strategy. Key findings include the microbiome's role in bone metabolism through hormone regulation and production of short-chain fatty acids, crucial for mineral absorption. The review also considers the effects of diet, probiotics, and fecal microbiota transplantation on gut microbiome composition and their implications for orthopedic health. While promising, challenges in translating microbiome research into clinical practice persist, necessitating further exploration and ethical consideration of microbiome-based therapies. This interdisciplinary research aims to link digestive health with musculoskeletal integrity, offering new insights into the prevention and management of bone and joint diseases.
Collapse
Affiliation(s)
- Naveen Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, Tamil Nadu, India
- Department of Orthopaedics, Orthopaedic Research Group, Coimbatore 641045, Tamil Nadu, India
| | - Madhan Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, Tamil Nadu, India
- Department of Orthopaedics, Orthopaedic Research Group, Coimbatore 641045, Tamil Nadu, India
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| | - Priya Dhanpal
- Department of General Medicine, Government Medical College, Omandurar Government Estate, Chennai 600002, Tamil Nadu, India
| | - Swaminathan Ramasubramanian
- Department of General Medicine, Government Medical College, Omandurar Government Estate, Chennai 600002, Tamil Nadu, India
| | - Lavanya Ragavanandam
- Department of Pharmacology, Faculty of Medicine - Sri Lalithambigai Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600095, Tamil Nadu, India
| | - Sathish Muthu
- Department of Orthopaedics, Orthopaedic Research Group, Coimbatore 641045, Tamil Nadu, India
- Department of Orthopaedics, Government Medical College and Hospital, Karur 639004, Tamil Nadu, India
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Gabriel Silva Santos
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| | - Lucas Furtado da Fonseca
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| | - José Fábio Lana
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| |
Collapse
|
39
|
Muruganandam A, Migliorini F, Jeyaraman N, Vaishya R, Balaji S, Ramasubramanian S, Maffulli N, Jeyaraman M. Molecular Mimicry Between Gut Microbiome and Rheumatoid Arthritis: Current Concepts. Med Sci (Basel) 2024; 12:72. [PMID: 39728421 PMCID: PMC11677576 DOI: 10.3390/medsci12040072] [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: 10/25/2024] [Revised: 12/02/2024] [Accepted: 12/09/2024] [Indexed: 12/28/2024] Open
Abstract
Rheumatoid arthritis (RA) represents an autoimmune condition impacted by a combination of genetic and environmental factors, with the gut microbiome (GMB) being one of the influential environmental factors. Patients with RA display notable modifications in the composition of their GMB, characterised by decreased diversity and distinct bacterial alterations. The GMB, comprising an extensive array of approximately 35,000 bacterial species residing within the gastrointestinal tract, has garnered considerable attention as a pivotal contributor to both human health and the pathogenesis of diseases. This article provides an in-depth exploration of the intricate involvement of the GMB in the context of RA. The oral-GMB axis highlights the complex role of bacteria in RA pathogenesis by producing antibodies to citrullinated proteins (ACPAs) through molecular mimicry. Dysbiosis affects Tregs, cytokine levels, and RA disease activity, suggesting that regulating cytokines could be a strategy for managing inflammation in RA. The GMB also has significant implications for drug responses and toxicity, giving rise to the field of pharmacomicrobiomics. The composition of the microbiota can impact the efficacy and toxicity of drugs, while the microbiota's metabolites can influence drug response. Recent research has identified specific bacteria, metabolites, and immune responses associated with RA, offering potential targets for personalised management. However, several challenges, including the variation in microbial composition, establishing causality, accounting for confounding factors, and translating findings into clinical practice, need to be addressed. Microbiome-targeted therapy is still in its early stages and requires further research and standardisation for effective implementation.
Collapse
Affiliation(s)
- Anandanarayan Muruganandam
- Department of Orthopaedics, Faculty of Medicine—Sri Lalithambigai Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600095, India;
| | - Filippo Migliorini
- Department of Orthopedics and Trauma Surgery, Academic Hospital of Bolzano (SABES-ASDAA), 39100 Bolzano, Italy
- Department of Life Sciences, Health, and Health Professions, Link Campus University, 00165 Rome, Italy
| | - Naveen Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, India;
| | - Raju Vaishya
- Department of Orthopaedics and Joint Replacement Surgery, Indraprastha Apollo Hospital, New Delhi 110076, India;
| | - Sangeetha Balaji
- Department of Orthopaedics, Government Medical College, Omandurar Government Estate, Chennai 600002, India; (S.B.); (S.R.)
| | - Swaminathan Ramasubramanian
- Department of Orthopaedics, Government Medical College, Omandurar Government Estate, Chennai 600002, India; (S.B.); (S.R.)
| | - Nicola Maffulli
- Department of Trauma and Orthopaedic Surgery, Faculty of Medicine and Psychology, University La Sapienza, 00185 Roma, Italy;
- School of Pharmacy and Bioengineering, Keele University Faculty of Medicine, Stoke on Trent ST4 7QB, UK
- Centre for Sports and Exercise Medicine, Barts and the London School of Medicine and Dentistry, Mile End Hospital, Queen Mary University of London, London E1 4DG, UK
| | - Madhan Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, India;
| |
Collapse
|
40
|
Ndiaye C, Bassene H, Fonkou MDM, Fenollar F, Lagier JC, Raoult D, Sokhna C. The Application of Culturomics to Explore African Skin Microbiota. Am J Trop Med Hyg 2024; 111:1331-1337. [PMID: 39353418 PMCID: PMC11619480 DOI: 10.4269/ajtmh.23-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 02/12/2024] [Indexed: 10/04/2024] Open
Abstract
Over the past 12 years, culturomics, a high-throughput culture method, has been developed, considerably widening the repertoire of known cultured bacteria. An exhaustive database, including a list of microbes isolated by culture from human skin, was recently established by performing a review of the literature. The aim of the present study was to use the culturomics approach to explore the African skin microbiota. Skin swabs from the palms of human hands were collected between January and December 2016 from healthy subjects from the villages of Dielmo and Ndiop in rural Senegal. Three culture media were selected for the isolation of bacteria in aerobic conditions. Bacterial colonies were subjected to matrix-assisted laser desorption ionization-time of flight mass spectroscopy and the 16 S rRNA gene was sequenced for unidentified colonies. A total of 176 bacterial species were isolated. This increased the repertoire of bacterial species on the skin by 14.0%, by adding 71 bacteria, including seven new species. The culturomics approach characterizing microbial diversity has significantly changed our view of the skin microbiota, raising many important questions about the host-microorganism relationship and its relevance to skin diseases. In particular, the difference between the palm microbiota of these African populations (composed mainly of the genera Staphylococcus, Arthrobacter, Bacillus, and Microbacterium) and that of Western populations, whose main genera are Staphylococcus, Propionibacterium, Micrococcus, Corynebacterium, Enhydrobacter, and Streptococcus. This study demonstrates the need to continue to explore the skin microbiome using the culturomics approach.
Collapse
Affiliation(s)
- Codou Ndiaye
- UMR VITROME, Campus International IRD-UCAD de l’IRD de Hann, Dakar, Senegal
| | - Hubert Bassene
- UMR VITROME, Campus International IRD-UCAD de l’IRD de Hann, Dakar, Senegal
| | - Maxime Descartes Mbogning Fonkou
- Aix Marseille Université, IRD, AP-HM, Microbes Evolution Phylogeny and Infections (MEPHI), IHU-Méditerranée Infection, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Univ, IRD, AP-HM, SSA, IHU-Méditerranée Infection, UMR Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Jean Christophe Lagier
- Aix Marseille Université, IRD, AP-HM, Microbes Evolution Phylogeny and Infections (MEPHI), IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, Microbes Evolution Phylogeny and Infections (MEPHI), IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- UMR VITROME, Campus International IRD-UCAD de l’IRD de Hann, Dakar, Senegal
- Aix-Marseille Univ, IRD, AP-HM, SSA, IHU-Méditerranée Infection, UMR Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| |
Collapse
|
41
|
Manokasemsan W, Jariyasopit N, Poungsombat P, Kaewnarin K, Wanichthanarak K, Kurilung A, Duangkumpha K, Limjiasahapong S, Pomyen Y, Chaiteerakij R, Tansawat R, Srisawat C, Sirivatanauksorn Y, Sirivatanauksorn V, Khoomrung S. Quantifying fecal and plasma short-chain fatty acids in healthy Thai individuals. Comput Struct Biotechnol J 2024; 23:2163-2172. [PMID: 38827233 PMCID: PMC11141283 DOI: 10.1016/j.csbj.2024.05.007] [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: 02/24/2024] [Revised: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 06/04/2024] Open
Abstract
Short-chain fatty acids (SCFAs) are involved in important physiological processes such as gut health and immune response, and changes in SCFA levels can be indicative of disease. Despite the importance of SCFAs in human health and disease, reference values for fecal and plasma SCFA concentrations in healthy individuals are scarce. To address this gap in current knowledge, we developed a simple and reliable derivatization-free GC-TOFMS method for quantifying fecal and plasma SCFAs in healthy individuals. We targeted six linear- and seven branched-SCFAs, obtaining method recoveries of 73-88% and 83-134% in fecal and plasma matrices, respectively. The developed methods are simpler, faster, and more sensitive than previously published methods and are well suited for large-scale studies. Analysis of samples from 157 medically confirmed healthy individuals showed that the total SCFAs in the feces and plasma were 34.1 ± 15.3 µmol/g and 60.0 ± 45.9 µM, respectively. In fecal samples, acetic acid (Ace), propionic acid (Pro), and butanoic acid (But) were all significant, collectively accounting for 89% of the total SCFAs, whereas the only major SCFA in plasma samples was Ace, constituting of 93% of the total plasma SCFAs. There were no statistically significant differences in the total fecal and plasma SCFA concentrations between sexes or among age groups. The data revealed, however, a positive correlation for several nutrients, such as carbohydrate, fat, iron from vegetables, and water, to most of the targeted SCFAs. This is the first large-scale study to report SCFA reference intervals in the plasma and feces of healthy individuals, and thereby delivers valuable data for microbiome, metabolomics, and biomarker research.
Collapse
Affiliation(s)
- Weerawan Manokasemsan
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Narumol Jariyasopit
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Patcha Poungsombat
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Khwanta Kaewnarin
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- SingHealth Duke-NUS Institute of Biodiversity Medicine, National Cancer Centre Singapore, Singapore
| | - Kwanjeera Wanichthanarak
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Alongkorn Kurilung
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kassaporn Duangkumpha
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Suphitcha Limjiasahapong
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Yotsawat Pomyen
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand
| | - Roongruedee Chaiteerakij
- Center of Excellence for Innovation and Endoscopy in Gastrointestinal Oncology, Division of Gastroenterology, Department of Medicine, Faculty of Medicine Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Rossarin Tansawat
- Thailand Metabolomics Society, Bangkok, Thailand
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Metabolomics for Life Sciences Research Unit, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Chatchawan Srisawat
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Vorapan Sirivatanauksorn
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
| | - Sakda Khoomrung
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Thailand Metabolomics Society, Bangkok, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, Thailand
| |
Collapse
|
42
|
Ejtahed HS, Hasani-Ranjbar S, Soroush AR, Siadat SD, Larijani B. Microbiota research in Iran; current knowledge and future perspective. J Diabetes Metab Disord 2024; 23:1479-1484. [PMID: 39610549 PMCID: PMC11599682 DOI: 10.1007/s40200-020-00703-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Objective As the gut microbiota has attracted considerable attention in recent years, the aim of the present study is introducing a new microbiota research group at Endocrinology and Metabolism Research Institute (EMRI) that collaborates with national and international research centers for microbiome research projects management. Methods All the documents from EMRI focused on the microbiota field were collected using PubMed, Scopus, and Web of Science electronic databases from the inception up to June 2020. Results Findings of the EMRI research projects on the microbiota field were reviewed in this study and we highlighted some specific primary results of gut microbiota composition in the Iranian population. Moreover, applications of the developed Microbiota Database are introduced. Conclusion Enhancement of investment in this field and interdisciplinary collaborations are needed to progress our knowledge about the Iranian gut microbiota composition and develop microbiota modulating interventions over the next decade.
Collapse
Affiliation(s)
- Hanieh-Sadat Ejtahed
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Hasani-Ranjbar
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad-Reza Soroush
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed-Davar Siadat
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
43
|
Gupta U, Dey P. The oral microbial odyssey influencing chronic metabolic disease. Arch Physiol Biochem 2024; 130:831-847. [PMID: 38145405 DOI: 10.1080/13813455.2023.2296346] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/26/2023]
Abstract
INTRODUCTION Since the oral cavity is the gateway to the gut, oral microbes likely hold the potential to influence metabolic disease by affecting the gut microbiota. METHOD A thorough review of literature has been performed to link the alterations in oral microbiota with chronic metabolic disease by influencing the gut microbiota. RESULT A strong correlation exists between abnormalities in oral microbiota and several systemic disorders, such as cardiovascular disease, diabetes, and obesity, which likely initially manifest as oral diseases. Ensuring adequate oral hygiene practices and cultivating diverse oral microflora are crucial for the preservation of general well-being. Oral bacteria have the ability to establish and endure in the gastrointestinal tract, leading to the development of prolonged inflammation and activation of the immune system. Oral microbe-associated prophylactic strategies could be beneficial in mitigating metabolic diseases. CONCLUSION Oral microbiota can have a profound impact on the gut microbiota and influence the pathogenesis of metabolic diseases.
Collapse
Affiliation(s)
- Upasana Gupta
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| |
Collapse
|
44
|
Ranjan A, Arora J, Chauhan A, Basniwal RK, Kumari A, Rajput VD, Prazdnova EV, Ghosh A, Mukerjee N, Mandzhieva SS, Sushkova S, Minkina T, Jindal T. Advances in characterization of probiotics and challenges in industrial application. Biotechnol Genet Eng Rev 2024; 40:3226-3269. [PMID: 36200338 DOI: 10.1080/02648725.2022.2122287] [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: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.
Collapse
Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Jayati Arora
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| | - Rupesh Kumar Basniwal
- Amity Institute of Advanced Research and Studies (M&D), Amity University, Noida, India
| | - Arpna Kumari
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Evgeniya V Prazdnova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, New South Wales, Australia
| | - Saglara S Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| |
Collapse
|
45
|
Millman JF, Kondrashina A, Walsh C, Busca K, Karawugodage A, Park J, Sirisena S, Martin FP, Felice VD, Lane JA. Biotics as novel therapeutics in targeting signs of skin ageing via the gut-skin axis. Ageing Res Rev 2024; 102:102518. [PMID: 39389239 DOI: 10.1016/j.arr.2024.102518] [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: 07/14/2024] [Revised: 09/02/2024] [Accepted: 09/19/2024] [Indexed: 10/12/2024]
Abstract
Skin ageing is a phenomenon resulting from the aggregative changes to skin structure and function and is clinically manifested by physical features such as wrinkles, hyperpigmentation, elastosis, telangiectasia, and deterioration of skin barrier integrity. One of the main drivers of skin ageing, UV radiation, negatively influences the homeostasis of cells and tissues comprising the skin by triggering production of immune-mediated reactive oxygen species (ROS) and pro-inflammatory cytokines, as well as a various hormones and neuropeptides. Interestingly, an established link between the gut and the skin coined the 'gut-skin axis' has been demonstrated, with dysbiosis and gut barrier dysfunction frequently observed in certain inflammatory skin conditions and more recently, implicated in skin ageing. Therapeutic use of 'biotics' including prebiotics, probiotics, postbiotics, and synbiotics, which modulate the gut microbiota and production of microbially associated metabolites, influence the activity of the gut mucosal and immune systems and are showing promise as key candidates in addressing signs of skin ageing. In this review we aim to focus on the structure and function of the gut-skin axis and showcase the recent in-vitro and clinical evidence demonstrating the beneficial effects of select biotics in targeting signs of skin ageing and discuss the proposed mechanisms mediated via the gut-skin axis underpinning these effects.
Collapse
Affiliation(s)
- Jasmine F Millman
- Health and Happiness (H&H) Group, H&H Research, Level 6 & 7, 88 Langridge St, Collingwood, VIC 3066, Australia.
| | - Alina Kondrashina
- Health and Happiness (H&H) Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co., Cork P61K202, Ireland
| | - Clodagh Walsh
- Health and Happiness (H&H) Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co., Cork P61K202, Ireland
| | - Kizkitza Busca
- Health and Happiness (H&H) Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co., Cork P61K202, Ireland
| | - Aneesha Karawugodage
- Health and Happiness (H&H) Group, H&H Research, Level 6 & 7, 88 Langridge St, Collingwood, VIC 3066, Australia
| | - Julia Park
- Health and Happiness (H&H) Group, H&H Research, Level 6 & 7, 88 Langridge St, Collingwood, VIC 3066, Australia
| | - Sameera Sirisena
- Health and Happiness (H&H) Group, H&H Research, Level 6 & 7, 88 Langridge St, Collingwood, VIC 3066, Australia
| | - Francois-Pierre Martin
- Health and Happiness (H&H) Group, H&H Research, Avenue Sécheron 15 Bat F2/F3, Geneva 1202, Switzerland
| | - Valeria D Felice
- Health and Happiness (H&H) Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co., Cork P61K202, Ireland
| | - Jonathan A Lane
- Health and Happiness (H&H) Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co., Cork P61K202, Ireland.
| |
Collapse
|
46
|
Basnet J, Eissa MA, Cardozo LLY, Romero DG, Rezq S. Impact of Probiotics and Prebiotics on Gut Microbiome and Hormonal Regulation. GASTROINTESTINAL DISORDERS 2024; 6:801-815. [PMID: 39649015 PMCID: PMC11623347 DOI: 10.3390/gidisord6040056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2024] Open
Abstract
The gut microbiome plays a crucial role in human health by influencing various physiological functions through complex interactions with the endocrine system. These interactions involve the production of metabolites, signaling molecules, and direct communication with endocrine cells, which modulate hormone secretion and activity. As a result, the microbiome can exert neuroendocrine effects and contribute to metabolic regulation, adiposity, and appetite control. Additionally, the gut microbiome influences reproductive health by altering levels of sex hormones such as estrogen and testosterone, potentially contributing to conditions like polycystic ovary syndrome (PCOS) and hypogonadism. Given these roles, targeting the gut microbiome offers researchers and clinicians novel opportunities to improve overall health and well-being. Probiotics, such as Lactobacillus and Bifidobacterium, are live beneficial microbes that help maintain gut health by balancing the microbiota. Prebiotics, non-digestible fibers, nourish these beneficial bacteria, promoting their growth and activity. When combined, probiotics and prebiotics form synbiotics, which work synergistically to enhance the gut microbiota balance and improve metabolic, immune, and hormonal health. This integrated approach shows promising potential for managing conditions related to hormonal imbalances, though further research is needed to fully understand their specific mechanisms and therapeutic potential.
Collapse
Affiliation(s)
- Jelina Basnet
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Mississippi Center of Excellence in Perinatal Research, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Women’s Health Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Cardiovascular-Renal Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Manar A. Eissa
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Mississippi Center of Excellence in Perinatal Research, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Women’s Health Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Cardiovascular-Renal Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Licy L. Yanes Cardozo
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Mississippi Center of Excellence in Perinatal Research, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Women’s Health Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Cardiovascular-Renal Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Medicine, University of Mississippi Medical Center, 2500 N. State Street, Jackson, MS 39216, USA
| | - Damian G. Romero
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Mississippi Center of Excellence in Perinatal Research, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Women’s Health Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Cardiovascular-Renal Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Samar Rezq
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Mississippi Center of Excellence in Perinatal Research, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Women’s Health Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Cardiovascular-Renal Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
| |
Collapse
|
47
|
Alhamlan FS, Albadawi IA, Al-Qahtani AA, Awartani KA, Obeid DA, Tulbah AM. Cervicovaginal and gastrointestinal microbiomes in gynecological cancers and their roles in therapeutic intervention. Front Microbiol 2024; 15:1489942. [PMID: 39664050 PMCID: PMC11631898 DOI: 10.3389/fmicb.2024.1489942] [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: 09/02/2024] [Accepted: 11/13/2024] [Indexed: 12/13/2024] Open
Abstract
Cancer remains a significant global health concern, and understanding factors that regulate cancer development is important. The microbiome, with its potential role in cancer development, progression, and treatment, has garnered increasing attention in recent years. The cervicovaginal and gastrointestinal microbiomes in females constitute complex biological ecosystems. Although the gut microbiome has been extensively studied, little is known about the cervicovaginal microbiome. The microbiome plays a crucial role in maintaining local microenvironments and tissue homeostasis, but dysbiosis can disrupt this fine balance and contribute to pathological ramifications leading to cancer. This review explores the current understanding of the microbiome's correlation with gynecological cancers and highlights the potential of microbiome-based interventions to improve outcomes in these cancers. In addition, this review underscores the gaps and limitations in the literature, such as findings in specific ethnicities compared with understudied ethnicities. In addition, discrepancies in molecular techniques and terminology (microbiome vs. microbiota) used in the literature are addressed. Emerging evidence linking gynecological cancers and dysbiosis underscores microbiota as a potential target for cancer prevention and therapy. Manipulating the microbiome, such as through the use of probiotics, prebiotics, antibiotics, or vaginal and fecal transplantation, has demonstrated benefits in the treatment of chronic and inflammatory conditions. Further translational research in this field is needed to integrate the benefits of beneficial microorganisms in the fight against gynecological cancers.
Collapse
Affiliation(s)
- Fatimah S. Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ismail A. Albadawi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Gynecology Oncology, Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Khalid A. Awartani
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Reproductive Medicine, Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Dalia A. Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Asma M. Tulbah
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| |
Collapse
|
48
|
McCune E, Sharma A, Johnson B, O'Meara T, Theiner S, Campos M, Heditsian D, Brain S, Gilbert JA, Esserman L, Campbell MJ. Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women. mSystems 2024; 9:e0123724. [PMID: 39470189 PMCID: PMC11575313 DOI: 10.1128/msystems.01237-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 10/05/2024] [Indexed: 10/30/2024] Open
Abstract
This study characterized and compared the fecal and oral microbiota from women with early-stage breast cancer (BC), women with ductal carcinoma in situ (DCIS), and healthy women. Fecal and oral samples were collected from newly diagnosed patients prior to any therapy and characterized using 16S rRNA sequencing. Measures of gut microbial alpha diversity were significantly lower in the BC vs healthy cohort. Beta diversity differed significantly between the BC or DCIS and healthy groups, and several differentially abundant taxa were identified. Clustering (non-negative matrix factorization) of the gut microbiota identified five bacterial guilds dominated by Prevotella, Enterobacteriaceae, Akkermansia, Clostridiales, or Bacteroides. The Bacteroides and Enterobacteriaceae guilds were significantly more abundant in the BC cohort compared to healthy controls, whereas the Clostridiales guild was more abundant in the healthy group. Finally, prediction of functional pathways identified 23 pathways that differed between the BC and healthy gut microbiota including lipopolysaccharide biosynthesis, glycan biosynthesis and metabolism, lipid metabolism, and sphingolipid metabolism. In contrast to the gut microbiomes, there were no significant differences in alpha or beta diversity in the oral microbiomes, and very few differentially abundant taxa were observed. Non-negative matrix factorization analysis of the oral microbiota samples identified seven guilds dominated by Veillonella, Prevotella, Gemellaceae, Haemophilus, Neisseria, Propionibacterium, and Streptococcus; however, none of these guilds were differentially associated with the different cohorts. Our results suggest that alterations in the gut microbiota may provide the basis for interventions targeting the gut microbiome to improve treatment outcomes and long-term prognosis. IMPORTANCE Emerging evidence suggests that the gut microbiota may play a role in breast cancer. Few studies have evaluated both the gut and oral microbiomes in women with breast cancer (BC), and none have characterized these microbiomes in women with ductal carcinoma in situ (DCIS). We surveyed the gut and oral microbiomes from women with BC or DCIS and healthy women and identified compositional and functional features of the gut microbiota that differed between these cohorts. In contrast, very few differential features were identified in the oral microbiota. Understanding the role of gut bacteria in BC and DCIS may open up new opportunities for the development of novel markers for early detection (or markers of susceptibility) as well as new strategies for prevention and/or treatment.
Collapse
Affiliation(s)
- Emma McCune
- Department of Surgery, University of California, San Francisco, California, USA
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Breanna Johnson
- Department of Surgery, University of California, San Francisco, California, USA
| | - Tess O'Meara
- Department of Surgery, University of California, San Francisco, California, USA
| | - Sarah Theiner
- Department of Surgery, University of California, San Francisco, California, USA
| | - Maribel Campos
- Department of Surgery, University of California, San Francisco, California, USA
| | - Diane Heditsian
- Department of Surgery, University of California, San Francisco, California, USA
| | - Susie Brain
- Department of Surgery, University of California, San Francisco, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Laura Esserman
- Department of Surgery, University of California, San Francisco, California, USA
| | - Michael J Campbell
- Department of Surgery, University of California, San Francisco, California, USA
| |
Collapse
|
49
|
Chen CM, Yang YCSH, Chou HC. Maternal diesel particle exposure alters gut microbiota and induces lung injury in rat offspring. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 287:117278. [PMID: 39522267 DOI: 10.1016/j.ecoenv.2024.117278] [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: 08/10/2024] [Revised: 10/24/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024]
Abstract
Maternal air pollutant exposure inhibits fetal lung development. Diesel exhaust particles (DEP) are one of the most substantial contributors to particulate matter pollution. The effects of maternal DEP exposure on gut microbiota in mothers and offspring and fetal lung development remain unclear. In this study, time-dated pregnant Sprague Dawley rats received intranasal administration of 100 μL phosphate-buffered saline (PBS) or DEP (250 μg) in 100 μL PBS from gestational days 16-21. The dams were permitted to deliver vaginally at term. On postnatal days 0 and 7, gut microbiota was sampled from the lower gastrointestinal tract. The right lung and terminal ileum were harvested for histological, cytokine, and 8-hydroxy-2'-deoxyguanosine (8-OHdG) analyses. On postnatal day 0, the dams exposed to DEP and rat offspring with maternal DEP exposure exhibited macrophages that phagocytized diesel particles and increased numbers of macrophages in the alveolar parenchyma. On postnatal days 0 and 7, the offspring of DEP-exposed dams exhibited significantly lower intestinal tight junction protein expression, higher lung 8-OHdG and cytokine levels, and substantial lung injury compared with the offspring of the control dams. No significant differences were observed in the microbiota composition and diversity between the control and DEP-exposed dams. Maternal DEP exposure altered the gut microbiota composition and diversity on postnatal days 0 and 7, with more significant effects observed in the offspring on postnatal day 7. Regarding the mechanism, lung injury in offspring may have been linked to altered gut microbiota communities and dysregulated metabolic pathways caused by maternal DEP exposure.
Collapse
Affiliation(s)
- Chung-Ming Chen
- Department of Pediatrics, Taipei Medical University Hospital, Taipei, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Yu-Chen S H Yang
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Hsiu-Chu Chou
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei, Taiwan
| |
Collapse
|
50
|
Jeyaraman N, Jeyaraman M, Mariappan T, Muthu S, Ramasubramanian S, Sharma S, Santos GS, da Fonseca LF, Lana JF. Insights of gut-liver axis in hepatic diseases: Mechanisms, clinical implications, and therapeutic potentials. World J Gastrointest Pharmacol Ther 2024; 15:98146. [PMID: 39534519 PMCID: PMC11551618 DOI: 10.4292/wjgpt.v15.i6.98146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/06/2024] [Accepted: 09/10/2024] [Indexed: 10/25/2024] Open
Abstract
With the rising prevalence of chronic liver diseases worldwide, there exists a need to diversify our artillery to incorporate a plethora of diagnostic and therapeutic methods to combat this disease. Currently, the most common causes of liver disease are non-alcoholic fatty liver disease, hepatitis, and alcoholic liver disease. Some of these chronic diseases have the potential to transform into hepatocellular carcinoma with advancing fibrosis. In this review, we analyse the relationship between the gut and liver and their significance in liver disease. This two-way relationship has interesting effects on each other in liver diseases. The gut microbiota, through its metabolites, influences the metabolism in numerous ways. Careful manipulation of its composition can lead to the discovery of numerous therapeutic potentials that can be applied in the treatment of various liver diseases. Numerous cohort studies with a pan-omics approach are required to understand the association between the gut microbiome and hepatic disease progression through which we can identify effective ways to deal with this issue.
Collapse
Affiliation(s)
- Naveen Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, Tamil Nadu, India
- Department of Research Methods, Orthopaedic Research Group, Coimbatore 641045, Tamil Nadu, India
| | - Madhan Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600077, Tamil Nadu, India
- Department of Research Methods, Orthopaedic Research Group, Coimbatore 641045, Tamil Nadu, India
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| | - Tejaswin Mariappan
- Department of Community Medicine, Government Stanley Medical College and Hospital, Chennai 600001, Tamil Nadu, India
| | - Sathish Muthu
- Department of Research Methods, Orthopaedic Research Group, Coimbatore 641045, Tamil Nadu, India
- Department of Orthopaedics, Government Medical College, Karur 639004, Tamil Nadu, India
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Swaminathan Ramasubramanian
- Department of Orthopaedics, Government Medical College, Omandurar Government Estate, Chennai 600002, Tamil Nadu, India
| | - Shilpa Sharma
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Gabriel Silva Santos
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| | - Lucas Furtado da Fonseca
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| | - José Fábio Lana
- Department of Orthopaedics, Brazilian Institute of Regenerative Medicine, Indaiatuba 13334-170, São Paulo, Brazil
| |
Collapse
|