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Corbin KD, Igudesman D, Smith SR, Zengler K, Krajmalnik-Brown R. Targeting the Gut Microbiota's Role in Host Energy Absorption With Precision Nutrition Interventions for the Prevention and Treatment of Obesity. Nutr Rev 2025:nuaf046. [PMID: 40233201 DOI: 10.1093/nutrit/nuaf046] [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] [Indexed: 04/17/2025] Open
Abstract
The field of precision nutrition aims to develop dietary approaches based on individual biological factors such as genomics or the gut microbiota. The gut microbiota, which is the highly individualized and complex community of microbes residing in the colon, is a key contributor to human physiology. Although gut microbes play multiple roles in the metabolism of nutrients, their role in modulating the absorption of dietary energy from foods that escape digestion in the small intestine has the potential to variably affect energy balance and, thus, body weight. The fate of this energy, and its subsequent impact on body weight, is well described in rodents and is emerging in humans. This narrative review is focused on recent clinical evidence of the role of the gut microbiota in human energy balance, specifically its impact on energy available to the human host. Despite recent progress, remaining gaps in knowledge present opportunities for developing and implementing strategies to understand causal microbial mechanisms related to energy balance. We propose that implementing rigorous microbiota-focused measurements in the context of innovative clinical trial designs will elucidate integrated diet-host-gut microbiota mechanisms. These mechanisms are primed to be targets for precision nutrition interventions to optimize energy balance to achieve desired weight outcomes. Given the magnitude and impact of the obesity epidemic, implementing these interventions within comprehensive weight management paradigms has the potential to be of public health significance.
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Affiliation(s)
- Karen D Corbin
- AdventHealth Translational Research Institute, Orlando, FL 32804, United States
| | - Daria Igudesman
- AdventHealth Translational Research Institute, Orlando, FL 32804, United States
| | - Steven R Smith
- AdventHealth Translational Research Institute, Orlando, FL 32804, United States
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, United States
| | - Rosa Krajmalnik-Brown
- Biodesign Center for Health through Microbiomes, Arizona State University, Tempe, AZ 85281, United States
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85281, United States
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Bao R, Guo Y, Hu Y, Ning G, Pan S, Wang W. Standardized assessment of energy excretion in healthy adults: a novel methodology. Am J Clin Nutr 2025; 121:470-477. [PMID: 39701422 DOI: 10.1016/j.ajcnut.2024.12.016] [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: 06/25/2024] [Revised: 12/10/2024] [Accepted: 12/16/2024] [Indexed: 12/21/2024] Open
Abstract
BACKGROUND Accurate monitoring of energy balance is essential for effective weight management, but the role of energy excretion is often neglected. OBJECTIVES This study aimed to develop and validate a standardized method for assessing energy excretion using dye-labeled meal replacement bars with consistent and stable ingredients. METHODS We utilized baseline data from a registered cross-over trial involving 12 healthy adults (7 females and 5 males) with a body mass index of 18-25 kg/m2. Participants consumed dye-labeled meal replacement bars under a standardized protocol, and their feces and urine were collected for energy measurement using bomb calorimetry. Correlation analysis was conducted to explore associations between these variables. RESULTS The total energy excretion rate averaged 10.48% [standard deviation (SD) 2.56%] of energy intake, with fecal and urinary excretion accounting for 7.95% (SD 2.67%) and 2.52% (SD 0.6%), respectively. Significant individual variability was observed, with total energy excretion ranging from 6.34% to 15.07%, resulting in a maximum difference of 209.64 kcal/d. Fecal energy excretion was positively correlated with fecal wet weight and energy density, whereas urinary energy excretion was associated with digestible energy. CONCLUSIONS This study presents a standardized and efficient methodology for accurately assessing energy excretion using dye-labeled replacement bars. The findings underscore the notable yet variable role of energy excretion in energy balance and suggest that this method could enhance the precision of future energy balance studies. REGISTRATION NUMBER This study was registered at chictr.org.cn as ChiCTR2000038421.
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Affiliation(s)
- Riqiang Bao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuhan Guo
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yixiang Hu
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shijia Pan
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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3
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Bouchez T, Liu B, Garza DR. Healthy gut microbiomes are host-controllable microbiomes. Front Microbiol 2025; 15:1497083. [PMID: 39845029 PMCID: PMC11751039 DOI: 10.3389/fmicb.2024.1497083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 12/23/2024] [Indexed: 01/24/2025] Open
Affiliation(s)
- Théodore Bouchez
- Université Paris-Saclay, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), PRocédés biOtechnologiques au Service de l'Environnement, Antony, France
| | - Bin Liu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Daniel Rios Garza
- Université Paris-Saclay, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), PRocédés biOtechnologiques au Service de l'Environnement, Antony, France
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4
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Castañeda-Monsalve V, Haange SB, Fröhlich LF, Fu Q, Rolle-Kampczyk U, von Bergen M, Jehmlich N. Food colorant brilliant blue causes persistent functional and structural changes in an in vitro simplified microbiota model system. ISME COMMUNICATIONS 2025; 5:ycaf050. [PMID: 40201425 PMCID: PMC11977461 DOI: 10.1093/ismeco/ycaf050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 01/23/2025] [Accepted: 03/19/2025] [Indexed: 04/10/2025]
Abstract
The human gut microbiota plays a vital role in maintaining host health by acting as a barrier against pathogens, supporting the immune system, and metabolizing complex carbon sources into beneficial compounds such as short-chain fatty acids. Brilliant blue E-133 (BB), is a common food dye that is not absorbed or metabolized by the body, leading to substantial exposure of the gut microbiota. Despite this, its effects on the microbiota are not well-documented. In this study, we cultivated the Simplified Human Microbiota Model (SIHUMIx) in a three-stage in vitro approach (stabilization, exposure, and recovery). Using metaproteomic and metabolomic approaches, we observed significant shifts in microbial composition, including an increase in the relative abundance of Bacteroides thetaiotaomicron and a decrease in beneficial species such as Bifidobacterium longum and Clostridium butyricum. We observed lower protein abundance in energy metabolism, metabolic end products, and particularly lactate and butyrate. Disturbance in key metabolic pathways related to energy production, stress response, and amino acid metabolism were also observed, with some pathways affected independently of bacterial abundance. These functional changes persisted during the recovery phase, indicating that the microbiota did not fully return to its pre-exposure state. Our findings suggest that BB has a lasting impact on gut microbiota structure and function, raising concerns about its widespread use in the food industry. This study underscores the need for further research into the long-term effects of food colorants on the gut microbiota and their potential health implications.
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Affiliation(s)
- Victor Castañeda-Monsalve
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research – UFZ GmbH, 04318 Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research – UFZ GmbH, 04318 Leipzig, Germany
| | - Laura-Fabienne Fröhlich
- Department of Environmental Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ GmbH, 04318 Leipzig, Germany
| | - Qiuguo Fu
- Department of Environmental Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ GmbH, 04318 Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research – UFZ GmbH, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research – UFZ GmbH, 04318 Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research – UFZ GmbH, 04318 Leipzig, Germany
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5
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Ferreira SCM, Jarquín-Díaz VH, Planillo A, Ďureje Ľ, Martincová I, Kramer-Schadt S, Forslund-Startceva SK, Heitlinger E. Eco-evolutionary dynamics of host-microbiome interactions in a natural population of closely related mouse subspecies and their hybrids. Proc Biol Sci 2024; 291:20241970. [PMID: 39689880 DOI: 10.1098/rspb.2024.1970] [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: 06/19/2024] [Revised: 11/01/2024] [Accepted: 11/08/2024] [Indexed: 12/19/2024] Open
Abstract
Closely related host species share similar symbionts, but the effects of host genetic admixture and environmental conditions on these communities remain largely unknown. We investigated the influence of host genetic admixture and environmental factors on the intestinal prokaryotic and eukaryotic communities (fungi, parasites) of two house mouse subspecies (Mus musculus domesticus and M. m. musculus) and their hybrids in two settings: (i) wild-caught mice from the European hybrid zone and (ii) wild-derived inbred mice in a controlled laboratory environment before and during a community perturbation (infection). In wild-caught mice, environmental factors strongly predicted the overall microbiome composition. Subspecies' genetic distance significantly influenced the overall microbiome composition, and each component (bacteria, parasites and fungi). While hybridization had a weak effect, it significantly impacted fungal composition. We observed similar patterns in wild-derived mice, where genetic distances and hybridization influenced microbiome composition, with fungi being more stable to infection-induced perturbations than other microbiome components. Subspecies' genetic distance has a stronger and consistent effect across microbiome components than differences in expected heterozygosity among hybrids, suggesting that host divergence and host filtering play a key role in microbiome divergence, influenced by environmental factors. Our findings offer new insights into the eco-evolutionary processes shaping host-microbiome interactions.
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Affiliation(s)
- Susana C M Ferreira
- Division of Computational Systems Biology, Center for Microbiology and Ecological Systems Science, University of Vienna, Djerassipl. 1, Vienna 1030, Austria
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13 Haus 14, Berlin 10115, Germany
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstraße 1, Vienna A-1160, Austria
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, Berlin 13125, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC). Robert-Rössle-Str. 10, Berlin 13125, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Aimara Planillo
- Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
| | - Ľudovít Ďureje
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Iva Martincová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Stephanie Kramer-Schadt
- Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
- Institute of Ecology, Chair of Planning-related Animal Ecology, Technische Universität Berlin (TUB), Rothenburgstr. 12, Berlin 12165, Germany
| | - Sofia K Forslund-Startceva
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, Berlin 13125, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC). Robert-Rössle-Str. 10, Berlin 13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Emanuel Heitlinger
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13 Haus 14, Berlin 10115, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
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6
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Vivekanandan KE, Kasimani R, Kumar PV, Meenatchisundaram S, Sundar WA. Overview of cloning in lactic acid bacteria: Expression and its application of probiotic potential in inflammatory bowel diseases. Biotechnol Appl Biochem 2024; 71:881-895. [PMID: 38576028 DOI: 10.1002/bab.2584] [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: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Inflammatory bowel disease (IBD) imposes a significant impact on the quality of life for affected individuals. However, there was a current lack of a systematic summary regarding the latest epidemic trends and the underlying pathogenesis of IBD. This highlights the need for a thorough examination of both the epidemiological aspects of IBD and the specific mechanisms by which lactic acid bacteria (LAB) contribute to mitigating this condition. In developed countries, higher incidences and death rates of IBD have been observed, influenced by a combination of environmental and genetic factors. LAB offer significant advantages and substantial potential for enhancing IBD treatment. LAB's capabilities include the production of bioactive metabolites, regulation of gut immunity, protection of intestinal mechanical barriers, inhibition of oxidative damage, and restoration of imbalanced gut microbiota. The review suggests that screening effective LAB using cell models and metabolites, optimizing LAB intake through dose-effect studies, enhancing utilization through nanoencapsulation and microencapsulation, investigating mechanisms to deepen the understanding of LAB, and refining clinical study designs. These efforts aim to contribute to comprehending the epidemic trend, pathogenesis, and treatment of IBD, ultimately fostering the development of targeted therapeutic products, such as LAB-based interventions.
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Affiliation(s)
- K E Vivekanandan
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - R Kasimani
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - P Vinoth Kumar
- Department of Microbiology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India
| | - S Meenatchisundaram
- Department of Microbiology, Shree Nehru Maha Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - William Arputha Sundar
- Department of Pharmaceuticals, Swamy Vivekananda College of Pharmacy, Namakkal, Tamil Nadu, India
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7
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Castañeda-Monsalve V, Fröhlich LF, Haange SB, Homsi MN, Rolle-Kampczyk U, Fu Q, von Bergen M, Jehmlich N. High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study. Front Microbiol 2024; 15:1349367. [PMID: 38444810 PMCID: PMC10912515 DOI: 10.3389/fmicb.2024.1349367] [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: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
The human gut microbiota is a complex microbial community with critical functions for the host, including the transformation of various chemicals. While effects on microorganisms has been evaluated using single-species models, their functional effects within more complex microbial communities remain unclear. In this study, we investigated the response of a simplified human gut microbiota model (SIHUMIx) cultivated in an in vitro bioreactor system in combination with 96 deep-well plates after exposure to 90 different xenobiotics, comprising 54 plant protection products and 36 food additives and dyes, at environmentally relevant concentrations. We employed metaproteomics and metabolomics to evaluate changes in bacterial abundances, the production of Short Chain Fatty Acids (SCFAs), and the regulation of metabolic pathways. Our findings unveiled significant changes induced by 23 out of 54 plant protection products and 28 out of 36 food additives across all three categories assessed. Notable highlights include azoxystrobin, fluroxypyr, and ethoxyquin causing a substantial reduction (log2FC < -0.5) in the concentrations of the primary SCFAs: acetate, butyrate, and propionate. Several food additives had significant effects on the relative abundances of bacterial species; for example, acid orange 7 and saccharin led to a 75% decrease in Clostridium butyricum, with saccharin causing an additional 2.5-fold increase in E. coli compared to the control. Furthermore, both groups exhibited up- and down-regulation of various pathways, including those related to the metabolism of amino acids such as histidine, valine, leucine, and isoleucine, as well as bacterial secretion systems and energy pathways like starch, sucrose, butanoate, and pyruvate metabolism. This research introduces an efficient in vitro technique that enables high-throughput screening of the structure and function of a simplified and well-defined human gut microbiota model against 90 chemicals using metaproteomics and metabolomics. We believe this approach will be instrumental in characterizing chemical-microbiota interactions especially important for regulatory chemical risk assessments.
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Affiliation(s)
- Victor Castañeda-Monsalve
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Laura-Fabienne Fröhlich
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Masun Nabhan Homsi
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Qiuguo Fu
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
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8
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Galgano S, Kettle H, Free A, Houdijk JGM. Estimating the contribution of the porcine fecal core microbiota to metabolite production via mathematical modeling and in vitro fermentation. mSystems 2024; 9:e0036623. [PMID: 38059648 PMCID: PMC10805034 DOI: 10.1128/msystems.00366-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023] Open
Abstract
The swine gut microbiota is a complex ecosystem found throughout the gastrointestinal tract, with multiple exchanges with the host and whose composition is linked to both external and internal factors, such as diet or breed. Diet, probiotic, or prebiotic interventions have been designed to boost beneficial host-microbiota interactions, such as the production of anti-inflammatory molecules, or the fermentation of otherwise undigested resources. In parallel, a smaller microbial population, shared among the same host species, independent of external or internal factors, has been described and defined as the "core microbiota." Therapies targeting the core microbiota could possibly lead to more precise and long-lasting effects. However, the metabolic role of the porcine core microbiota, especially in relation to the rest of the microbial community, is currently missing. We present here the first dynamic model of the porcine core microbiota, which we used to estimate the core-microbiota metabolite production and to forecast the effect of a synbiotic intervention targeting the core genera of the core microbiota. We developed a community model in which a total of 17 microbial groups were established based on culture-based information of representative species. First, the model parameters were estimated, and the resulting model simulations were compared favorably with in vitro experimentation. The model was then used to predict the microbial dynamics of the core and non-core members under different experimental conditions. Therefore, it was able to theorize the main-metabolite core microbiota contribution, hypothesizing that it could be mainly responsible for acetate and propionate, but not for butyrate production.IMPORTANCECurrently, little information is present in the literature to describe the generic metabolic role of the porcine core microbiota or to inform on the effect of interventions targeting the core genera. Moreover, both in vitro and in vivo experimentations aiming to explore the core microbiota dynamics are technically demanding, expensive, or restricted by ethical considerations. Modeling approaches can be used as an initial exploratory tool to develop hypotheses for targeted experimentation. Our mathematical model provides initial information on the microbial and metabolite dynamics of the core microbiota in relation to diet and therapeutic intervention.
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Affiliation(s)
- Salvatore Galgano
- Monogastric Science Research Centre, Scotland's Rural College, Edinburgh, Scotland, United Kingdom
| | - Helen Kettle
- Biomathematics and Statistics Scotland, Edinburgh, Scotland, United Kingdom
| | - Andrew Free
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jos G. M. Houdijk
- Monogastric Science Research Centre, Scotland's Rural College, Edinburgh, Scotland, United Kingdom
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9
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Yan W, Luo J, Yu Z, Xu B. A critical review on intestinal mucosal barrier protection effects of dietary polysaccharides. Food Funct 2024; 15:481-492. [PMID: 38197139 DOI: 10.1039/d3fo03412g] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Studies have shown that dietary polysaccharides, which are widely present in natural foods, have an important impact on the intestinal mucosal barrier. Dietary polysaccharides can maintain the intestinal barrier function through multiple mechanisms. The intestinal barrier is composed of mechanical, chemical, immune, and biological barriers, and dietary polysaccharides, as a bioactive component, can promote and regulate these four barriers. Dietary polysaccharides can enhance the expression of tight junction proteins and mucins such as occludin-1 and zonula occludens-1 (ZO-1) between intestinal epithelial cells, inhibit inflammatory response and oxidative stress, increase the growth of beneficial bacteria, produce beneficial metabolites such as short chain fatty acids (SCFAs), and promote the proliferation and metabolism of immune cells. Given the critical role of the intestinal mucosal system in health and disease, the protective effects of dietary polysaccharides may be potentially valuable for the prevention and treatment of gut-related diseases. Therefore, it is of great significance to further study the mechanism and application prospects of the intestinal mucosal barrier derived from plant, animal, fungal and bacterial sources.
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Affiliation(s)
- Weiqi Yan
- Food Science and Technology Program, Department of Life Sciences, BNU-HKBU United International College, China.
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Jinhai Luo
- Food Science and Technology Program, Department of Life Sciences, BNU-HKBU United International College, China.
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhiling Yu
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Baojun Xu
- Food Science and Technology Program, Department of Life Sciences, BNU-HKBU United International College, China.
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10
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Sayol-Altarriba A, Aira A, Villasante A, Albarracín R, Faneca J, Casals G, Villanueva-Cañas JL, Casals-Pascual C. Normalization of short-chain fatty acid concentration by bacterial count of stool samples improves discrimination between eubiotic and dysbiotic gut microbiota caused by Clostridioides difficile infection. Gut Microbes 2024; 16:2415488. [PMID: 39395000 PMCID: PMC11485779 DOI: 10.1080/19490976.2024.2415488] [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: 08/01/2024] [Revised: 09/23/2024] [Accepted: 10/07/2024] [Indexed: 10/14/2024] Open
Abstract
Short-chain fatty acids (SCFAs) represent a cornerstone of gut health, serving as critical mediators of immune modulation and overall host homeostasis. Patients with dysbiosis caused by Clostridioides difficile infection (CDI) typically exhibit lower SCFAs levels compared to healthy stool donors and, thus, the concentration of SCFAs has been proposed as a proxy marker of a healthy microbiota. However, there is no consistency in the methods used to quantify SCFAs in stool samples and usually, the results are normalized by the weight of the stool samples, which does not address differences in water and fiber content and ignores bacterial counts in the sample (the main component of stool that contributes to the composition of these metabolites in the sample). Here, we show that normalized SCFAs concentrations by the bacterial count improve discrimination between healthy and dysbiotic samples (patients with CDI), particularly when using acetate and propionate levels. After normalization, butyrate is the metabolite that best discriminates eubiotic and dysbiotic samples according to the area under the receiver operating characteristic (ROC) curve (AUC-ROC = 0.860, [95% CI: 0.786-0.934], p < .0001).
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Affiliation(s)
- Anna Sayol-Altarriba
- Faculty of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
- ISGlobal, Barcelona, Spain
- Department of Clinical Microbiology, Centre for Biomedical Diagnosis, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Andrea Aira
- ISGlobal, Barcelona, Spain
- Department of Clinical Microbiology, Centre for Biomedical Diagnosis, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Barcelona, Spain
| | - Anna Villasante
- Department of Clinical Microbiology, Centre for Biomedical Diagnosis, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Rosa Albarracín
- Department of Clinical Microbiology, Centre for Biomedical Diagnosis, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Joana Faneca
- Department of Biochemistry and Molecular Genetics, Centre for Biomedical Diagnosis, Hospital Clínic de Barcelona, IDIBAPS, Barcelona, Spain
| | - Gregori Casals
- Department of Biochemistry and Molecular Genetics, Centre for Biomedical Diagnosis, Hospital Clínic de Barcelona, IDIBAPS, Barcelona, Spain
| | | | - Climent Casals-Pascual
- Faculty of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
- ISGlobal, Barcelona, Spain
- Department of Clinical Microbiology, Centre for Biomedical Diagnosis, Hospital Clínic de Barcelona, Barcelona, Spain
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11
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Thiele Orberg E, Meedt E, Hiergeist A, Xue J, Heinrich P, Ru J, Ghimire S, Miltiadous O, Lindner S, Tiefgraber M, Göldel S, Eismann T, Schwarz A, Göttert S, Jarosch S, Steiger K, Schulz C, Gigl M, Fischer JC, Janssen KP, Quante M, Heidegger S, Herhaus P, Verbeek M, Ruland J, van den Brink MRM, Weber D, Edinger M, Wolff D, Busch DH, Kleigrewe K, Herr W, Bassermann F, Gessner A, Deng L, Holler E, Poeck H. Bacteria and bacteriophage consortia are associated with protective intestinal metabolites in patients receiving stem cell transplantation. NATURE CANCER 2024; 5:187-208. [PMID: 38172339 DOI: 10.1038/s43018-023-00669-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/13/2023] [Indexed: 01/05/2024]
Abstract
The microbiome is a predictor of clinical outcome in patients receiving allogeneic hematopoietic stem cell transplantation (allo-SCT). Microbiota-derived metabolites can modulate these outcomes. How bacteria, fungi and viruses contribute to the production of intestinal metabolites is still unclear. We combined amplicon sequencing, viral metagenomics and targeted metabolomics from stool samples of patients receiving allo-SCT (n = 78) and uncovered a microbiome signature of Lachnospiraceae and Oscillospiraceae and their associated bacteriophages, correlating with the production of immunomodulatory metabolites (IMMs). Moreover, we established the IMM risk index (IMM-RI), which was associated with improved survival and reduced relapse. A high abundance of short-chain fatty acid-biosynthesis pathways, specifically butyric acid via butyryl-coenzyme A (CoA):acetate CoA-transferase (BCoAT, which catalyzes EC 2.8.3.8) was detected in IMM-RI low-risk patients, and virome genome assembly identified two bacteriophages encoding BCoAT as an auxiliary metabolic gene. In conclusion, our study identifies a microbiome signature associated with protective IMMs and provides a rationale for considering metabolite-producing consortia and metabolite formulations as microbiome-based therapies.
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Affiliation(s)
- Erik Thiele Orberg
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany.
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Elisabeth Meedt
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Medical Center, Regensburg, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Zentrum Munich, Munich, Germany
- Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Paul Heinrich
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Zentrum Munich, Munich, Germany
- Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Sakhila Ghimire
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Oriana Miltiadous
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah Lindner
- Department of Immunology, Sloan Kettering Institute, New York, NY, USA
| | - Melanie Tiefgraber
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Sophia Göldel
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Tina Eismann
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Alix Schwarz
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Sascha Göttert
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany
- Comparative Experimental Pathology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Schulz
- Department of Internal Medicine II, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Michael Gigl
- Bavarian Center for Biomolecular Mass Spectrometry, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julius C Fischer
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar TUM, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar TUM, Munich, Germany
| | - Michael Quante
- Department of Internal Medicine II, University Medical Center, Freiburg, Germany
| | - Simon Heidegger
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Peter Herhaus
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Mareike Verbeek
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Marcel R M van den Brink
- Department of Immunology, Sloan Kettering Institute, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Daniela Weber
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Matthias Edinger
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Daniel Wolff
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Florian Bassermann
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Medical Center, Regensburg, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum Munich, Munich, Germany
- Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ernst Holler
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany.
- Leibniz Institute for Immunotherapy, Regensburg, Germany.
- Bavarian Cancer Research Center (BZKF), Regensburg, Germany.
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12
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Amieva-Balmori M, García-Mazcorro JF, Martínez-Conejo A, Hernández-Ramírez GA, García-Zermeño KR, Rodríguez-Aguilera O, Aja-Cadena M, Barradas-Cortés M, Quigley EMM, Remes-Troche JM. Fecal bacterial microbiota in constipated patients before and after eight weeks of daily Bifidobacterium infantis 35624 administration. REVISTA DE GASTROENTEROLOGIA DE MEXICO (ENGLISH) 2023; 88:369-380. [PMID: 35810091 DOI: 10.1016/j.rgmxen.2022.06.014] [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: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION AND AIM In recent years, probiotics have been used in functional gastrointestinal disorders, including chronic constipation (CC). The effect of Bifidobacterium infantis strain 35624 on the gut microbiota of CC patients has not been previously studied. Our aim was to analyze the fecal microbiota of constipated patients, before and after consuming a single-strain probiotic (B. infantis strain 35624). MATERIALS AND METHODS We used 16S rRNA gene high-throughput sequencing to analyze the fecal microbiota of female patients (n=13) with CC. Patients were instructed to ingest one capsule of Alflorex® (containing 1×109 CFUs/g B. infantis strain 35624) daily for eight weeks. Fecal samples were obtained at the baseline and end (final) of probiotic administration. RESULTS Alpha diversity metrics did not differ between the baseline and final periods. The butyrate producer, Oscillospira, was the taxon most strongly correlated with amplicon sequence variants (R2=0.55, p<0.0001). Except for a few bacterial taxa, there were no significant differences in relative abundance between the baseline and final periods. Beta-diversity measures also showed limited evidence for the differences between the two time periods. CONCLUSIONS The results suggest that the fecal bacterial microbiota remains stable in constipated women consuming a single-strain probiotic. Those findings may be helpful in better understanding probiotic functioning in patients with digestive disorders.
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Affiliation(s)
- M Amieva-Balmori
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - J F García-Mazcorro
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - A Martínez-Conejo
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - G A Hernández-Ramírez
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - K R García-Zermeño
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - O Rodríguez-Aguilera
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - M Aja-Cadena
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - M Barradas-Cortés
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - E M M Quigley
- Lynda K and David M Underwood Center for Digestive Disorders, Houston Methodist Hospital and Weill Cornell Medical College, Houston, TX, USA
| | - J M Remes-Troche
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México.
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13
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Walker AW, Hoyles L. Human microbiome myths and misconceptions. Nat Microbiol 2023; 8:1392-1396. [PMID: 37524974 DOI: 10.1038/s41564-023-01426-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/15/2023] [Indexed: 08/02/2023]
Abstract
Over the past two decades, interest in human microbiome research has increased exponentially. Regrettably, this increased activity has brought with it a degree of hype and misinformation, which can undermine progress and public confidence in the research. Here we highlight selected human microbiome myths and misconceptions that lack a solid evidence base. By presenting these examples, we hope to draw increased attention to the implications of inaccurate dogma becoming embedded in the literature, and the importance of acknowledging nuance when describing the complex human microbiome.
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Affiliation(s)
- Alan W Walker
- Microbiome, Food Innovation and Food Security Research Theme, Rowett Institute, University of Aberdeen, Aberdeen, UK.
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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14
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Szukiewicz D. Insight into the Potential Mechanisms of Endocrine Disruption by Dietary Phytoestrogens in the Context of the Etiopathogenesis of Endometriosis. Int J Mol Sci 2023; 24:12195. [PMID: 37569571 PMCID: PMC10418522 DOI: 10.3390/ijms241512195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Phytoestrogens (PEs) are estrogen-like nonsteroidal compounds derived from plants (e.g., nuts, seeds, fruits, and vegetables) and fungi that are structurally similar to 17β-estradiol. PEs bind to all types of estrogen receptors, including ERα and ERβ receptors, nuclear receptors, and a membrane-bound estrogen receptor known as the G protein-coupled estrogen receptor (GPER). As endocrine-disrupting chemicals (EDCs) with pro- or antiestrogenic properties, PEs can potentially disrupt the hormonal regulation of homeostasis, resulting in developmental and reproductive abnormalities. However, a lack of PEs in the diet does not result in the development of deficiency symptoms. To properly assess the benefits and risks associated with the use of a PE-rich diet, it is necessary to distinguish between endocrine disruption (endocrine-mediated adverse effects) and nonspecific effects on the endocrine system. Endometriosis is an estrogen-dependent disease of unknown etiopathogenesis, in which tissue similar to the lining of the uterus (the endometrium) grows outside of the uterus with subsequent complications being manifested as a result of local inflammatory reactions. Endometriosis affects 10-15% of women of reproductive age and is associated with chronic pelvic pain, dysmenorrhea, dyspareunia, and infertility. In this review, the endocrine-disruptive actions of PEs are reviewed in the context of endometriosis to determine whether a PE-rich diet has a positive or negative effect on the risk and course of endometriosis.
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Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
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15
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Kriger-Sharabi O, Malnick SDH, Fisher D. Manipulation of the intestinal microbiome-a slow journey to primetime. World J Clin Cases 2023; 11:4975-4988. [PMID: 37583860 PMCID: PMC10424025 DOI: 10.12998/wjcc.v11.i21.4975] [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: 03/23/2023] [Revised: 05/17/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023] Open
Abstract
The gut microbiota has important functions in the regulation of normal body functions. Alterations of the microbiota are being increasingly linked to various disease states. The microbiome has been manipulated via the administration of stool from animals or humans, for more than 1000 years. Currently, fecal microbiota transplantation can be performed via endoscopic administration of fecal matter to the duodenum or colon or via capsules of lyophilized stools. More recently fecal microbial transplantation has been shown to be very effective for recurrent Clostridoides difficile infection (CDI). In addition there is some evidence of efficacy in the metabolic syndrome and its hepatic manifestation, metabolic associated fatty liver disease (MAFLD), irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). We review the current literature regarding the microbiome and the pathogenesis and treatment of CDI, MAFLD, IBS and IBD.
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Affiliation(s)
- Ofra Kriger-Sharabi
- Institute of Gastroenterology, Assuta Medical Center, Ashdod 7747629, Israel
| | - Stephen D H Malnick
- Department of Internal Medicine, Kaplan Medical Center, Rehovot 76100, Israel
| | - David Fisher
- Department of Endocrinology, Soroka Medical Center, Beer Sheva POB 151, Israel
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16
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Blachier F. Amino Acid-Derived Bacterial Metabolites in the Colorectal Luminal Fluid: Effects on Microbial Communication, Metabolism, Physiology, and Growth. Microorganisms 2023; 11:1317. [PMID: 37317289 DOI: 10.3390/microorganisms11051317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Undigested dietary and endogenous proteins, as well as unabsorbed amino acids, can move from the terminal part of the ileum into the large intestine, where they meet a dense microbial population. Exfoliated cells and mucus released from the large intestine epithelium also supply nitrogenous material to this microbial population. The bacteria in the large intestine luminal fluid release amino acids from the available proteins, and amino acids are then used for bacterial protein synthesis, energy production, and in other various catabolic pathways. The resulting metabolic intermediaries and end products can then accumulate in the colorectal fluid, and their concentrations appear to depend on different parameters, including microbiota composition and metabolic activity, substrate availability, and the capacity of absorptive colonocytes to absorb these metabolites. The aim of the present review is to present how amino acid-derived bacterial metabolites can affect microbial communication between both commensal and pathogenic microorganisms, as well as their metabolism, physiology, and growth.
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Affiliation(s)
- François Blachier
- Université Paris-Saclay, AgroParisTech, INRAe, UMR PNCA, 91120 Palaiseau, France
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17
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Gut Microbiome Proteomics in Food Allergies. Int J Mol Sci 2023; 24:ijms24032234. [PMID: 36768555 PMCID: PMC9917015 DOI: 10.3390/ijms24032234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Food allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) tract microbiome as alterations in the gut microbiota can lead to dysbiosis, causing inflammation and pathogenic intestinal conditions that result in the development of FA. Although there is currently not enough knowledge to fully understand how the interactions between gut microbiota, host responses and the environment cause food allergies, recent advances in '-omics' technologies (i.e., proteomics, genomics, metabolomics) and in approaches involving systems biology suggest future headways that would finally allow the scientific understanding of the relationship between gut microbiome and FA. This review summarizes the current knowledge in the field of FA and insights into the future advances that will be achieved by applying proteomic techniques to study the GI tract microbiome in the field of FA and their medical treatment. Metaproteomics, a proteomics experimental approach of great interest in the study of GI tract microbiota, aims to analyze and identify all the proteins in complex environmental microbial communities; with shotgun proteomics, which uses liquid chromatography (LC) for separation and tandem mass spectrometry (MS/MS) for analysis, as it is the most promising technique in this field.
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18
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Daniel H. Gut physiology meets microbiome science. GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2022; 4:e1. [PMID: 39295899 PMCID: PMC11406389 DOI: 10.1017/gmb.2022.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 09/21/2024]
Abstract
Research on the gut microbiome has gained high popularity and almost every disease has meanwhile been linked to alterations in microbiome composition. Typically assessed via stool samples, the microbiome displays a huge diversity with a multitude of environmental parameters already identified as contributing to its character. Despite impressive scientific progress, normal microbiome diversity remains largely unexplained and it is tempting to speculate some of the yet unexplained variance is hidden in normal gut physiology. Although a few genome/phenome-wide associations studies have recently highlighted physiological parameters such as stool frequency, known as contributing to microbiome diversity, there is a large knowledge base from decades of basic research on gut functions that can be explored for possible links to stool features and microbiome characteristics. And, when extrapolating findings from faecal samples to the biology in the intestinal lumen or the mucosal microenvironment, gut anatomy and physiology features need to be considered. Similarly, differences in anatomy and physiology between rodents and humans need attention when discussing findings in animals in relation to human physiology and nutrition.
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Affiliation(s)
- Hannelore Daniel
- ex. School of Life Sciences, Technical University of Munich, Gregor-Mendel-Strasse 2, 85354 Freising, Germany
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19
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Aalam SMM, Crasta DN, Roy P, Miller AL, Gamb SI, Johnson S, Till LM, Chen J, Kashyap P, Kannan N. Genesis of fecal floatation is causally linked to gut microbial colonization in mice. Sci Rep 2022; 12:18109. [PMID: 36302811 PMCID: PMC9613883 DOI: 10.1038/s41598-022-22626-x] [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: 01/22/2022] [Accepted: 10/18/2022] [Indexed: 12/30/2022] Open
Abstract
The origin of fecal floatation phenomenon remains poorly understood. Following our serendipitous discovery of differences in buoyancy of feces from germ-free and conventional mice, we characterized microbial and physical properties of feces from germ-free and gut-colonized (conventional and conventionalized) mice. The gut-colonization associated differences were assessed in feces using DNA, bacterial-PCR, scanning electron microscopy, FACS, thermogravimetry and pycnometry. Based on the differences in buoyancy of feces, we developed levô in fimo test (LIFT) to distinguish sinking feces (sinkers) of germ-free mice from floating feces (floaters) of gut-colonized mice. By simultaneous tracking of microbiota densities and gut colonization kinetics in fecal transplanted mice, we provide first direct evidence of causal relationship between gut microbial colonization and fecal floatation. Rare discordance in LIFT and microbiota density indicated that enrichment of gasogenic gut colonizers may be necessary for fecal floatation. Finally, fecal metagenomics analysis of 'floaters' from conventional and syngeneic fecal transplanted mice identified colonization of > 10 gasogenic bacterial species including highly prevalent B. ovatus, an anaerobic commensal bacteria linked with flatulence and intestinal bowel diseases. The findings reported here will improve our understanding of food microbial biotransformation and gut microbial regulators of fecal floatation in human health and disease.
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Affiliation(s)
- Syed Mohammed Musheer Aalam
- grid.66875.3a0000 0004 0459 167XDivision of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905 USA
| | - Daphne Norma Crasta
- grid.66875.3a0000 0004 0459 167XDivision of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905 USA
| | - Pooja Roy
- grid.66875.3a0000 0004 0459 167XDivision of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905 USA
| | - A. Lee Miller
- grid.66875.3a0000 0004 0459 167XDepartment of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905 USA
| | - Scott I. Gamb
- grid.66875.3a0000 0004 0459 167XMicroscopy and Cell Analysis Core, Mayo Clinic, Rochester, MN 55905 USA
| | - Stephen Johnson
- grid.66875.3a0000 0004 0459 167XDivision of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905 USA
| | - Lisa M. Till
- grid.66875.3a0000 0004 0459 167XDepartment of Gastroenterology, Mayo Clinic, Rochester, MN 55905 USA
| | - Jun Chen
- grid.66875.3a0000 0004 0459 167XDivision of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905 USA
| | - Purna Kashyap
- grid.66875.3a0000 0004 0459 167XDepartment of Gastroenterology, Mayo Clinic, Rochester, MN 55905 USA
| | - Nagarajan Kannan
- grid.66875.3a0000 0004 0459 167XDivision of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905 USA ,grid.66875.3a0000 0004 0459 167XCenter for Regenerative Biotherapeutics, Mayo Clinic, Rochester, MN 55905 USA ,grid.66875.3a0000 0004 0459 167XMayo Clinic Cancer Center, Mayo Clinic, Rochester, MN 55905 USA
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20
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Chriswell ME, Lefferts AR, Clay MR, Hsu AR, Seifert J, Feser ML, Rims C, Bloom MS, Bemis EA, Liu S, Maerz MD, Frank DN, Demoruelle MK, Deane KD, James EA, Buckner JH, Robinson WH, Holers VM, Kuhn KA. Clonal IgA and IgG autoantibodies from individuals at risk for rheumatoid arthritis identify an arthritogenic strain of Subdoligranulum. Sci Transl Med 2022; 14. [PMID: 36288282 PMCID: PMC9804515 DOI: 10.1126/scitranslmed.abn5166 10.1126/scitranslmed.abn5166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The mucosal origins hypothesis of rheumatoid arthritis (RA) proposes a central role for mucosal immune responses in the initiation or perpetuation of the systemic autoimmunity that occurs with disease. However, the connection between the mucosa and systemic autoimmunity in RA remains unclear. Using dual immunoglobulin A (IgA) and IgG family plasmablast-derived monoclonal autoantibodies obtained from peripheral blood of individuals at risk for RA, we identified cross-reactivity between RA-relevant autoantigens and bacterial taxa in the closely related families Lachnospiraceae and Ruminococcaceae. After generating bacterial isolates within the Lachnospiraceae/Ruminococcaceae genus Subdoligranulum from the feces of an individual, we confirmed monoclonal antibody binding and CD4+ T cell activation in individuals with RA compared to control individuals. In addition, when Subdoligranulum isolate 7 but not isolate 1 colonized germ-free mice, it stimulated TH17 cell expansion, serum RA-relevant IgG autoantibodies, and joint swelling reminiscent of early RA, with histopathology characterized by antibody deposition and complement activation. Systemic immune responses were likely due to mucosal invasion along with the generation of colon-isolated lymphoid follicles driving increased fecal and serum IgA by isolate 7, because B and CD4+ T cell depletion not only halted intestinal immune responses but also eliminated detectable clinical disease. In aggregate, these findings demonstrate a mechanism of RA pathogenesis through which a specific intestinal strain of bacteria can drive systemic autoantibody generation and joint-centered antibody deposition and immune activation.
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Affiliation(s)
- Meagan E. Chriswell
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Adam R. Lefferts
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael R. Clay
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Alex Ren Hsu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Jennifer Seifert
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marie L. Feser
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Cliff Rims
- Benaroya Research Institute, Seattle, WA 98101
| | - Michelle S. Bloom
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Elizabeth A. Bemis
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Sucai Liu
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | | | - Daniel N. Frank
- Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - M. Kristen Demoruelle
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Kevin D. Deane
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | | | | | - William H. Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - V. Michael Holers
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Kristine A. Kuhn
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045,Corresponding Author:
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21
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Chriswell ME, Lefferts AR, Clay MR, Hsu AR, Seifert J, Feser ML, Rims C, Bloom MS, Bemis EA, Liu S, Maerz MD, Frank DN, Demoruelle MK, Deane KD, James EA, Buckner JH, Robinson WH, Holers VM, Kuhn KA. Clonal IgA and IgG autoantibodies from individuals at risk for rheumatoid arthritis identify an arthritogenic strain of Subdoligranulum. Sci Transl Med 2022; 14:eabn5166. [PMID: 36288282 PMCID: PMC9804515 DOI: 10.1126/scitranslmed.abn5166] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The mucosal origins hypothesis of rheumatoid arthritis (RA) proposes a central role for mucosal immune responses in the initiation or perpetuation of the systemic autoimmunity that occurs with disease. However, the connection between the mucosa and systemic autoimmunity in RA remains unclear. Using dual immunoglobulin A (IgA) and IgG family plasmablast-derived monoclonal autoantibodies obtained from peripheral blood of individuals at risk for RA, we identified cross-reactivity between RA-relevant autoantigens and bacterial taxa in the closely related families Lachnospiraceae and Ruminococcaceae. After generating bacterial isolates within the Lachnospiraceae/Ruminococcaceae genus Subdoligranulum from the feces of an individual, we confirmed monoclonal antibody binding and CD4+ T cell activation in individuals with RA compared to control individuals. In addition, when Subdoligranulum isolate 7 but not isolate 1 colonized germ-free mice, it stimulated TH17 cell expansion, serum RA-relevant IgG autoantibodies, and joint swelling reminiscent of early RA, with histopathology characterized by antibody deposition and complement activation. Systemic immune responses were likely due to mucosal invasion along with the generation of colon-isolated lymphoid follicles driving increased fecal and serum IgA by isolate 7, because B and CD4+ T cell depletion not only halted intestinal immune responses but also eliminated detectable clinical disease. In aggregate, these findings demonstrate a mechanism of RA pathogenesis through which a specific intestinal strain of bacteria can drive systemic autoantibody generation and joint-centered antibody deposition and immune activation.
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Affiliation(s)
- Meagan E. Chriswell
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Adam R. Lefferts
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael R. Clay
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Alex Ren Hsu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Jennifer Seifert
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marie L. Feser
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Cliff Rims
- Benaroya Research Institute, Seattle, WA 98101
| | - Michelle S. Bloom
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Elizabeth A. Bemis
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Sucai Liu
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | | | - Daniel N. Frank
- Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - M. Kristen Demoruelle
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Kevin D. Deane
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | | | | | - William H. Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - V. Michael Holers
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Kristine A. Kuhn
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045,Corresponding Author:
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22
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Carpinteyro-Espín P, Santes O, Moctezuma-Velazquez P, Navarro-Iñiguez JA, Navarro-Navarro A, Salgado-Nesme N. Deloyers procedure compared to ileorectal anastomosis as restoration techniques of bowel continuity after extended left colon resection. ANZ J Surg 2022; 93:956-962. [PMID: 36196846 DOI: 10.1111/ans.18084] [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: 08/15/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Restoration of bowel continuity after left extended colectomy may be challenging because the remaining colon may not reach the rectal stump without tension to perform a safe anastomosis. Performing a total colectomy with ileorectal anastomosis (IRA) is an option, but the quality of life can be significantly impaired due to loose stools and an increase in bowel frequency. In contrast, the preservation of the right colon and ileocaecal valve in the Deloyers procedure (DP) might ensure a better stool consistency and bowel transit, and therefore a superior quality of life. MATERIALS AND METHODS A transverse study comparing patients that underwent DP versus patients with an IRA was performed. Postoperative morbidity, mortality, functional outcomes, and quality of life were analysed between groups. Quality of life after the surgical procedure was assessed with the SF-36 V2® health survey. RESULTS A total of 16 patients with DP and 32 with IRA were included. The groups had similar demographic characteristics concerning age, sex, body mass index, ASA classification, diagnosis and Charlson comorbidity index. The median follow-up was 55 months for DP and 99 months for IRA. Postoperative complications were similar in both groups. Patients in the DP group had fewer bowel movements (P = 0.01), tenesmus (P = 0.04) and use of loperamide (P = 0.03). DP patients achieved better scores in physical pain (P = 0.02) and general health (P < 0.01) than IRA patients. CONCLUSIONS DP for intestinal continuity restoration after extended left colon resection is a safe and feasible alternative, possibly achieving better functional outcomes and quality-of-life compared to IRA.
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Affiliation(s)
- Paulina Carpinteyro-Espín
- Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Oscar Santes
- Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Paulina Moctezuma-Velazquez
- Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julio A Navarro-Iñiguez
- Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Adolfo Navarro-Navarro
- Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Noel Salgado-Nesme
- Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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23
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Kettle H, Louis P, Flint HJ. Process-based modelling of microbial community dynamics in the human colon. J R Soc Interface 2022; 19:20220489. [PMCID: PMC9554726 DOI: 10.1098/rsif.2022.0489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/16/2022] [Indexed: 12/15/2024] Open
Abstract
The human colon contains a dynamic microbial community whose composition has important implications for human health. In this work, we build a process-based model of the colonic microbial ecosystem and compare with general empirical observations and the results of in vivo experiments. Our model comprises a complex microbial ecosystem along with absorption of short chain fatty acids (SCFA) and water by the host through the gut wall, variations in incoming dietary substrates (in the form of ‘meals’ whose composition varies in time), bowel movements, feedback on microbial growth from changes in pH resulting from SCFA production and multiple compartments to represent the proximal, transverse and distal colon. We verify our model against a number of observed criteria, e.g. total SCFA concentrations, SCFA ratios, mass of bowel movements, pH and water absorption over the transit time; and then run simulations investigating the effect of colonic transit time, and the composition and amount of indigestible carbohydrate in the host diet, which we compare with in vivo studies. The code is available as an R package (microPopGut) to aid future research.
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Affiliation(s)
- Helen Kettle
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Petra Louis
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Harry J. Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
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24
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Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota. Proc Natl Acad Sci U S A 2022; 119:e2114931119. [PMID: 35787046 PMCID: PMC9282425 DOI: 10.1073/pnas.2114931119] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The genetic composition of the gut microbiota is constantly reshaped by ecological and evolutionary forces. These strain-level dynamics are challenging to understand because they depend on complex spatial growth processes that take place within a host. Here we introduce a population genetic framework to predict how stochastic evolutionary forces emerge from simple models of microbial growth in spatially extended environments like the intestinal lumen. Our framework shows how fluid flow and longitudinal variation in growth rate combine to shape the frequencies of genetic variants in simulated fecal samples, yielding analytical expressions for the effective generation times, selection coefficients, and rates of genetic drift. We find that over longer timescales, the emergent evolutionary dynamics can often be captured by well-mixed models that lack explicit spatial structure, even when there is substantial spatial variation in species-level composition. By applying these results to the human colon, we find that continuous fluid flow and simple forms of wall growth alone are unlikely to create sufficient bottlenecks to allow large fluctuations in mutant frequencies within a host. We also find that the effective generation times may be significantly shorter than expected from traditional average growth rate estimates. Our results provide a starting point for quantifying genetic turnover in spatially extended settings like the gut microbiota and may be relevant for other microbial ecosystems where unidirectional fluid flow plays an important role.
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25
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Emetere ME, Chikwendu L, Afolalu SA. Improved Biogas Production from Human Excreta Using Chicken Feather Powder: A Sustainable Option to Eradicating Poverty. GLOBAL CHALLENGES (HOBOKEN, NJ) 2022; 6:2100117. [PMID: 35712022 PMCID: PMC9189137 DOI: 10.1002/gch2.202100117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/08/2022] [Indexed: 06/15/2023]
Abstract
It has been proposed that providing energy for cooking and lighting would solve over 65% of energy needs in rural communities. The use of biomass resources has been found not sustainable as other bioproducts such as biodiesel and bioethanol depend on it. More so that there is a depletion of bioresources in some parts of the world. The shift into animal waste such as poultry droppings and cattle dung has huge prospects, but it is not sustainable in the long term as rural farmers depend on it. The use of human excreta is the most available and sustainable due to the human population. This research aims to provide a workable blueprint of biogas production to meet energy needs. The research considers a laboratory-scale experiment whose result is used to project the medium-scale biodigester. Microbial culturing from human waste is used to initiate the codigestion of human excreta and powdered chicken feathers. It is observed that this procedure drastically reduces the high nitrogen content in the biogas and improves its methane and carbon dioxide content. It is observed that the scaled-up biodigester in a worst case scenario can function at 67%. Design parameters are documented for the onward adoption of the technique.
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Affiliation(s)
- Moses E. Emetere
- Department of Mechanical Engineering ScienceUniversity of JohannesburgJohannesburg2006South Africa
| | - L. Chikwendu
- Department of PhysicsCovenant University Canaan landOtaPMB 1023Nigeria
| | - S. A. Afolalu
- Department of Mechanical EngineeringAfe Babalola UniversityAdo Ekiti360102Nigeria
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26
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Watanabe Y, Mizushima T, Okumura R, Fujino S, Ogino T, Miyoshi N, Takahashi H, Uemura M, Matsuda C, Yamamoto H, Takeda K, Doki Y, Eguchi H. Fecal Stream Diversion Changes Intestinal Environment, Modulates Mucosal Barrier, and Attenuates Inflammatory Cells in Crohn's Disease. Dig Dis Sci 2022; 67:2143-2157. [PMID: 34041649 DOI: 10.1007/s10620-021-07060-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/11/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The intestinal environment plays important roles in mucosal barrier homeostasis and intestinal inflammation, as clarified in studies using experimental animals but not in humans. AIMS We investigated whether environmental changes in the fecal stream cause phenotypic changes in the human mucosal barrier. METHODS We obtained human ileal samples after fecal stream diversions in patients with rectal cancer or Crohn's disease. We investigated the bacterial load and diversity in the human defunctioned ileum, defined as the anal side of the ileum relative to the ileostomy. We also examined the epithelium and lamina propria cell phenotypes in the defunctioned ileum. RESULTS After fecal stream diversion, bacterial loads decreased significantly in the defunctioned ileum. Based on the Chao1, Shannon, and observed species indices, the diversity of mucosa-associated microbiota was lower in the defunctioned ileum than in the functional ileum. Moreover, the healthy defunctioned ileum showed reductions in villous height, goblet cell numbers, and Ki-67+ cell numbers. Additionally, interferon-γ+, interleukin-17+, and immunoglobulin A+ cell abundance in the lamina propria decreased. After the intestinal environment was restored with an ileostomy closure, the impaired ileal homeostasis recovered. The defunctioned ileum samples from patients with Crohn's disease also showed reductions in interferon-γ+ and interleukin-17+ cell numbers. CONCLUSIONS Fecal stream diversion reduced the abundance and diversity of intestinal bacteria. It also altered the intestinal mucosal barrier, similar to the alterations observed in germ-free animals. In patients with Crohn's disease, Th1 and Th17 cell numbers were attenuated, which suggests that the host-microbiome interaction is important in disease pathogenesis.
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Affiliation(s)
- Yoshifumi Watanabe
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Therapeutics for Inflammatory Bowel Diseases, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka, Japan.
| | - Ryu Okumura
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
- Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
| | - Shiki Fujino
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takayuki Ogino
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Chu Matsuda
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kiyoshi Takeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
- Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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27
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Peppelenbosch MP, Janmaat VT. Editorial on "A systematic review of microbial markers for risk prediction of colorectal neoplasia" by Yu and coauthors. Br J Cancer 2022; 126:1239-1240. [PMID: 35292757 PMCID: PMC9043177 DOI: 10.1038/s41416-022-01774-x] [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: 01/24/2022] [Revised: 02/04/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
Yu and colleagues show microbial markers are correlated with CRC and to a lesser degree with adenomas. Moreover, faecal microbial markers can be isolated from quantitative fecal immunochemical test cartridges and appear to improve results. If studies become less heterogeneous, it appears feasible to apply microbial markers in screening programmes.
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Affiliation(s)
- Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Vincent T Janmaat
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
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28
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Fornasaro S, Esposito A, Florian F, Pallavicini A, De Leo L, Not T, Lagatolla C, Mezzarobba M, Di Silvestre A, Sergo V, Bonifacio A. Spectroscopic investigation of faeces with surface-enhanced Raman scattering: a case study with coeliac patients on gluten-free diet. Anal Bioanal Chem 2022; 414:3517-3527. [PMID: 35258650 PMCID: PMC9018641 DOI: 10.1007/s00216-022-03975-y] [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: 12/07/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 11/06/2022]
Abstract
Surface-enhanced Raman scattering (SERS) spectra of faecal samples can be obtained by adding AuNP to their methanol extracts according to the reported protocol, and display bands that are due to bilirubin-like species but also to xanthine and hypoxanthine, two metabolic products secreted by gut bacteria. A total of 27 faecal samples from three different groups, i.e. coeliac patients (n = 9), coeliac patients on gluten-free diet (n = 10) and a control group (n = 8), were characterized with both SERS spectroscopy and 16S rRNA sequencing analysis. Significant differences are present between SERS spectra of coeliac patients and those on gluten-free diet, with a marked increase in the relative intensity of both xanthine and hypoxanthine for the latter. Interestingly, these differences do not correlate with bacterial composition as derived from 16S rRNA sequencing.
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Affiliation(s)
- Stefano Fornasaro
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Alessandro Esposito
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Fiorella Florian
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Luigina De Leo
- Institute for Maternal Child Health-IRCCS "Burlo Garofolo" Trieste, via dell'Istria 65/1, 34100, Trieste, Italy
| | - Tarcisio Not
- Institute for Maternal Child Health-IRCCS "Burlo Garofolo" Trieste, via dell'Istria 65/1, 34100, Trieste, Italy
| | - Cristina Lagatolla
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Marica Mezzarobba
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Alessia Di Silvestre
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Valter Sergo
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Alois Bonifacio
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy.
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29
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A Short-Term Low-Fiber Diet Reduces Body Mass in Healthy Young Men: Implications for Weight-Sensitive Sports. Int J Sport Nutr Exerc Metab 2022; 32:256-264. [PMID: 35313275 DOI: 10.1123/ijsnem.2021-0324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/13/2022] [Accepted: 02/10/2022] [Indexed: 11/18/2022]
Abstract
Athletes from weight-sensitive sports are reported to consume low-fiber diets (LOW) to induce acute reductions in body mass (BM). However, evidence supporting their efficacy is anecdotal. Therefore, we aimed to determine the effect of a LOW on acute changes in BM. Nineteen healthy males (32 ± 10 years, 1.79 ± 0.07 m, 77.5 ± 8.1 kg) consumed their habitual diet (∼30 g fiber/day) for 7 consecutive days followed by 4 days of a LOW (<10 g fiber/day) that was matched for energy and macronutrient content. Participants also matched their daily exercise load during LOW to that completed during habitual diet (p = .669, average 257 ± 141 arbitrary units). BM was significantly reduced in LOW versus habitual diet after 4 days (Δ = 0.40 ± 0.77 kg or 0.49% ± 0.91%, p < .05, effect size [ES] [95% confidence interval] = -0.53 [-1.17, 0.12]) and on the morning of Day 5 (Δ = 0.58 ± 0.83 kg or 0.74% ± 0.99%, p < .01, ES = -0.69 [-1.34, -0.03]). LOW resulted in moderately higher hunger (Δ = 5 ± 9 mm, p = .015, ES = 0.55 [-0.09, 1.20]), a decline in stool frequency from 2 ± 0 to 1 ± 0 bowel movements per day (p = .012, ES = 0.64 [-0.02, 1.29]) and stool softness decrease (p = .005). Nonetheless, participants reported the diet to be tolerable (n = 18/19) and were willing to repeat it (n = 16/19). Data demonstrate for the first time that consumption of a short-term LOW induces reductions in BM.
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30
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Gehrig JL, Portik DM, Driscoll MD, Jackson E, Chakraborty S, Gratalo D, Ashby M, Valladares R. Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data. Microb Genom 2022; 8:000794. [PMID: 35302439 PMCID: PMC9176275 DOI: 10.1099/mgen.0.000794] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A long-standing challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiota's impact on health and disease. With a growing number of live microbial interventions in clinical development, this challenge is renewed by a need to understand the pharmacokinetics and pharmacodynamics of therapeutic candidates. While short-read sequencing of the bacterial 16S rRNA gene has been the standard for microbiota profiling, recent improvements in the fidelity of long-read sequencing underscores the need for a re-evaluation of the value of distinct microbiome-sequencing approaches. We leveraged samples from participants enrolled in a phase 1b clinical trial of a novel live biotherapeutic product to perform a comparative analysis of short-read and long-read amplicon and metagenomic sequencing approaches to assess their utility for generating clinical microbiome data. Across all methods, overall community taxonomic profiles were comparable and relationships between samples were conserved. Comparison of ubiquitous short-read 16S rRNA amplicon profiling to long-read profiling of the 16S-ITS-23S rRNA amplicon showed that only the latter provided strain-level community resolution and insight into novel taxa. All methods identified an active ingredient strain in treated study participants, though detection confidence was higher for long-read methods. Read coverage from both metagenomic methods provided evidence of active-ingredient strain replication in some treated participants. Compared to short-read metagenomics, approximately twice the proportion of long reads were assigned functional annotations. Finally, compositionally similar bacterial metagenome-assembled genomes (MAGs) were recovered from short-read and long-read metagenomic methods, although a greater number and more complete MAGs were recovered from long reads. Despite higher costs, both amplicon and metagenomic long-read approaches yielded added microbiome data value in the form of higher confidence taxonomic and functional resolution and improved recovery of microbial genomes compared to traditional short-read methodologies.
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Affiliation(s)
| | | | | | - Eric Jackson
- Shoreline Biome, 400 Farmington Ave, Farmington, CT 06032, USA
| | | | - Dawn Gratalo
- Shoreline Biome, 400 Farmington Ave, Farmington, CT 06032, USA
| | - Meredith Ashby
- Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA 93025, USA
| | - Ricardo Valladares
- Siolta Therapeutics, 930 Brittan Ave, San Carlos, CA 94070, USA
- *Correspondence: Ricardo Valladares,
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Afrizal A, Hitch TCA, Viehof A, Treichel N, Riedel T, Abt B, Buhl EM, Kohlheyer D, Overmann J, Clavel T. Anaerobic single-cell dispensing facilitates the cultivation of human gut bacteria. Environ Microbiol 2022; 24:3861-3881. [PMID: 35233904 DOI: 10.1111/1462-2920.15935] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
Cultivation via classical agar plate (CAP) approaches is widely used to study microbial communities, but they are time-consuming. An alternative approach is the application of single-cell dispensing (SCD), which allows high-throughput, label-free sorting of microscopic particles. We aimed to develop a new anaerobic SCD workflow to cultivate human gut bacteria and compared it with CAP using faecal communities on three rich culture media. We found that the SCD approach significantly decreased the experimental time to obtain pure cultures from 17 ± 4 to 5 ± 0 days, while the isolate diversity and relative abundance coverage were comparable for both approaches. We further tested the total captured fraction by sequencing the sorted bacteria directly after growth as bulk biomass from 2400 dispensed single cells without downstream identification of individual strains. In this approach, the cultured fraction increased from 35.2% to 52.2% for SCD, highlighting the potential for deeper cultivation projects from single samples. SCD-based cultivation also captured species not detected by sequencing (16 ± 5 per sample, including seven novel taxa). From this work, 82 human gut bacterial species across five phyla (Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes and Proteobacteria) and 24 families were obtained, including the first cultured member of 11 novel genera and 10 novel species that were fully characterized taxonomically.
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Affiliation(s)
- Afrizal Afrizal
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Alina Viehof
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Nicole Treichel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Birte Abt
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Eva M Buhl
- Electron Microscopy Facility, Institute of Pathology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.,Aachener Verfahrenstechnik (AVT-MSB), RWTH Aachen University, Aachen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
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Consumption of multi-fiber enriched yogurt is associated with increase of Bifidobacterium animalis and butyrate producing bacteria in human fecal microbiota. J Funct Foods 2022. [DOI: 10.1016/j.jff.2021.104899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Christiansen CB, Veedfald S, Hartmann B, Gauguin AM, Møller S, Moritz T, Madsbad S, Holst JJ. Colonic Lactulose Fermentation Has No Impact on Glucagon-like Peptide-1 and Peptide-YY Secretion in Healthy Young Men. J Clin Endocrinol Metab 2022; 107:77-87. [PMID: 34508600 DOI: 10.1210/clinem/dgab666] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Indexed: 01/14/2023]
Abstract
CONTEXT The colon houses most of humans' gut microbiota, which ferments indigestible carbohydrates. The products of fermentation have been proposed to influence the secretion of glucagon-like peptide-1 (GLP-1) and peptide YY (PYY) from the many endocrine cells in the colonic epithelium. However, little is known about the colonic contribution to fasting or postprandial plasma levels of L-cell products. OBJECTIVE To determine the impact of colonic lactulose fermentation on gut peptide secretion and to evaluate whether colonic endocrine secretion contributes to gut hormone concentrations measurable in the fasting state. METHODS Ten healthy young men were studied on 3 occasions after an overnight fast. On 2 study days, lactulose (20 g) was given orally and compared to water intake on a third study day. For 1 of the lactulose visits, participants underwent a full colonic evacuation. Over a 6-h study protocol, lactulose fermentation was assessed by measuring exhaled hydrogen, and gut peptide secretion, paracetamol, and short-chain fatty acid levels were measured in plasma. RESULTS Colonic evacuation markedly reduced hydrogen exhalation after lactulose intake (P = 0.013). Our analysis suggests that the colon does not account for the measurable amounts of GLP-1 and PYY present in the circulation during fasting and that fermentation and peptide secretion are not acutely related. CONCLUSION Whether colonic luminal contents affect colonic L-cell secretion sufficiently to influence circulating concentrations requires further investigation. Colonic evacuation markedly reduced lactulose fermentation, but hormone releases were unchanged in the present study.
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Affiliation(s)
- Charlotte Bayer Christiansen
- Novo Nordic Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Veedfald
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Endocrinology, Copenhagen University Hospital at Hvidovre, Hvidovre, Denmark
| | - Bolette Hartmann
- Novo Nordic Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Astrid Marie Gauguin
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Møller
- Center for Functional and Diagnostic Imaging and Research, Department of Clinical Physiology and Nuclear Medicine 260, Copenhagen University Hospital at Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Moritz
- Novo Nordic Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sten Madsbad
- Department of Endocrinology, Copenhagen University Hospital at Hvidovre, Hvidovre, Denmark
| | - Jens Juul Holst
- Novo Nordic Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Hernalsteens S, Huang S, Cong HH, Chen XD. The final fate of food: On the establishment of in vitro colon models. Food Res Int 2021; 150:110743. [PMID: 34865762 DOI: 10.1016/j.foodres.2021.110743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
The search for life/health quality has driven the search for a better understanding of food components on the overall individual health, which turns to be intrinsically related to the digestive system. In vitro digestion models are considered an alternative for the in vivo studies for a variety of practical reasons, but further research is still needed concerning the colon model establishment. An effective in vitro colon model should consider all unit operations and transport phenomena, together with chemical and biochemical reactions, material handling and reactor design. Due to the different techniques and dependence on the donor microbiota, it is difficult to obtain a standard protocol with results reproductible in time and space. Furthermore, the colon model should be fed with a representative substrate, thus what happens in upper digestion tract and absorption prior to colon is also of crucial importance. Essentially, there are two ways to think about how to achieve a good and useful in vitro colon model: a complex biomimetic system that provides results comparable with the in vivo studies or a simple system, that despite the fact it could not give physiologically relevant data, it is sufficient to understand the fate of some specific components.
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Affiliation(s)
- Saartje Hernalsteens
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
| | | | - Hai Hua Cong
- College of Food Science and Engineering - Dalian Ocean University, China
| | - Xiao Dong Chen
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
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Dharmaratne P, Rahman N, Leung A, Ip M. Is there a role of faecal microbiota transplantation in reducing antibiotic resistance burden in gut? A systematic review and Meta-analysis. Ann Med 2021; 53:662-681. [PMID: 34170204 PMCID: PMC8238059 DOI: 10.1080/07853890.2021.1927170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/03/2021] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES The aim of current systematic review and meta-analysis is to provide insight into the therapeutic efficacy of fecal microbiota transplantation (FMT) for the decolonization of antimicrobial-resistant (AMR) bacteria from the gut. METHODS The protocol for this Systematic Review was prospectively registered with PROSPERO (CRD42020203634). Four databases (EMBASE, MEDLINE, SCOPUS, and WEB of SCIENCE) were consulted up until September 2020. A total of fourteen studies [in vivo (n = 2), case reports (n = 7), case series without control arm (n = 3), randomized clinical trials (RCT, n = 2)], were reviewed. Data were synthesized narratively for the case reports, along with a proportion meta-analysis for the case series studies (n = 102 subjects) without a control arm followed by another meta-analysis for case series studies with a defined control arm (n = 111 subjects) for their primary outcomes. RESULTS Overall, seven non-duplicate case reports (n = 9 participants) were narratively reviewed and found to have broad AMR remission events at the 1-month time point. Proportion meta-analysis of case series studies showed an overall 0.58 (95% CI: 0.42-0.74) AMR remission. Additionally, a significant difference in AMR remission was observed in FMT vs treatment naïve (RR = 0.44; 95% CI: 0.20-0.99) and moderate heterogeneity (I2=65%). A subgroup analysis of RCTs (n = 2) revealed FMT with further benefits of AMR remission with low statistical heterogeneity (RR = 0.37; 95% CI: 0.18-0.79; I2 =23%). CONCLUSION More rigorous RCTs with larger sample size and standardized protocols on FMTs for gut decolonization of AMR organisms are warranted.KEY MESSAGEExisting studies in this subject are limited and of low quality with moderate heterogeneity, and do not allow definitive conclusions to be drawn.More rigorous RCTs with larger sample size and standardized protocols on FMTs for gut decolonization of AMR organisms are warranted.
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Affiliation(s)
- Priyanga Dharmaratne
- Faculty of Medicine, Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Sha Tin, China
| | - Nannur Rahman
- Faculty of Medicine, Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Sha Tin, China
| | - Anthony Leung
- Faculty of Medicine, Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Sha Tin, China
| | - Margaret Ip
- Faculty of Medicine, Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Sha Tin, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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36
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Krueger BC, Fowler GD, Templeton MR, Septien S. Faecal sludge pyrolysis: Understanding the relationships between organic composition and thermal decomposition. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 298:113456. [PMID: 34364246 DOI: 10.1016/j.jenvman.2021.113456] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Sludge treatment is an integral part of faecal sludge management in non-sewered sanitation settings. Development of pyrolysis as a suitable sludge treatment method requires thorough knowledge about the properties and thermal decomposition mechanisms of the feedstock. This study aimed to improve the current lack of understanding concerning relevant sludge properties and their influence on the thermal decomposition characteristics. Major organic compounds (hemicellulose, cellulose, lignin, protein, oil and grease, other carbohydrates) were quantified in 30 faecal sludge samples taken from different sanitation technologies, providing the most comprehensive organic faecal sludge data set to date. This information was used to predict the sludge properties crucial to pyrolysis (calorific value, fixed carbon, volatile matter, carbon, hydrogen). Samples were then subjected to thermogravimetric analysis to delineate the influence of organic composition on thermal decomposition. Septic tanks showed lower median fractions of lignin (9.4%dwb) but higher oil and grease (10.7%dwb), compared with ventilated improved pit latrines (17.4%dwb and 4.6%dwb respectively) and urine diverting dry toilets (17.9%dwb and 4.7%dwb respectively). High fixed carbon fractions in lignin (45.1%dwb) and protein (18.8%dwb) suggested their importance for char formation, while oil and grease fully volatilised. For the first time, this study provided mechanistic insights into faecal sludge pyrolysis as a function of temperature and feedstock composition. Classification into the following three phases was proposed: decomposition of hemicellulose, cellulose, other carbohydrates, proteins and, partially, lignin (200-380 °C), continued decomposition of lignin and thermal cracking of oil and grease (380-500 °C) and continued carbonisation (>500 °C). The findings will facilitate the development and optimisation of faecal sludge pyrolysis, emphasising the importance of considering the organic composition of the feedstock.
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Affiliation(s)
- Benedict C Krueger
- Department of Civil and Environmental Engineering, Imperial College London, SW7 2AZ, UK.
| | - Geoffrey D Fowler
- Department of Civil and Environmental Engineering, Imperial College London, SW7 2AZ, UK
| | - Michael R Templeton
- Department of Civil and Environmental Engineering, Imperial College London, SW7 2AZ, UK
| | - Santiago Septien
- Water, Sanitation & Hygiene Research & Development Centre, University of KwaZulu-Natal, Durban, 4041, South Africa
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37
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Understanding the physiology of human defaecation and disorders of continence and evacuation. Nat Rev Gastroenterol Hepatol 2021; 18:751-769. [PMID: 34373626 DOI: 10.1038/s41575-021-00487-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 02/07/2023]
Abstract
The act of defaecation, although a ubiquitous human experience, requires the coordinated actions of the anorectum and colon, pelvic floor musculature, and the enteric, peripheral and central nervous systems. Defaecation is best appreciated through the description of four phases, which are, temporally and physiologically, reasonably discrete. However, given the complexity of this process, it is unsurprising that disorders of defaecation are both common and problematic; almost everyone will experience constipation at some time in their life and many will develop faecal incontinence. A detailed understanding of the normal physiology of defaecation and continence is critical to inform management of disorders of defaecation. During the past decade, there have been major advances in the investigative tools used to assess colonic and anorectal function. This Review details the current understanding of defaecation and continence. This includes an overview of the relevant anatomy and physiology, a description of the four phases of defaecation, and factors influencing defaecation (demographics, stool frequency/consistency, psychobehavioural factors, posture, circadian rhythm, dietary intake and medications). A summary of the known pathophysiology of defaecation disorders including constipation, faecal incontinence and irritable bowel syndrome is also included, as well as considerations for further research in this field.
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38
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Abd El-Wahab A, Meyer L, Kölln M, Chuppava B, Wilke V, Visscher C, Kamphues J. Insect Larvae Meal ( Hermetia illucens) as a Sustainable Protein Source of Canine Food and Its Impacts on Nutrient Digestibility and Fecal Quality. Animals (Basel) 2021; 11:ani11092525. [PMID: 34573490 PMCID: PMC8466710 DOI: 10.3390/ani11092525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/28/2022] Open
Abstract
Insect larvae meal has been proposed as a sustainable protein source for animal diets. This study aimed to provide information on including black soldier fly larvae meal (BSFL; Hermetia illucens) in comparison to poultry meal (PM) in the canine diet with regard to digestibility and fecal characteristics. In light of this trend, the levels of PM or BSFL meal were added to replace about 30% of dry matter of the basic extruded diet. Six Beagle dogs (BW 9.64 kg) were included in a cross-over experiment. Dogs fed a BSFL meal-based diet showed higher (p < 0.05) apparent protein digestibility (82.3%) compared to those offered a PM-based diet (80.5%). Apparent digestibility for fat was higher (p < 0.05) in groups fed the BSFL meal-based diet (94.5%) compared to those offered the PM-based diet (91.6%). The fecal consistency scores for dogs fed both diets were within an acceptable range (well-formed and firm). Fecal dry matter content was higher (p < 0.05) for dogs fed the PM-based diet (33.0%) compared to those offered the BSFL meal-based diet (28.0%). Including BSFL meal in dog food can be an appropriate source of protein without any negative effects on nutrient digestibility and fecal quality.
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Affiliation(s)
- Amr Abd El-Wahab
- Department of Nutrition and Nutritional Deficiency Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt;
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany; (L.M.); (M.K.); (B.C.); (V.W.); (J.K.)
| | - Laura Meyer
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany; (L.M.); (M.K.); (B.C.); (V.W.); (J.K.)
| | - Mareike Kölln
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany; (L.M.); (M.K.); (B.C.); (V.W.); (J.K.)
| | - Bussarakam Chuppava
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany; (L.M.); (M.K.); (B.C.); (V.W.); (J.K.)
| | - Volker Wilke
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany; (L.M.); (M.K.); (B.C.); (V.W.); (J.K.)
| | - Christian Visscher
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany; (L.M.); (M.K.); (B.C.); (V.W.); (J.K.)
- Correspondence:
| | - Josef Kamphues
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany; (L.M.); (M.K.); (B.C.); (V.W.); (J.K.)
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Tsutaya T, Ogawa NO, Nomura T, Shimizu M, Ohkouchi N, Kuze N. Carbon and nitrogen stable isotopic offsets between diet and hair/feces in captive orangutans. Primates 2021; 62:945-954. [PMID: 34415484 DOI: 10.1007/s10329-021-00940-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Estimating stable isotopic offset values is crucial for dietary reconstructions. Although research into stable isotope ecology of wild nonhuman primates is increasing overall, only a minority of studies involve laboratory experiments. This study is the first to report the carbon and nitrogen stable isotopic offset values in hair and feces of orangutans. During an experiment lasting 1 week, the weight of each consumed food item was recorded for each of six captive Bornean orangutan (Pongo pygmaeus) individuals. The food, hair, and fecal samples were collected for a few days, and their stable carbon and nitrogen isotope ratios were measured using an elemental analyzer/isotope ratio mass spectrometer. Subsamples of feces were treated with ethanol during the preservation process. Monte Carlo analyses showed that the 95% confidence intervals (CIs) of the carbon and nitrogen offset values between hair and diet were +0.9‰ to +3.9‰ and +2.3‰ to +4.5‰, respectively. The 95% CIs of the carbon and nitrogen offset values between feces and diet were -3.7‰ to -0.9‰ and +0.3‰ to +2.7‰, respectively. The effect of ethanol treatment on the stable isotope ratios of feces was unclear and inconclusive. The computed offset values of hair in captive orangutans are similar to those reported in other nonhuman primates, although those of feces showed greater interspecies variations. The offset values estimated in this study contribute to isotopic studies into the feeding ecology of free-ranging orangutans who are critically endangered in most wild settings.
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Affiliation(s)
- Takumi Tsutaya
- Department of Evolutionary Studies of Biosystems, the Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa, 240-0193, Japan. .,Japan Agency for Marine-Earth Science and Technology, Biogeochemistry Research Center, Research Institute for Marine Resources Utilization, Natsushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Nanako O Ogawa
- Japan Agency for Marine-Earth Science and Technology, Biogeochemistry Research Center, Research Institute for Marine Resources Utilization, Natsushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan
| | - Toshiya Nomura
- Tama Zoological Park, Hodokubo 7-1-1, Hino, Tokyo, 191-0042, Japan
| | - Mika Shimizu
- Tama Zoological Park, Hodokubo 7-1-1, Hino, Tokyo, 191-0042, Japan.,Present address: Ikimonosha, Maya 714, Akaiwa, Okayama, 709-0825, Japan
| | - Naohiko Ohkouchi
- Japan Agency for Marine-Earth Science and Technology, Biogeochemistry Research Center, Research Institute for Marine Resources Utilization, Natsushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan
| | - Noko Kuze
- Department of Anthropology, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki, 305-0005, Japan
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Dwivedi M, Powali S, Rastogi S, Singh A, Gupta DK. Microbial community in human gut: a therapeutic prospect and implication in health and diseases. Lett Appl Microbiol 2021; 73:553-568. [PMID: 34365651 DOI: 10.1111/lam.13549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
The interest in the working and functionality of the human gut microbiome has increased drastically over the years. Though the existence of gut microbes has long been speculated for long over the last few decades, a lot of research has sprung up in studying and understanding the role of gut microbes in the human digestive tract. The microbes present in the gut are highly instrumental in maintaining the metabolism in the body. Further research is going on in this field to understand how gut microbes can be employed as potential sources of novel therapeutics; moreover, probiotics have also elucidated their significant place in this direction. As regards the clinical perspective, microbes can be engineered to afford defence mechanisms while interacting with foreign pathogenic bodies. More investigations in this field may assist us to evaluate and understand how these cells communicate with human cells and promote immune interactions. Here we elaborate on the possible implication of human gut microbiota into the immune system as well as explore the probiotics in the various human ailments. Comprehensive information on the human gut microbiome at the same platform may contribute effectively to our understanding of the human microbiome and possible mechanisms of associated human diseases.
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Affiliation(s)
- M Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - S Powali
- Maulana Abdul Kalam Azad University of Technology, Kolkatta, India
| | - S Rastogi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - A Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - D K Gupta
- Department of Biochemistry, University of Allahabad, Prayagraj, India
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Minnebo Y, De Paepe K, Raes J, Van de Wiele T. Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem. FEMS Microbiol Ecol 2021; 97:6329685. [PMID: 34320208 DOI: 10.1093/femsec/fiab111] [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: 03/08/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
A recently introduced quantitative framework for gut microbiota analysis indicated that microbial load alterations can be linked to various diseases, making it essential to pinpoint its determinants. We identified nutrient load as a main driver of the quantitative microbial community composition and functionality in vitro by stepwise decreasing standardised feed concentrations from 100% to 33, 20 and 10% in five-day intervals. While the proportional composition and metabolic profile were mainly determined by the inter-individual variability (35 and 41%), nutrient load accounted for 58%, 23% and 65% of the observed variation in the microbial load, quantitative composition and net daily metabolite production, respectively. After the tenfold nutrient reduction, the microbial load decreased by 79.72 ± 9% and 82.96 ± 1.66% in the proximal and distal colon, respectively, while the net total short-chain fatty acid production dropped by 79.42 ± 4.42% and 84.58 ± 2.42%, respectively. The majority of microbial taxa quantitatively decreased, whereas a select group of nutritional specialists, such as Akkermansia muciniphila and Bilophila wadsworthia and a number of opportunistic pathogens remained unaffected. This shows that nutrient load is an important driver of the human gut microbiome and should be considered in future in vitro and in vivo dietary research.
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Affiliation(s)
- Yorick Minnebo
- Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Kim De Paepe
- Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.,Center for Microbiology, VIB, Herestraat 49, 3000 Leuven, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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James WPT. A Dissenter's Journey. Annu Rev Nutr 2021; 41:1-18. [PMID: 34115517 DOI: 10.1146/annurev-nutr-101220-114101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
After I studied medicine, my career took an early and unusual course when I was offered a clinical research post in Jamaica dealing with childhood malnutrition, of which I knew nothing. My subsequent nutritional explorations allowed gastrointestinal and metabolic analyses to have an impact on several public health policies. The biggest challenges came from unexpected political demands: coping with poor school performers in the Caribbean; addressing UK public health initiatives in health education; breaking the siege of Sarajevo; developing a Food Standards Agency as a sudden need for Tony Blair as incoming prime minister; dealing with widespread bovine spongiform encephalopathy in Europe; and responding to a United Nations request to assess global malnutrition. This last task revealed the need for a lifelong approach to nutrition, which also encompassed pregnancy. But perhaps the biggest challenge was establishing the criteria for obesity assessment, management, and prevention for policy makers across the globe. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- W Philip T James
- Department of Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom;
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Ibrahim HS, Shehab AY, Allam AF, Mohamed MA, Farag HF, Tolba MM. Detection and Molecular Identification of Cryptosporidium Species Among Children with Malignancies. Acta Parasitol 2021; 66:377-383. [PMID: 33025352 DOI: 10.1007/s11686-020-00250-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/25/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Cryptosporidiosis represents a major health problem worldwide particularly among children. Its diagnosis is still difficult and demands sensitive methods. In Egypt, there is little documentation of infection among children with malignancies. This work was designed to study the infection rate of Cryptosporidium among children with malignancies, compare the performance of modified Ziehl-Neelsen (MZN) stain with nested polymerase chain reaction (PCR) and identify the species subtypes of positive cases. METHODS The study was conducted on 100 children with malignancies (leukemia, lymphoma and solid tumors), below 10 years of age, from El-Shatby hospital, Alexandria University. After obtaining the informed consent, their stool samples were collected and examined microscopically following MZN stain for the diagnosis of Cryptosporidium spp. All samples were then subjected to nested PCR. Restriction fragment length polymorphism (RFLP) targeting the Cryptosporidium oocyst wall protein (COWP) gene was applied to positive cases, using restriction enzyme RsaI for digestion of nested PCR products. RESULTS Out of the 100 examined children, MZN detected higher positive cases compared to nested PCR. Six cases (6%) were diagnosed positive by MZN stain, three of which (3%) were concordantly positive by nested PCR. All positives were among children with acute lymphoblastic leukemia (ALL). Fair agreement was found between the two tests (K = 0.36). Genotyping results revealed that positive samples were of Cryptosporidium parvum (C. parvum) type II. CONCLUSIONS Low Cryptosporidium infection rate was detected among children with malignancies. MZN diagnosed more positive cases compared to nested PCR. C. parvum type II was the identified species among the examined children. Further optimization of PCR steps is needed.
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Fecal microbiota transplantation in human metabolic diseases: From a murky past to a bright future? Cell Metab 2021; 33:1098-1110. [PMID: 34077717 DOI: 10.1016/j.cmet.2021.05.005] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/26/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022]
Abstract
Fecal microbiota transplantation (FMT) is gaining considerable traction as a therapeutic approach to influence the course of a plethora of chronic conditions, ranging from metabolic syndrome and malignancies to auto-immune and neurological diseases, and helped to establish the contribution of the gut microbiome to these conditions. Although FMT procedures have yielded important mechanistic insights, their use in clinical practice may be limited due to practical objections in the setting of metabolic diseases. While its applicability is established to treat recurrent Clostridiodes difficile, FMT is emerging in ulcerative colitis and various other diseases. A particularly new insight is that FMTs may not only alter insulin sensitivity but may also alter the course of type 1 diabetes by attenuating underlying auto-immunity. In this review, we will outline the major principles and pitfalls of FMT and where optimization of study design and the procedure itself will further advance the field of cardiometabolic medicine.
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Gut amino acid absorption in humans: Concepts and relevance for postprandial metabolism. CLINICAL NUTRITION OPEN SCIENCE 2021. [DOI: 10.1016/j.nutos.2020.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Wu ZC, Wu L, Zhang M, Zhou W. Genome sequence and annotation of Bacteroides sp aff. Thetaiotaomicron strain isolated from blood. INFECTION GENETICS AND EVOLUTION 2021; 91:104816. [PMID: 33771725 DOI: 10.1016/j.meegid.2021.104816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/13/2021] [Accepted: 03/21/2021] [Indexed: 11/27/2022]
Abstract
This study is focused on genome sequence and annotation of the Bacteroides strain isolated from the blood of a patient with descending colon cancer. According to a comparison of the 16S ribosomal RNA sequence with the National Center for Biotechnology Information database, this strain was identified as Bacteroides sp. aff. Thetaiotaomicron. The next-generation sequencing of the strain was performed in a GENEWIZ laboratory (Jiangsu, China) on Illumina HiSeq device. According to CAZy classification, metabolic pathways related to carbohydrate metabolism of this strain engage the following enzymes: 427 glycosylhydrolases, 277 glycosyltransferases, 137 carbohydrate-binding modules, 48 carbohydrate esterases, and 24 polysaccharide lyases. According to the KEGG pathway database, Bacteroides sp. aff thetaiotaomicron strain is reported to incorporate 199 pathway associated genes. Bacteroides sp. aff. Thetaiotaomicron exposes the capacity of metabolizing a variety of polysaccharides. Its genome is enriched with an expanded repertoire of enzymes for the hydrolysis of glycosidic bonds and, thus, likely to hydrolyze most of glycosidic bonds in biological polysaccharides. The advanced capabilities of the studied strain to recognize and respond to environmental signals are expressed in the rich representation of one- and two-component signal transduction systems.
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Affiliation(s)
- Zhi Cheng Wu
- Clinical Laboratory, The First Affiliated Hospital of Hainan Medical University, 31 Longhua Road, Haikou, Hainan Province 570102, China.
| | - Lin Wu
- School of Tropical and Laboratory Medicine, Hainan Medical University, 31 Longhua Road, Haikou City, Hainan Province 571199, China; Faculty of Biotechnology and Biotechnics, National Technical University of Ukraine, Kyiv, Ukraine; Key Laboratory of Tropical Translational Medicine, Ministry of Education, Hainan Medical University, Haikou City, Hainan Province, China.
| | - Meng Zhang
- Sanya People's Hospital, Jiefang Third Road, 558, Sanya City, Hainan Province 572000, China
| | - WeiLan Zhou
- Clinical Laboratory, The First Affiliated Hospital of Hainan Medical University, 31 Longhua Road, Haikou, Hainan Province 570102, China
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The distribution of cellular turnover in the human body. Nat Med 2021; 27:45-48. [PMID: 33432173 DOI: 10.1038/s41591-020-01182-9] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 11/16/2020] [Indexed: 01/28/2023]
Abstract
We integrated ubiquity, mass and lifespan of all major cell types to achieve a comprehensive quantitative description of cellular turnover. We found a total cellular mass turnover of 80 ± 20 grams per day, dominated by blood cells and gut epithelial cells. In terms of cell numbers, close to 90% of the (0.33 ± 0.02) × 1012 cells per day turnover was blood cells.
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Effects of Low and High FODMAP Diets on Human Gastrointestinal Microbiota Composition in Adults with Intestinal Diseases: A Systematic Review. Microorganisms 2020; 8:microorganisms8111638. [PMID: 33114017 PMCID: PMC7690730 DOI: 10.3390/microorganisms8111638] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 10/18/2020] [Indexed: 12/12/2022] Open
Abstract
A diet high in non-digestible carbohydrates is known to promote health, in part through its effect on the gut microbiome. While substantially proven for healthy individuals, these effects are more ambiguous in subjects with intestinal diseases. At the same time, a diet low in these fermentable carbohydrates, the low FODMAP (acronym for Fermentable Oligo-, Di-, Mono-saccharides, And Polyols) diet, is gaining popularity as a treatment option for symptom relief in irritable bowel syndrome and inflammatory bowel disease. There are, however, several indications that this diet induces effects opposite to those of prebiotic supplementation, resulting in gut microbiome changes that might be detrimental. Here, we provide a systematic review of the effects of low and high FODMAP diets on human gastrointestinal microbiota composition in adults with intestinal diseases, through literature screening using the databases PubMed, Embase, and Web of Science. We summarize study findings on dietary impact in patients, including the effect on bacterial taxa and diversity. In general, similar to healthy subjects, restricting non-digestible carbohydrate intake in patients with intestinal diseases has opposite effects compared to prebiotic supplementation, causing a reduction in bifidobacteria and an increase in bacteria associated with dysbiosis. Future studies should focus on assessing whether the induced microbial changes persist over time and have adverse effects on long-term colonic health.
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Reitsema LJ, Jones CE, Gilbert HR, Fragaszy D, Izar P. Isotopic and elemental corroborates for wild bearded capuchin (Sapajus libidinosus) omnivorous dietary adaptation at Fazenda Boa Vista, Brazil. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8856. [PMID: 32526804 DOI: 10.1002/rcm.8856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/15/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE This study analyzes variability in the diets of wild bearded capuchin monkeys, Sapajus libidinosus, by analyzing stable carbon (δ13 C) and nitrogen (δ15 N) isotope ratios and elemental concentrations (%C and %N) of fecal samples and food items. Developing isotopic and elemental correlates for diets of habituated subjects is a necessary step towards applying similar methods to interpret diets of unhabituated or cryptic subjects. METHODS Fecal samples from wild capuchins and their foods were collected at Fazenda Boa Vista, Brazil. Fecal samples from laboratory-housed Sapajus spp. and their foods were analyzed to establish diet-feces offsets for δ13 C, δ15 N, %C, and %N. Samples were dried, powdered, and measured for isotopic and elemental values. A Bayesian mixing model commutes isotopic and elemental data from wild capuchins into likely proportions of different food categories. RESULTS The captive study shows small diet-feces spaces for Sapajus spp. of -0.8 ± 0.7‰ for δ13 C, -0.2 ± 0.4‰ for δ15 N, -6.1 ± 1.7% for %C, and -1.0 ± 0.6% for %N. The wild study shows omnivorous diets based on C3 , C4 , and CAM plants, and fauna. Subject diets are highly varied within and between days. Fecal data show age-related differences in diet and crop-raiding. There is no consistent isotopic or elemental difference between mothers and infants. CONCLUSIONS Fecal stable isotope and elemental evidence employed in a Bayesian mixing model reflects the highly varied diets of capuchin monkeys in an isotopically heterogeneous environment. The isotopic and elemental variability reported here will aid similar diet reconstructions among unhabituated subjects in the future, but precludes tracking weaning isotopically among capuchins in this environment.
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Affiliation(s)
| | - Caroline E Jones
- Department of Psychology, University of Georgia, Athens, GA, USA
| | - Hannah R Gilbert
- Department of Chemistry, University of Georgia, Athens, GA, USA
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Dorothy Fragaszy
- Department of Psychology, University of Georgia, Athens, GA, USA
| | - Patrícia Izar
- Department of Experimental Psychology, University of Sao Paulo, Sao Paulo, BRAZIL
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Lemay JA, Yamamoto M, Kroezen Z, Shanmuganathan M, Ly R, Hart L, Pai N, Britz-McKibbin P. Lyophilized fecal short-chain fatty acid and electrolyte determination by capillary electrophoresis with indirect UV detection for assessment of pediatric inflammatory bowel disease. J Pharm Biomed Anal 2020; 192:113658. [PMID: 33091761 DOI: 10.1016/j.jpba.2020.113658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 12/19/2022]
Abstract
Short-chain fatty acids (SCFAs) and electrolytes are major constituents of human feces involved in maintaining gastrointestinal homeostasis that underlie complex diet, host and microbiome interactions. Reliable quantification of SCFAs and electrolytes is challenging given the heterogeneity of stool specimens from pediatric patients with diarrhea-predominate inflammatory bowel disease (IBD). Herein, we introduce two validated methods for determination of 3 SCFAs and 5 electrolytes consistently quantified from fecal extracts when using capillary electrophoresis with indirect UV detection (CE-iUV), where concentrations are normalized to total dried weight (mmol/kg d.w.). Lyophilization facilitates sample handling and extraction of heterogeneous stool specimens (∼ 15 mg) from a cohort of children with Crohn's disease (CD, n = 12) and ulcerative colitis (UC, n = 10) treated with exclusive enteral nutrition (EEN) or corticosteroid (CS) therapy to induce remission, respectively. Good technical precision (mean CV = 13 %, n = 14) and accuracy (recovery from 84 to 116%) is demonstrated for SCFAs and electrolytes from freeze dried stool extracts using a modified Bligh-Dyer protocol with low micromolar detection limits (∼ 2-15 μM). Fecal butyrate is 2.6-fold higher in CD as compared to UC patients (effect size = 1.51; p = 0.00291), and there is a strong co-linearity between fecal butyrate and acetate (r = 0.835) unlike propionate, which is correlated with fecal calprotectin (r = 0.517), a protein biomarker of intestinal inflammation. Also, a longitudinal study of matching stool samples collected from a sub-set of IBD patients revealed about a 7-fold enrichment in magnesium and calcium following 4 weeks of EEN as compared to baseline (F > 4.1 ; p < 0.05) unlike the CS treatment arm with no changes in other fecal SCFAs and electrolytes, including sodium, potassium, and ammonium. CE-iUV enables rapid fecal SCFA and electrolyte determination as required for new insights into the role of gut dysbiosis in IBD, as well as treatment monitoring of nutritional interventions that stabilize the disease course in affected children.
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Affiliation(s)
- Julie-Anne Lemay
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Mai Yamamoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Zachary Kroezen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Ritchie Ly
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Lara Hart
- Department of Pediatrics, Division of Pediatric Gastroenterology, McMaster University, Hamilton, ON, Canada
| | - Nikhil Pai
- Department of Pediatrics, Division of Pediatric Gastroenterology, McMaster University, Hamilton, ON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada.
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