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Chatterjee P, Dassama LMK. Unveiling of a messenger: Gut microbes make a neuroactive signal. Cell 2024; 187:2903-2904. [PMID: 38848674 DOI: 10.1016/j.cell.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
Abstract
Gut microbes are known to impact host physiology in several ways. However, key molecular players in host-commensal interactions remain to be uncovered. In this issue of Cell, McCurry et al. reveal that gut bacteria perform 21-dehydroxylation to convert abundant biliary corticoids to neurosteroids using readily available H2 in their environment.
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Affiliation(s)
- Poulami Chatterjee
- Department of Chemistry, Stanford University, Stanford, CA, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Laura M K Dassama
- Department of Chemistry, Stanford University, Stanford, CA, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, USA.
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2
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McCurry MD, D'Agostino GD, Walsh JT, Bisanz JE, Zalosnik I, Dong X, Morris DJ, Korzenik JR, Edlow AG, Balskus EP, Turnbaugh PJ, Huh JR, Devlin AS. Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas. Cell 2024; 187:2952-2968.e13. [PMID: 38795705 PMCID: PMC11179439 DOI: 10.1016/j.cell.2024.05.005] [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: 07/19/2023] [Revised: 02/03/2024] [Accepted: 05/02/2024] [Indexed: 05/28/2024]
Abstract
Recent studies suggest that human-associated bacteria interact with host-produced steroids, but the mechanisms and physiological impact of such interactions remain unclear. Here, we show that the human gut bacteria Gordonibacter pamelaeae and Eggerthella lenta convert abundant biliary corticoids into progestins through 21-dehydroxylation, thereby transforming a class of immuno- and metabo-regulatory steroids into a class of sex hormones and neurosteroids. Using comparative genomics, homologous expression, and heterologous expression, we identify a bacterial gene cluster that performs 21-dehydroxylation. We also uncover an unexpected role for hydrogen gas production by gut commensals in promoting 21-dehydroxylation, suggesting that hydrogen modulates secondary metabolism in the gut. Levels of certain bacterial progestins, including allopregnanolone, better known as brexanolone, an FDA-approved drug for postpartum depression, are substantially increased in feces from pregnant humans. Thus, bacterial conversion of corticoids into progestins may affect host physiology, particularly in the context of pregnancy and women's health.
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Affiliation(s)
- Megan D McCurry
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriel D D'Agostino
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jasmine T Walsh
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jordan E Bisanz
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, State College, PA 16802, USA
| | - Ines Zalosnik
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Xueyang Dong
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - David J Morris
- Emeritus Professor of Pathology and Laboratory Medicine, Brown University Alpert School of Medicine, Providence, RI 02903, USA
| | - Joshua R Korzenik
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Andrea G Edlow
- Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Emily P Balskus
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA
| | - Jun R Huh
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - A Sloan Devlin
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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3
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Basuray N, Deehan EC, Vieira FT, Avedzi HM, Duke RL, Colín-Ramírez E, Tun HM, Zhang Z, Wine E, Madsen KL, Field CJ, Haqq AM. Dichotomous effect of dietary fiber in pediatrics: a narrative review of the health benefits and tolerance of fiber. Eur J Clin Nutr 2024:10.1038/s41430-024-01429-5. [PMID: 38480843 DOI: 10.1038/s41430-024-01429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Dietary fibers are associated with favorable gastrointestinal, immune, and metabolic health outcomes when consumed at sufficient levels. Despite the well-described benefits of dietary fibers, children and adolescents continue to fall short of daily recommended levels. This gap in fiber intake (i.e., "fiber gap") might increase the risk of developing early-onset pediatric obesity and obesity-related comorbidities such as type 2 diabetes mellitus into adulthood. The structure-dependent physicochemical properties of dietary fiber are diverse. Differences in solubility, viscosity, water-holding capacity, binding capability, bulking effect, and fermentability influence the physiological effects of dietary fibers that aid in regulating appetite, glycemic and lipidemic responses, and inflammation. Of growing interest is the fermentation of fibers by the gut microbiota, which yields both beneficial and less favorable end-products such as short-chain fatty acids (e.g., acetate, propionate, and butyrate) that impart metabolic and immunomodulatory properties, and gases (e.g., hydrogen, carbon dioxide, and methane) that cause gastrointestinal symptoms, respectively. This narrative review summarizes (1) the implications of fibers on the gut microbiota and the pathophysiology of pediatric obesity, (2) some factors that potentially contribute to the fiber gap with an emphasis on undesirable gastrointestinal symptoms, (3) some methods to alleviate fiber-induced symptoms, and (4) the therapeutic potential of whole foods and commonly marketed fiber supplements for improved health in pediatric obesity.
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Affiliation(s)
- Nandini Basuray
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Edward C Deehan
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
- Nebraska Food for Health Center, Lincoln, NE, USA
| | - Flávio T Vieira
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Hayford M Avedzi
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Reena L Duke
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | - Hein M Tun
- JC School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Zhengxiao Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Eytan Wine
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Catherine J Field
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Andrea M Haqq
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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4
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Li J, Huang G, Wang J, Wang S, Yu Y. Hydrogen Regulates Ulcerative Colitis by Affecting the Intestinal Redox Environment. J Inflamm Res 2024; 17:933-945. [PMID: 38370464 PMCID: PMC10871146 DOI: 10.2147/jir.s445152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
The redox balance in the intestine plays an important role in maintaining intestinal homeostasis, and it is closely related to the intestinal mucosal barrier, intestinal inflammation, and the gut microbiota. Current research on the treatment of ulcerative colitis has focused on immune disorders, excessive inflammation, and oxidative stress. However, an imbalance in intestinal redox reaction plays a particularly critical role. Hydrogen is produced by some anaerobic bacteria via hydrogenases in the intestine. Increasing evidence suggests that hydrogen, as an inert gas, is crucial for immunity, inflammation, and oxidative stress and plays a protective role in ulcerative colitis. Hydrogen maintains the redox state balance in the intestine in ulcerative colitis and reduces damage to intestinal epithelial cells by exerting its selective antioxidant ability. Hydrogen also regulates the intestinal flora, reduces the harmful effects of bacteria on the intestinal epithelial barrier, promotes the restoration of normal anaerobic bacteria in the intestines, and ultimately improves the integrity of the intestinal epithelial barrier. The present review focuses on the therapeutic mechanisms of hydrogen-targeting ulcerative colitis.
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Affiliation(s)
- Jiayi Li
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Gang Huang
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Juexin Wang
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Sui Wang
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Yanbo Yu
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, Shandong, People’s Republic of China
- Shandong Provincial Clinical Research Center for Digestive Disease, Qilu Hospital of Shandong University, Jinan, Shandong, People’s Republic of China
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Villanueva-Millan MJ, Leite G, Morales W, Sanchez M, Parodi G, Weitsman S, Celly S, Cohrs D, Do H, Barlow GM, Mathur R, Rezaie A, Pimentel M. Hydrogen Sulfide Producers Drive a Diarrhea-Like Phenotype and a Methane Producer Drives a Constipation-Like Phenotype in Animal Models. Dig Dis Sci 2024; 69:426-436. [PMID: 38060167 PMCID: PMC10861391 DOI: 10.1007/s10620-023-08197-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/23/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND We recently demonstrated that diarrhea-predominant irritable bowel syndrome (IBS-D) subjects have higher relative abundance (RA) of hydrogen sulfide (H2S)-producing Fusobacterium and Desulfovibrio species, and constipation-predominant IBS (IBS-C) subjects have higher RA of methanogen Methanobrevibacter smithii. AIMS In this study, we investigate the effects of increased methanogens or H2S producers on stool phenotypes in rat models. METHODS Adult Sprague-Dawley rats were fed high-fat diet (HFD) for 60 days to increase M. smithii levels, then gavaged for 10 days with water (controls) or methanogenesis inhibitors. To increase H2S producers, rats were gavaged with F. varium or D. piger. Stool consistency (stool wet weight (SWW)) and gas production were measured. 16S rRNA gene sequencing was performed on stool samples. RESULTS In HFD diet-fed rats (N = 30), stool M. smithii levels were increased (P < 0.001) after 52 days, correlating with significantly decreased SWW (P < 0.0001) at 59 days (R = - 0.38, P = 0.037). Small bowel M. smithii levels decreased significantly in lovastatin lactone-treated rats (P < 0.0006), and SWW increased (normalized) in lovastatin hydroxyacid-treated rats (P = 0.0246), vs. controls (N = 10/group). SWW increased significantly in D. piger-gavaged rats (N = 16) on day 10 (P < 0.0001), and in F. varium-gavaged rats (N = 16) at all timepoints, vs. controls, with increased stool H2S production. 16S sequencing revealed stool microbiota alterations in rats gavaged with H2S producers, with higher relative abundance (RA) of other H2S producers, particularly Lachnospiraceae and Bilophila in F. varium-gavaged rats, and Sutterella in D. piger-gavaged rats. CONCLUSIONS These findings suggest that increased M. smithii levels result in a constipation-like phenotype in a rat model that is partly reversible with methanogenesis inhibitors, whereas gavage with H2S producers D. piger or F. varium results in increased colonization with other H2S producers and diarrhea-like phenotypes. This supports roles for the increased RA of methanogens and H2S producers identified in IBS-C and IBS-D subjects, respectively, in contributing to stool phenotypes.
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Affiliation(s)
- Maria J Villanueva-Millan
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Gabriela Leite
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Walter Morales
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Maritza Sanchez
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Stacy Weitsman
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Shreya Celly
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Daniel Cohrs
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Huongly Do
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Gillian M Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai, Los Angeles, CA, USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai, Los Angeles, CA, USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, 770 N. San Vicente Blvd, Suite G271, West Hollywood, CA, 90069, USA.
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai, Los Angeles, CA, USA.
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Deehan EC, Zhang Z, Nguyen NK, Perez-Muñoz ME, Cole J, Riva A, Berry D, Prado CM, Walter J. Adaptation to tolerate high doses of arabinoxylan is associated with fecal levels of Bifidobacterium longum. Gut Microbes 2024; 16:2363021. [PMID: 38860973 PMCID: PMC11174067 DOI: 10.1080/19490976.2024.2363021] [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: 12/18/2023] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Dietary fiber supplements are a strategy to close the 'fiber gap' and induce targeted modulations of the gut microbiota. However, higher doses of fiber supplements cause gastrointestinal (GI) symptoms that differ among individuals. What determines these inter-individual differences is insufficiently understood. Here we analyzed findings from a six-week randomized controlled trial that evaluated GI symptoms to corn bran arabinoxylan (AX; n = 15) relative to non-fermentable microcrystalline cellulose (MCC; n = 16) at efficacious supplement doses of 25 g/day (females) or 35 g/day (males) in adults with excess weight. Self-reported flatulence, bloating, and stomach aches were evaluated weekly. Bacterial taxa involved in AX fermentation were identified by bioorthogonal non-canonical amino acid tagging. Associations between GI symptoms, fecal microbiota features, and diet history were systematically investigated. AX supplementation increased symptoms during the first three weeks relative to MCC (p < 0.05, Mann-Whitney tests), but subjects 'adapted' with symptoms reverting to baseline levels toward the end of treatment. Symptom adaptations were individualized and correlated with the relative abundance of Bifidobacterium longum at baseline (rs = 0.74, p = 0.002), within the bacterial community that utilized AX (rs = 0.69, p = 0.006), and AX-induced shifts in acetate (rs = 0.54, p = 0.039). Lower baseline consumption of animal-based foods and higher whole grains associated with less severity and better adaptation. These findings suggest that humans do 'adapt' to tolerate efficacious fiber doses, and this process is linked to their microbiome and dietary factors known to interact with gut microbes, providing a basis for the development of strategies for improved tolerance of dietary fibers.
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Affiliation(s)
- Edward C. Deehan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA
| | - Zhengxiao Zhang
- Department of Medicine, University of Alberta, Edmonton, Canada
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Nguyen K. Nguyen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), WEL Research Institute, Wavre, Belgium
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Janis Cole
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Alessandra Riva
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Carla M. Prado
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork – National University of Ireland, Cork, Ireland
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Zünd JN, Plüss S, Mujezinovic D, Menzi C, von Bieberstein PR, de Wouters T, Lacroix C, Leventhal GE, Pugin B. A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors. ISME COMMUNICATIONS 2024; 4:ycae035. [PMID: 38562261 PMCID: PMC10982853 DOI: 10.1093/ismeco/ycae035] [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: 11/01/2023] [Revised: 11/13/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.
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Affiliation(s)
- Janina N Zünd
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Serafina Plüss
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Denisa Mujezinovic
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Carmen Menzi
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
- PharmaBiome AG, 8952 Schlieren, Switzerland
| | - Philipp R von Bieberstein
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
- PharmaBiome AG, 8952 Schlieren, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | | | - Benoit Pugin
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
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8
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Little AS, Younker IT, Schechter MS, Bernardino PN, Méheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramanswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH. Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nat Microbiol 2024; 9:55-69. [PMID: 38177297 PMCID: PMC11055453 DOI: 10.1038/s41564-023-01560-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.
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Affiliation(s)
- Alexander S Little
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Isaac T Younker
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Matthew S Schechter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Paola Nol Bernardino
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Joshua Stemczynski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Kaylie Scorza
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | | | - Deepti Sharan
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - William Leiter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Matthew A Odenwald
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Section of Infectious Diseases & Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenbug, Germany
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
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9
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Wang T, Leibrock N, Plugge CM, Smidt H, Zoetendal EG. In vitro interactions between Blautia hydrogenotrophica, Desulfovibrio piger and Methanobrevibacter smithii under hydrogenotrophic conditions. Gut Microbes 2023; 15:2261784. [PMID: 37753963 PMCID: PMC10538451 DOI: 10.1080/19490976.2023.2261784] [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: 02/25/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This in vitro study cocultured Blautia hydrogenotrophica (reductive acetogen), Desulfovibrio piger (sulfate reducer) and Methanobrevibacter smithii (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by B. hydrogenotrophica and M. smithii. D. piger inhibited the growth of B. hydrogenotrophica and M. smithii after 10 h incubations, and the inhibition on M. smithii was associated with increased sulfide concentration. Remarkably, M. smithii growth lag phase was shortened by coculturing with B. hydrogenotrophica and D. piger. Formate was rapidly used by M. smithii under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.
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Affiliation(s)
- Taojun Wang
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Nils Leibrock
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Wetsus European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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10
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Nie S, Ge Y. The link between the gut microbiome, inflammation, and Parkinson's disease. Appl Microbiol Biotechnol 2023; 107:6737-6749. [PMID: 37736791 DOI: 10.1007/s00253-023-12789-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
As our society ages, the growing number of people with Parkinson's disease (PD) puts tremendous pressure on our society. Currently, there is no effective treatment for PD, so there is an urgent need to find new treatment options. In recent years, increasing studies have shown a strong link between gut microbes and PD. In this review, recent advances in research on gut microbes in PD patients were summarized. Increased potential pro-inflammatory microbes and decreased potential anti-inflammatory microbes are prominent features of gut microbiota in PD patients. These changes may lead to an increase in pro-inflammatory substances (such as lipopolysaccharide and H2S) and a decrease in anti-inflammatory substances (such as short-chain fatty acids) to promote inflammation in the gut. This gut microbiota-mediated inflammation will lead to pathological α-synuclein accumulation in the gut, and the inflammation and α-synuclein can spread to the brain via the microbiota-gut-brain axis, thereby promoting neuroinflammation, apoptosis of dopaminergic neurons, and ultimately the development of PD. This review also showed that therapies based on gut microbiota may have a bright future for PD. However, more research and new approaches are still needed to clarify the causal relationship between gut microbes and PD and to determine whether therapies based on gut microbiota are effective in PD patients. KEY POINTS: • There is a strong association between gut microbes and PD. • Inflammation mediated by gut microbes may promote the development of PD. • Therapies based on the gut microbiome provide a promising strategy for PD prevention.
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Affiliation(s)
- Shiqing Nie
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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11
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Wielgosz-Grochowska JP, Domanski N, Drywień ME. Influence of Body Composition and Specific Anthropometric Parameters on SIBO Type. Nutrients 2023; 15:4035. [PMID: 37764818 PMCID: PMC10535553 DOI: 10.3390/nu15184035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/04/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Recent observations have shown that Small Intestinal Bacterial Overgrowth (SIBO)affects the host through various mechanisms. While both weight loss and obesity have been reported in the SIBO population due to alterations in the gut microbiome, very little is known about the influence of SIBO type on body composition. This study aimed to evaluate whether there is a link between the three types of SIBO: methane dominant (M+), hydrogen dominant (H+), and methane-hydrogen dominant (H+/M+) and specific anthropometric parameters. This observational study included 67 participants (W = 53, M = 14) with gastrointestinal symptoms and SIBO confirmed by lactulose hydrogen-methane breath tests (LHMBTs) using the QuinTron device. Participants underwent a body composition assessment by Bioelectrical Impedance Analysis (BIA) using the InBody Analyzer. In the H+/M+ group, body weight (p = 0.010), BMI (p = 0.001), body fat in kg (p = 0.009), body fat in % (p = 0.040), visceral fat (p = 0.002), and mineral bone content (p = 0.049) showed an inverse correlation with hydrogen (H2) gas production. These findings suggest that body weight, BMI, body fat, and mineral bone content may be inversely linked to the production of hydrogen and the risk of hydrogen-methane SIBO.
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Affiliation(s)
| | - Nicole Domanski
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
| | - Małgorzata Ewa Drywień
- Department of Human Nutrition, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, 02-776 Warsaw, Poland;
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12
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Meiller L, Sauvinet V, Breyton AE, Ranaivo H, Machon C, Mialon A, Meynier A, Bischoff SC, Walter J, Neyrinck AM, Laville M, Delzenne NM, Vinoy S, Nazare JA. Metabolic signature of 13C-labeled wheat bran consumption related to gut fermentation in humans: a pilot study. Eur J Nutr 2023; 62:2633-2648. [PMID: 37222787 DOI: 10.1007/s00394-023-03161-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE The aim of this pilot study was to analyze concomitantly the kinetics of production of 13C-labeled gut-derived metabolites from 13C-labeled wheat bran in three biological matrices (breath, plasma, stools), in order to assess differential fermentation profiles among subjects. METHODS Six healthy women consumed a controlled breakfast containing 13C-labeled wheat bran biscuits. H2, CH4 and 13CO2, 13CH4 24 h-concentrations in breath were measured, respectively, by gas chromatography (GC) and GC-isotope ratio mass spectrometry (GC-IRMS). Plasma and fecal concentrations of 13C-short-chain fatty acids (linear SCFAs: acetate, propionate, butyrate, valerate; branched SCFAs: isobutyrate, isovalerate) were quantified using GC-combustion-IRMS. Gut microbiota composition was assessed by16S rRNA gene sequencing analysis. RESULTS H2 and CH4 24 h-kinetics distinguished two groups in terms of fermentation-related gas excretion: high-CH4 producers vs low-CH4 producers (fasting concentrations: 45.3 ± 13.6 ppm vs 6.5 ± 3.6 ppm). Expired 13CH4 was enhanced and prolonged in high-CH4 producers compared to low-CH4 producers. The proportion of plasma and stool 13C-butyrate tended to be higher in low-CH4 producers, and inversely for 13C-acetate. Plasma branched SCFAs revealed different kinetics of apparition compared to linear SCFAs. CONCLUSION This pilot study allowed to consider novel procedures for the development of biomarkers revealing dietary fiber-gut microbiota interactions. The non-invasive assessment of exhaled gas following 13C-labeled fibers ingestion enabled to decipher distinct fermentation profiles: high-CH4 producers vs low-CH4 producers. The isotope labeling permits a specific in vivo characterisation of the dietary fiber impact consumption on microbiota metabolite production. CLINICAL TRIAL REGISTRATION The study has been registered under the number NCT03717311 at ClinicalTrials.gov on October 24, 2018.
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Affiliation(s)
- Laure Meiller
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Valérie Sauvinet
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Anne-Esther Breyton
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France
| | - Harimalala Ranaivo
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France
| | - Christelle Machon
- Service de Biochimie et Biologie Moléculaire, Hospices Civils de Lyon, Pierre Bénite, France
| | - Anne Mialon
- Service de Biochimie et Biologie Moléculaire, Hospices Civils de Lyon, Pierre Bénite, France
| | | | - Stephan C Bischoff
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Jens Walter
- Department of Medicine, School of Microbiology, APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Audrey M Neyrinck
- Metabolism and Nutrition Research Group, UCLouvain, Brussels, Belgium
| | - Martine Laville
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France
- Service d'Endocrinologie Diabète Nutrition, Hospices Civils de Lyon, Pierre Bénite, France
| | | | - Sophie Vinoy
- Nutrition Research, Mondelez International, Saclay, France
| | - Julie-Anne Nazare
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France.
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France.
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13
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Katagiri S, Ohsugi Y, Shiba T, Yoshimi K, Nakagawa K, Nagasawa Y, Uchida A, Liu A, Lin P, Tsukahara Y, Iwata T, Tohara H. Homemade blenderized tube feeding improves gut microbiome communities in children with enteral nutrition. Front Microbiol 2023; 14:1215236. [PMID: 37680532 PMCID: PMC10482415 DOI: 10.3389/fmicb.2023.1215236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
Enteral nutrition for children is supplied through nasogastric or gastrostomy tubes. Diet not only influences nutritional intake but also interacts with the composition and function of the gut microbiota. Homemade blenderized tube feeding has been administered to children receiving enteral nutrition, in addition to ready-made tube feeding. The purpose of this study was to evaluate the oral/gut microbial communities in children receiving enteral nutrition with or without homemade blenderized tube feeding. Among a total of 30 children, 6 receiving mainly ready-made tube feeding (RTF) and 5 receiving mainly homemade blenderized tube feeding (HBTF) were analyzed in this study. Oral and gut microbiota community profiles were evaluated through 16S rRNA sequencing of saliva and fecal samples. The α-diversity representing the number of observed features, Shannon index, and Chao1 in the gut were significantly increased in HBTF only in the gut microbiome but not in the oral microbiome. In addition, the relative abundances of the phylum Proteobacteria, class Gammaproteobacteria, and genus Escherichia-Shigella were significantly low, whereas that of the genus Ruminococcus was significantly high in the gut of children with HBTF, indicating HBTF altered the gut microbial composition and reducing health risks. Metagenome prediction showed enrichment of carbon fixation pathways in prokaryotes at oral and gut microbiomes in children receiving HBTF. In addition, more complex network structures were observed in the oral cavity and gut in the HBTF group than in the RTF group. In conclusion, HBTF not only provides satisfaction and enjoyment during meals with the family but also alters the gut microbial composition to a healthy state.
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Affiliation(s)
- Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Kanako Yoshimi
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazuharu Nakagawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuki Nagasawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Aritoshi Uchida
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Anhao Liu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Peiya Lin
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuta Tsukahara
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Haruka Tohara
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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14
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Hu H, Zhu H, Yang H, Yao W, Zheng W. In vitro fermentation properties of magnesium hydride and related modulation effects on broiler cecal microbiome and metabolome. Front Microbiol 2023; 14:1175858. [PMID: 37621394 PMCID: PMC10445219 DOI: 10.3389/fmicb.2023.1175858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Magnesium hydride (MGH), a highly promising hydrogen-producing substance/additive for hydrogen production through its hydrolysis reaction, has the potential to enhance broiler production. However, before incorporating MGH as a hydrogen-producing additive in broiler feed, it is crucial to fully understand its impact on microbiota and metabolites. In vitro fermentation models provide a fast, reproducible, and direct assessment tool for microbiota metabolism and composition. This study aims to investigate the effects of MGH and coated-magnesium hydride (CMG) on fermentation characteristics, as well as the microbiota and metabolome in the culture of in vitro fermentation using cecal inocula from broilers. After 48 h of incubation, it was observed that the presence of MGH had a significant impact on various factors. Specifically, the content of N-NH3 decreased, while the total hydrogen gas and total SCFAs increased. Furthermore, the presence of MGH promoted the abundance of SCFA-producing bacteria such as Ruminococcus, Blautia, Coprobacillus, and Dysgonomonas. On the other hand, the presence of CMG led to an increase in the concentration of lactic acid, acetic acid, and valeric acid. Additionally, CMG affected the diversity of microbiota in the culture, resulting in an enrichment of the relative abundance of Firmicutes, as well as genera of Lactobacillus, Coprococcus, and Eubacterium. Conversely, the relative abundance of the phylum Proteobacteria and pathogenic bacteria Shigella decreased. Metabolome analysis revealed that MGH and CMG treatment caused significant changes in 21 co-regulated metabolites, primarily associated with lipid, amino acid, benzenoids, and organooxygen compounds. Importantly, joint correlation analysis revealed that MGH or CMG treatments had a direct impact on the microbiota, which in turn indirectly influenced metabolites in the culture. In summary, the results of this study suggested that both MGH and coated-MGH have similar yet distinct positive effects on the microbiota and metabolites of the broiler cecal in an in vitro fermentation model.
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Affiliation(s)
- Heng Hu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - He Zhu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Haiyan Yang
- Center of Hydrogen Science, Shanghai Jiao Tong University, Shanghai, China
| | - Wen Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Weijiang Zheng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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15
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Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community. Nat Commun 2023; 14:4780. [PMID: 37553336 PMCID: PMC10409746 DOI: 10.1038/s41467-023-40372-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
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Affiliation(s)
- Anna S Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa S Niedermeier
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Alexandra von Strempel
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Anna G Burrichter
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chiara Lincetto
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Johannes Hübner
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany.
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16
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Khan MT, Dwibedi C, Sundh D, Pradhan M, Kraft JD, Caesar R, Tremaroli V, Lorentzon M, Bäckhed F. Synergy and oxygen adaptation for development of next-generation probiotics. Nature 2023; 620:381-385. [PMID: 37532933 PMCID: PMC10412450 DOI: 10.1038/s41586-023-06378-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/27/2023] [Indexed: 08/04/2023]
Abstract
The human gut microbiota has gained interest as an environmental factor that may contribute to health or disease1. The development of next-generation probiotics is a promising strategy to modulate the gut microbiota and improve human health; however, several key candidate next-generation probiotics are strictly anaerobic2 and may require synergy with other bacteria for optimal growth. Faecalibacterium prausnitzii is a highly prevalent and abundant human gut bacterium associated with human health, but it has not yet been developed into probiotic formulations2. Here we describe the co-isolation of F. prausnitzii and Desulfovibrio piger, a sulfate-reducing bacterium, and their cross-feeding for growth and butyrate production. To produce a next-generation probiotic formulation, we adapted F. prausnitzii to tolerate oxygen exposure, and, in proof-of-concept studies, we demonstrate that the symbiotic product is tolerated by mice and humans (ClinicalTrials.gov identifier: NCT03728868 ) and is detected in the human gut in a subset of study participants. Our study describes a technology for the production of next-generation probiotics based on the adaptation of strictly anaerobic bacteria to tolerate oxygen exposures without a reduction in potential beneficial properties. Our technology may be used for the development of other strictly anaerobic strains as next-generation probiotics.
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Affiliation(s)
- Muhammad Tanweer Khan
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Metabogen, Mölndal, Sweden
| | - Chinmay Dwibedi
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Sundh
- Sahlgrenska Osteoporosis Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Meenakshi Pradhan
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jamie D Kraft
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Robert Caesar
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Geriatric Medicine Clinic, Sahlgrenska University Hospital Mölndal, Mölndal, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
- Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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17
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Campbell A, Gdanetz K, Schmidt AW, Schmidt TM. H 2 generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers. MICROBIOME 2023; 11:133. [PMID: 37322527 PMCID: PMC10268494 DOI: 10.1186/s40168-023-01565-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Hydrogen gas (H2) is a common product of carbohydrate fermentation in the human gut microbiome and its accumulation can modulate fermentation. Concentrations of colonic H2 vary between individuals, raising the possibility that H2 concentration may be an important factor differentiating individual microbiomes and their metabolites. Butyrate-producing bacteria (butyrogens) in the human gut usually produce some combination of butyrate, lactate, formate, acetate, and H2 in branched fermentation pathways to manage reducing power generated during the oxidation of glucose to acetate and carbon dioxide. We predicted that a high concentration of intestinal H2 would favor the production of butyrate, lactate, and formate by the butyrogens at the expense of acetate, H2, and CO2. Regulation of butyrate production in the human gut is of particular interest due to its role as a mediator of colonic health through anti-inflammatory and anti-carcinogenic properties. RESULTS For butyrogens that contained a hydrogenase, growth under a high H2 atmosphere or in the presence of the hydrogenase inhibitor CO stimulated production of organic fermentation products that accommodate reducing power generated during glycolysis, specifically butyrate, lactate, and formate. Also as expected, production of fermentation products in cultures of Faecalibacterium prausnitzii strain A2-165, which does not contain a hydrogenase, was unaffected by H2 or CO. In a synthetic gut microbial community, addition of the H2-consuming human gut methanogen Methanobrevibacter smithii decreased butyrate production alongside H2 concentration. Consistent with this observation, M. smithii metabolic activity in a large human cohort was associated with decreased fecal butyrate, but only during consumption of a resistant starch dietary supplement, suggesting the effect may be most prominent when H2 production in the gut is especially high. Addition of M. smithii to the synthetic communities also facilitated the growth of E. rectale, resulting in decreased relative competitive fitness of F. prausnitzii. CONCLUSIONS H2 is a regulator of fermentation in the human gut microbiome. In particular, high H2 concentration stimulates production of the anti-inflammatory metabolite butyrate. By consuming H2, gut methanogenesis can decrease butyrate production. These shifts in butyrate production may also impact the competitive fitness of butyrate producers in the gut microbiome. Video Abstract.
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Affiliation(s)
- Austin Campbell
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kristi Gdanetz
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Alexander W Schmidt
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, MI, 48109, Ann Arbor, USA
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Ecology & Evolutionary Biology, University of Michigan, MI, 48109, Ann Arbor, USA.
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, MI, 48109, Ann Arbor, USA.
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18
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García Mendez D, Sanabria J, Wist J, Holmes E. Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6213-6225. [PMID: 37070710 PMCID: PMC10143624 DOI: 10.1021/acs.jafc.2c08146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 05/03/2023]
Abstract
Since the early 1980s, multiple researchers have contributed to the development of in vitro models of the human gastrointestinal system for the mechanistic interrogation of the gut microbiome ecology. Using a bioreactor for simulating all the features and conditions of the gastrointestinal system is a massive challenge. Some conditions, such as temperature and pH, are readily controlled, but a more challenging feature to simulate is that both may vary in different regions of the gastrointestinal tract. Promising solutions have been developed for simulating other functionalities, such as dialysis capabilities, peristaltic movements, and biofilm growth. This research field is under constant development, and further efforts are needed to drive these models closer to in vivo conditions, thereby increasing their usefulness for studying the gut microbiome impact on human health. Therefore, understanding the influence of key operational parameters is fundamental for the refinement of the current bioreactors and for guiding the development of more complex models. In this review, we performed a systematic search for operational parameters in 229 papers that used continuous bioreactors seeded with human feces. Despite the reporting of operational parameters for the various bioreactor models being variable, as a result of a lack of standardization, the impact of specific operational parameters on gut microbial ecology is discussed, highlighting the advantages and limitations of the current bioreactor systems.
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Affiliation(s)
- David
Felipe García Mendez
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
| | - Janeth Sanabria
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
- Environmental
Microbiology and Biotechnology Laboratory, Engineering School of Environmental
& Natural Resources, Engineering Faculty, Universidad del Valle—Sede Meléndez, Cali, Colombia 76001
| | - Julien Wist
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
- Chemistry
Department, Universidad del Valle, 76001, Cali, Colombia
| | - Elaine Holmes
- Australian
National Phenome Centre and Computational and Systems Medicine, Health
Futures Institute, Murdoch University, Harry Perkins Building, Perth, Australia WA6150
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19
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Ramires T, Wilson R, Padilha da Silva W, Bowman JP. Identification of pH-specific protein expression responses by Campylobacter jejuni strain NCTC 11168. Res Microbiol 2023:104061. [PMID: 37055003 DOI: 10.1016/j.resmic.2023.104061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
In this study a data dependent acquisition label-free based proteomics approach was used to identify pH-dependent proteins that respond in a growth phase independent manner in C. jejuni reference strain NCTC 11168. NCTC 11168 was grown within its pH physiological normal growth range (pH 5.8, 7.0 and 8.0, μ = ∼0.5 h-1) and exposed to pH 4.0 shock for 2 hours. It was discovered that gluconate 2-dehydrogenase GdhAB, NssR-regulated globins Cgb and Ctb, cupin domain protein Cj0761, cytochrome c protein CccC (Cj0037c), and phosphate-binding transporter protein PstB all show acidic pH dependent abundance increases but are not activated by sub-lethal acid shock. Glutamate synthase (GLtBD) and the MfrABC and NapAGL respiratory complexes were induced in cells grown at pH 8.0. The response to pH stress by C. jejuni is to bolster microaerobic respiration and at pH 8.0 this is assisted by accumulation of glutamate the conversion of which could bolster fumarate respiration. The pH dependent proteins linked to growth in C. jejuni NCTC 11168 aids cellular energy conservation maximising growth rate and thus competitiveness and fitness.
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Affiliation(s)
- Tassiana Ramires
- Departamento de Ciência e Tecnologia Agroindustrial, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - Wladimir Padilha da Silva
- Departamento de Ciência e Tecnologia Agroindustrial, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia.
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20
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Cisek AA, Dolka B, Bąk I, Cukrowska B. Microorganisms Involved in Hydrogen Sink in the Gastrointestinal Tract of Chickens. Int J Mol Sci 2023; 24:ijms24076674. [PMID: 37047647 PMCID: PMC10095559 DOI: 10.3390/ijms24076674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Hydrogen sink is a beneficial process, which has never been properly examined in chickens. Therefore, the aim of this study was to assess the quantity and quality of microbiota involved in hydrogen uptake with the use of real-time PCR and metagenome sequencing. Analyses were carried out in 50 free-range chickens, 50 commercial broilers, and 54 experimental chickens isolated from external factors. The median values of acetogens, methanogens, sulfate-reducing bacteria (SRB), and [NiFe]-hydrogenase utilizers measured in the cecum were approx. 7.6, 0, 0, and 3.2 log10/gram of wet weight, respectively. For the excreta samples, these values were 5.9, 4.8, 4, and 3 log10/gram of wet weight, respectively. Our results showed that the acetogens were dominant over the other tested groups of hydrogen consumers. The quantities of methanogens, SRB, and the [NiFe]-hydrogenase utilizers were dependent on the overall rearing conditions, being the result of diet, environment, agrotechnical measures, and other factors combined. By sequencing of the 16S rRNA gene, archaea of the genus Methanomassiliicoccus (Candidatus Methanomassiliicoccus) were discovered in chickens for the first time. This study provides some indication that in chickens, acetogenesis may be the main metabolic pathway responsible for hydrogen sink.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Beata Dolka
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Iwona Bąk
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Bożena Cukrowska
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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21
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Kim JE, Tun HM, Bennett DC, Leung FC, Cheng KM. Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae). Sci Rep 2023; 13:4488. [PMID: 36934111 PMCID: PMC10024708 DOI: 10.1038/s41598-023-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 03/20/2023] Open
Abstract
Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.
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Affiliation(s)
- Ji Eun Kim
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Hein M Tun
- School of Public Health, Li Ka Shing, Faculty of Medicine, HKU-Pasteur Research Pole, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- JC School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Darin C Bennett
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Animal Science Department, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Frederick C Leung
- School of Biological Sciences, Faculty of Science, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kimberly M Cheng
- Avian Research Centre, Faculty of Land and Food Systems, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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22
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Lim J, Rezaie A. Pros and Cons of Breath Testing for Small Intestinal Bacterial Overgrowth and Intestinal Methanogen Overgrowth. Gastroenterol Hepatol (N Y) 2023; 19:140-146. [PMID: 37706108 PMCID: PMC10496284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Breath testing is the most widely utilized modality to diagnose small intestinal bacterial overgrowth (SIBO) and/or intestinal methanogen overgrowth (IMO). Although SIBO can be diagnosed with small bowel aspiration and breath testing, IMO can only be diagnosed with breath testing in clinical practice. Breath testing can tailor antibiotic therapy and predict response to treatment; however, the test is limited by its indirect method of measurement and concerns about the variability of orocecal transit time. Like any clinical test, breath testing has inherent strengths and limitations, and results must be interpreted with consideration of the clinical context and influencing factors. Recent studies have demonstrated the expanding clinical utility of breath testing in the diagnosis, management, and prediction of treatment response in SIBO and particularly in IMO along with the identification of distinct breath test patterns such as flat-line and high baseline hydrogen. This article reviews the strengths and limitations of breath testing in diagnosing SIBO and IMO as well as its expanding utility in clinical practice.
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Affiliation(s)
- Jane Lim
- GI Motility Program, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ali Rezaie
- GI Motility Program, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
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23
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Bonvegna S, Cilia R. Disease mechanisms as subtypes: Microbiome. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:107-131. [PMID: 36803806 DOI: 10.1016/b978-0-323-85555-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Abnormalities in gut microbiota have been suggested to be involved in the pathophysiology and progression of Parkinson's disease (PD). Gastrointestinal nonmotor symptoms often precede the onset of motor features in PD, suggesting a role for gut dysbiosis in neuroinflammation and α-synuclein (α-syn) aggregation. In the first part of this chapter, we analyze critical features of healthy gut microbiota and factors (environmental and genetic) that modify its composition. In the second part, we focus on the mechanisms underlying the gut dysbiosis and how it alters anatomically and functionally the mucosal barrier, triggering neuroinflammation and subsequently α-syn aggregation. In the third part, we describe the most common alterations in the gut microbiota of PD patients, dividing the gastrointestinal system in higher and lower tract to examine the association between microbiota abnormalities and clinical features. In the final section, we report on current and future therapeutic approaches to gut dysbiosis aiming to either reduce the risk for PD, modify the disease course, or improve the pharmacokinetic profile of dopaminergic therapies. We also suggest that further studies will be needed to clarify the role of the microbiome in PD subtyping and of pharmacological and nonpharmacological interventions in modifying specific microbiota profiles in individualizing disease-modifying treatments in PD.
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Affiliation(s)
- Salvatore Bonvegna
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy
| | - Roberto Cilia
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy.
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24
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Qusa MH, Abdelwahed KS, Hill RA, El Sayed KA. S-(-)-Oleocanthal Ex Vivo Modulatory Effects on Gut Microbiota. Nutrients 2023; 15:nu15030618. [PMID: 36771326 PMCID: PMC9920009 DOI: 10.3390/nu15030618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Compelling evidence points to the critical role of bioactive extra-virgin olive oil (EVOO) phenolics and gut microbiota (GM) interplay, but reliable models for studying the consequences thereof remain to be developed. Herein, we report an optimized ex vivo fecal anaerobic fermentation model to study the modulation of GM by the most bioactive EVOO phenolic S-(-)-oleocanthal (OC), and impacts therefrom, focusing on OC biotransformation in the gut. This model will also be applicable for characterization of GM interactions with other EVOO phenolics, and moreover, for a broadly diverse range of bioactive natural products. The fecal fermentation media and time, and mouse type and gender, were the major factors varied and optimized to provide better understanding of GM-OC interplay. A novel resin entrapment technique (solid-phase extraction) served to selectively entrap OC metabolites, degradation products, and any remaining fraction of OC while excluding interfering complex fecal medium constituents. The effects of OC on GM compositions were investigated via shallow shotgun DNA sequencing. Robust metabolome analyses identified GM bacterial species selectively altered (population numbers/fraction) by OC. Finally, the topmost OC-affected gut bacterial species of the studied mice were compared with those known to be extant in humans and distributions of these bacteria at different human body sites. OC intake caused significant quantitative and qualitative changes to mice GM, which was also comparable with human GM. Results clearly highlight the potential positive health outcomes of OC as a prospective nutraceutical.
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25
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The Association of the Oral Microbiota with the Effects of Acid Stress Induced by an Increase of Brain Lactate in Schizophrenia Patients. Biomedicines 2023; 11:biomedicines11020240. [PMID: 36830777 PMCID: PMC9953675 DOI: 10.3390/biomedicines11020240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/28/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
The altered cerebral energy metabolism central to schizophrenia can be linked to lactate accumulation. Lactic acid is produced by gastrointestinal bacteria, among others, and readily crosses the blood-brain barrier, leading to the brain acidity. This study aimed to examine the association of the oral microbiota with the effects of acid stress induced by an increase of brain lactate in schizophrenia patients. The study included patients with a diagnosis of acute polyphasic psychotic disorder meeting criteria for schizophrenia at 3-month follow-up. Results: Individuals with a significantly higher total score on the Positive and Negative Syndrome Scale had statistically significantly lower lactate concentrations compared to those with a lower total score and higher brain lactate. We observed a positive correlation between Actinomyces and lactate levels in the anterior cingulate cap and a negative correlation between bacteria associated with lactate metabolism and some clinical assessment scales. Conclusions: Shifts in the oral microbiota in favour of lactate-utilising bacterial genera may represent a compensatory mechanism in response to increased lactate production in the brain. Assessment of neuronal function mediated by ALA-LAC-dependent NMDA regulatory mechanisms may, thus, support new therapies for schizophrenia, for which acidosis has become a differentiating feature of individuals with schizophrenia endophenotypes.
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26
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Yao H, Flanagan BM, Williams BA, Mikkelsen D, Gidley MJ. Lactate and buyrate proportions, methanogen growth and gas production during in vitro dietary fibre fermentation all depend on fibre concentration. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Kurt F, Leventhal GE, Spalinger MR, Anthamatten L, Rogalla von Bieberstein P, Menzi C, Reichlin M, Meola M, Rosenthal F, Rogler G, Lacroix C, de Wouters T. Co-cultivation is a powerful approach to produce a robust functionally designed synthetic consortium as a live biotherapeutic product (LBP). Gut Microbes 2023; 15:2177486. [PMID: 36794804 PMCID: PMC9980632 DOI: 10.1080/19490976.2023.2177486] [Citation(s) in RCA: 2] [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: 10/19/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
The success of fecal microbiota transplants (FMT) has provided the necessary proof-of-concept for microbiome therapeutics. Yet, feces-based therapies have many associated risks and uncertainties, and hence defined microbial consortia that modify the microbiome in a targeted manner have emerged as a promising safer alternative to FMT. The development of such live biotherapeutic products has important challenges, including the selection of appropriate strains and the controlled production of the consortia at scale. Here, we report on an ecology- and biotechnology-based approach to microbial consortium construction that overcomes these issues. We selected nine strains that form a consortium to emulate the central metabolic pathways of carbohydrate fermentation in the healthy human gut microbiota. Continuous co-culturing of the bacteria produces a stable and reproducible consortium whose growth and metabolic activity are distinct from an equivalent mix of individually cultured strains. Further, we showed that our function-based consortium is as effective as FMT in counteracting dysbiosis in a dextran sodium sulfate mouse model of acute colitis, while an equivalent mix of strains failed to match FMT. Finally, we showed robustness and general applicability of our approach by designing and producing additional stable consortia of controlled composition. We propose that combining a bottom-up functional design with continuous co-cultivation is a powerful strategy to produce robust functionally designed synthetic consortia for therapeutic use.
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Affiliation(s)
- Fabienne Kurt
- PharmaBiome AG, Schlieren, Switzerland
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Marianne Rebecca Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Laura Anthamatten
- PharmaBiome AG, Schlieren, Switzerland
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | | | | | | | | | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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28
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Intestinal gas production by the gut microbiota: A review. J Funct Foods 2023. [DOI: 10.1016/j.jff.2022.105367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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29
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Holscher HD, Chumpitazi BP, Dahl WJ, Fahey GC, Liska DJ, Slavin JL, Verbeke K. Perspective: Assessing Tolerance to Nondigestible Carbohydrate Consumption. Adv Nutr 2022; 13:2084-2097. [PMID: 36041178 PMCID: PMC9776727 DOI: 10.1093/advances/nmac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/28/2023] Open
Abstract
Human intestinal enzymes do not hydrolyze nondigestible carbohydrates (NDCs), and thus, they are not digested and absorbed in the small intestine. Instead, NDCs are partially to completely fermented by the intestinal microbiota. Select NDCs are associated with health benefits such as laxation and lowering of blood cholesterol and glucose. NDCs provide functional attributes to processed foods, including sugar or fat replacers, thickening agents, and bulking agents. Additionally, NDCs are incorporated into processed foods to increase their fiber content. Although consumption of NDCs can benefit health and contribute functional characteristics to foods, they can cause gastrointestinal symptoms, such as flatulence and bloating. As gastrointestinal symptoms negatively affect consumer well-being and their acceptance of foods containing NDC ingredients, it is crucial to consider tolerance when designing food products and testing their physiological health benefits in clinical trials. This perspective provides recommendations for the approach to assess gastrointestinal tolerance to NDCs, with a focus on study design, population criteria, intervention, comparator, and outcome. Special issues related to studies in children and implications for stakeholders are also discussed. It is recommended that the evaluation of gastrointestinal tolerance to NDCs be conducted in randomized, blinded, controlled crossover studies using standard gastrointestinal questionnaires, with attention to study participant background diets, health status, lifestyle, and medications.
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Affiliation(s)
| | - Bruno P Chumpitazi
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Children's Nutrition Research Center, United States Department of Agriculture, Houston, TX, USA
| | - Wendy J Dahl
- Department of Food Science and Human Nutrition, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - George C Fahey
- Department of Animal Sciences, University of Illinois, Urbana, IL USA
| | | | - Joanne L Slavin
- Department of Food Science and Nutrition, University of Minnesota, Twin Cities, MN USA
| | - Kristin Verbeke
- Translational Research in Gastrointestinal Disorders, KU Leuven, Targid, Leuven, Belgium; and Leuven Food Science and Nutrition Research Centre, Leuven, Belgium
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30
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Wang T, van Dijk L, Rijnaarts I, Hermes GDA, de Roos NM, Witteman BJM, de Wit NJW, Govers C, Smidt H, Zoetendal EG. Methanogen Levels Are Significantly Associated with Fecal Microbiota Composition and Alpha Diversity in Healthy Adults and Irritable Bowel Syndrome Patients. Microbiol Spectr 2022; 10:e0165322. [PMID: 36321894 PMCID: PMC9769613 DOI: 10.1128/spectrum.01653-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Hydrogenotrophic microbes, primarily including the three functional groups methanogens, sulfate-reducing bacteria, and reductive acetogens, use hydrogen as an energy source and play an important role in maintaining the hydrogen balance in gut ecosystems. A distorted hydrogen balance has been associated with irritable bowel syndrome (IBS). However, the role of hydrogenotrophic microbes in overall microbiota composition and function remains largely unknown. This study aims to assess the distribution and stability of hydrogenotrophic functional groups in healthy adults (HAs) and IBS patients and their association with overall microbiota composition and IBS symptoms. A two-time-point study with 4 weeks in between was performed with 27 HAs and 55 IBS patients included. Our observations revealed that methanogens showed a bimodal distribution across samples. A high-level methanogen microbiota was consistently associated with higher alpha diversity, and its composition was significantly different from that of individuals with a low-level methanogen microbiota. In general, these associations were more pronounced in IBS patients than in HAs. The differences in the copy numbers of genes indicative of total bacteria and acetogens between HAs and IBS patients and their correlations with IBS symptom severity, anxiety, depression, and quality of life (QoL) were sampling time dependent. Hydrogenotrophic functional groups did not show negative abundance correlations with each other in HAs and IBS patients. These findings suggest that methanogen levels in the gut have a pronounced association with microbiota alpha diversity and composition, and the interactions between hydrogenotrophic functional groups are complex in gut ecosystems. IMPORTANCE Hydrogenotrophic microbes play an essential role in the disposal of hydrogen and the maintenance of the hydrogen balance in gut ecosystems. Their abundances vary between individuals and have been reported to be associated with human gut disorders such as irritable bowel disease. This study confirms that methanogen levels show a bimodal distribution. Moreover, a high-level methanogen microbiota was associated with higher alpha diversity, and its composition was different from that of individuals with a low-level methanogen microbiota. These associations are more pronounced in IBS patients than in healthy subjects. In addition, associations between hydrogenotrophic microbes and IBS symptom scores vary over time, which argues for the use of longitudinal study designs. Last but not least, this study suggests that the different hydrogenotrophic microbes coexist with each other and do not necessarily compete for hydrogen in the gut. The findings in this study highlight the impact of methanogens on overall microbiota composition and function.
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Affiliation(s)
- Taojun Wang
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Leander van Dijk
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Iris Rijnaarts
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Gerben D. A. Hermes
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Nicole M. de Roos
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Ben J. M. Witteman
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
- Department of Gastroenterology and Hepatology, Hospital Gelderse Vallei, Ede, the Netherlands
| | - Nicole J. W. de Wit
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Coen Govers
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, the Netherlands
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
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31
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Interpreting tree ensemble machine learning models with endoR. PLoS Comput Biol 2022; 18:e1010714. [PMID: 36516158 PMCID: PMC9797088 DOI: 10.1371/journal.pcbi.1010714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 12/28/2022] [Accepted: 11/07/2022] [Indexed: 12/15/2022] Open
Abstract
Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.
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Han Q, Bai Y, Zhou C, Dong B, Li Y, Luo N, Chen H, Yu Y. Effect of molecular hydrogen treatment on Sepsis-Associated encephalopathy in mice based on gut microbiota. CNS Neurosci Ther 2022; 29:633-645. [PMID: 36468415 PMCID: PMC9873526 DOI: 10.1111/cns.14043] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/09/2022] Open
Abstract
INTRODUCTION In our experiments, male wild-type mice were randomly divided into four groups: the sham, SAE, SAE + 2% hydrogen gas inhalation (H2 ), and SAE + hydrogen-rich water (HW) groups. The feces of the mice were collected for 16 S rDNA analysis 24 h after the models were established, and the serum and brain tissue of the mice were collected for nontargeted metabolomics analysis. AIM Destruction of the intestinal microbiota is a risk factor for sepsis and subsequent organ dysfunction, and up to 70% of severely ill patients with sepsis exhibit varying degrees of sepsis-associated encephalopathy (SAE). The pathogenesis of SAE remains unclear. We aimed to explore the changes in gut microbiota in SAE and the regulatory mechanism of molecular hydrogen. RESULTS Molecular hydrogen treatment significantly improved the functional outcome of SAE and downregulated inflammatory reactions in both the brain and the gut. In addition, molecular hydrogen treatment improved gut microbiota dysbiosis and partially amended metabolic disorder after SAE. CONCLUSIONS Molecular hydrogen treatment promotes functional outcomes after SAE in mice, which may be attributable to increasing beneficial bacteria, repressing harmful bacteria, and metabolic disorder, and reducing inflammation.
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Affiliation(s)
- Qingqing Han
- Department of AnaesthesiologyTianjin Medical University General Hospital, Tianjin Research Institute of AnaesthesiologyTianjinChina
| | - Yuanyuan Bai
- Department of AnesthesiologyTianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical UniversityTianjinChina
| | - Chunjing Zhou
- Department of AnaesthesiologyTianjin 4 center hospitalTianjinChina
| | - Beibei Dong
- Department of AnaesthesiologyTianjin Medical University General Hospital, Tianjin Research Institute of AnaesthesiologyTianjinChina
| | - Yingning Li
- Department of AnaesthesiologyTianjin Medical University General Hospital, Tianjin Research Institute of AnaesthesiologyTianjinChina
| | - Ning Luo
- Department of AnaesthesiologyTianjin Medical University General Hospital, Tianjin Research Institute of AnaesthesiologyTianjinChina
| | - Hongguang Chen
- Department of AnaesthesiologyTianjin Medical University General Hospital, Tianjin Research Institute of AnaesthesiologyTianjinChina
| | - Yonghao Yu
- Department of AnaesthesiologyTianjin Medical University General Hospital, Tianjin Research Institute of AnaesthesiologyTianjinChina
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Methanogens and Hydrogen Sulfide Producing Bacteria Guide Distinct Gut Microbe Profiles and Irritable Bowel Syndrome Subtypes. Am J Gastroenterol 2022; 117:2055-2066. [PMID: 36114762 PMCID: PMC9722381 DOI: 10.14309/ajg.0000000000001997] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Irritable bowel syndrome (IBS) includes diarrhea-predominant (IBS-D) and constipation-predominant (IBS-C) subtypes. We combined breath testing and stool microbiome sequencing to identify potential microbial drivers of IBS subtypes. METHODS IBS-C and IBS-D subjects from 2 randomized controlled trials (NCT03763175 and NCT04557215) were included. Baseline breath carbon dioxide, hydrogen (H 2 ), methane (CH 4 ), and hydrogen sulfide (H 2 S) levels were measured by gas chromatography, and baseline stool microbiome composition was analyzed by 16S rRNA sequencing. Microbial metabolic pathways were analyzed using Kyoto Encyclopedia of Genes and Genomes collection databases. RESULTS IBS-C subjects had higher breath CH 4 that correlated with higher gut microbial diversity and higher relative abundance (RA) of stool methanogens, predominantly Methanobrevibacter , as well as higher absolute abundance of Methanobrevibacter smithii in stool. IBS-D subjects had higher breath H 2 that correlated with lower microbial diversity and higher breath H 2 S that correlated with higher RA of H 2 S-producing bacteria, including Fusobacterium and Desulfovibrio spp. The predominant H 2 producers were different in these distinct microtypes, with higher RA of Ruminococcaceae and Christensenellaceae in IBS-C/CH 4 + (which correlated with Methanobacteriaceae RA) and higher Enterobacteriaceae RA in IBS-D. Finally, microbial metabolic pathway analysis revealed enrichment of Kyoto Encyclopedia of Genes and Genomes modules associated with methanogenesis and biosynthesis of methanogenesis cofactor F420 in IBS-C/CH 4 + subjects, whereas modules associated with H 2 S production, including sulfate reduction pathways, were enriched in IBS-D. DISCUSSION Our findings identify distinct gut microtypes linked to breath gas patterns in IBS-C and IBS-D subjects, driven by methanogens such as M. smithii and H 2 S producers such as Fusobacterium and Desulfovibrio spp, respectively.
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Emerging insights between gut microbiome dysbiosis and Parkinson's disease: Pathogenic and clinical relevance. Ageing Res Rev 2022; 82:101759. [PMID: 36243356 DOI: 10.1016/j.arr.2022.101759] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/28/2022] [Accepted: 10/09/2022] [Indexed: 01/31/2023]
Abstract
Parkinson's disease (PD) is a complicated neurodegenerative disease, of which gastrointestinal disturbance appears prior to motor symptoms. Numerous studies have shed light on the roles of gastrointestinal tract and its neural connection to brain in PD pathology. In the past decades, the fields of microbiology and neuroscience have become ever more entwined. The emergence of gut microbiome has been considered as one of the key regulators of gut-brain function. With the advent of multi-omics sequencing techniques, gut microbiome of PD patients has been shown unique characteristics. The resident gut microbiota can exert considerable effects in PD and there are suggestions of a link between gut microbiome dysbiosis and PD progression. In this review, we summarize the latest progresses of gut microbiome dysbiosis in PD pathogenesis, further highlight the clinical relevance of gut microbiota and its metabolites in both the non-motor and motor symptoms of PD. Furthermore, we draw attention to the complex interplay between gut microbiota and PD drugs, with the purpose of improving drug efficacy and prescription accordingly. Further studies at specific strain level and longitudinal prospective clinical trials using optimized methods are still needed for the development of diagnostic markers and novel therapeutic regimens for PD.
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Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome. Nat Med 2022; 28:2344-2352. [PMID: 36138151 DOI: 10.1038/s41591-022-01965-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/22/2022] [Indexed: 01/14/2023]
Abstract
The gut microbiota shapes the response to immune checkpoint inhibitors (ICIs) in cancer, however dietary and geographic influences have not been well-studied in prospective trials. To address this, we prospectively profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events (irAEs). Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline. Together, these data provide insight into the relevance of native gut microbiota signatures, dietary intake and systemic inflammation in shaping the response to and toxicity from ICIs, prompting the need for further studies in this area.
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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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Nugroho FAA, Bai P, Darmadi I, Castellanos GW, Fritzsche J, Langhammer C, Gómez Rivas J, Baldi A. Inverse designed plasmonic metasurface with parts per billion optical hydrogen detection. Nat Commun 2022; 13:5737. [PMID: 36180437 PMCID: PMC9525276 DOI: 10.1038/s41467-022-33466-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
Plasmonic sensors rely on optical resonances in metal nanoparticles and are typically limited by their broad spectral features. This constraint is particularly taxing for optical hydrogen sensors, in which hydrogen is absorbed inside optically-lossy Pd nanostructures and for which state-of-the-art detection limits are only at the low parts-per-million (ppm) range. Here, we overcome this limitation by inversely designing a plasmonic metasurface based on a periodic array of Pd nanoparticles. Guided by a particle swarm optimization algorithm, we numerically identify and experimentally demonstrate a sensor with an optimal balance between a narrow spectral linewidth and a large field enhancement inside the nanoparticles, enabling a measured hydrogen detection limit of 250 parts-per-billion (ppb). Our work significantly improves current plasmonic hydrogen sensor capabilities and, in a broader context, highlights the power of inverse design of plasmonic metasurfaces for ultrasensitive optical (gas) detection. Plasmonic hydrogen sensors have limited sensitivity due to broad spectral features. Here, the authors use a particle swarm optimization algorithm to inversely design a plasmonic metasurface based on a periodic array of Pd nanoparticles, and demonstrate hydrogen detection limit of 250 ppb.
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Affiliation(s)
- Ferry Anggoro Ardy Nugroho
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands. .,Department of Physics, Universitas Indonesia, 16424, Depok, Indonesia.
| | - Ping Bai
- Department of Applied Physics and Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Iwan Darmadi
- Department of Physics, Chalmers University of Technology, 412 96, Göteborg, Sweden
| | - Gabriel W Castellanos
- Department of Applied Physics and Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, 412 96, Göteborg, Sweden
| | - Christoph Langhammer
- Department of Physics, Chalmers University of Technology, 412 96, Göteborg, Sweden.
| | - Jaime Gómez Rivas
- Department of Applied Physics and Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
| | - Andrea Baldi
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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Aoki C, Imai K, Mizutani T, Sugiyama D, Miki R, Koya Y, Kobayashi T, Ushida T, Iitani Y, Nakamura N, Owaki T, Nishikawa H, Toyokuni S, Kajiyama H, Kotani T. Molecular hydrogen has a positive impact on pregnancy maintenance through enhancement of mitochondrial function and immunomodulatory effects on T cells. Life Sci 2022; 308:120955. [PMID: 36115583 DOI: 10.1016/j.lfs.2022.120955] [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: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/09/2022] [Indexed: 10/31/2022]
Abstract
AIMS Molecular hydrogen (H2) has attracted growing interest because of its implications in various diseases. However, the molecular mechanisms underlying the remarkable effect of a small amount of H2 remain elusive. No knowledge has been available on the role of H2 in the etiology of pregnancy disorders or its direct influence on human immune cells. Since maternal immunity, T cells in particular, plays a critical role in pregnancy maintenance. We investigated the effects of H2 on T cells and its relation to preterm birth (PTB). MAIN METHODS Exhaled H2 concentrations in pregnant women were measured and correlated with cytokine concentrations in maternal and umbilical cord blood. H2 was added to T cells collected from healthy donors, and differentiation and proliferation were examined. Energy metabolism was also examined. H2 was administered to mice and cytokine expression was compared. KEY FINDINGS Our prospective observational study revealed that maternal production of H2 is significantly lower in pregnant women with PTB, suggesting its potential as a biomarker for predicting PTB. We found that H2 has clear associations with several maternal cytokines, and acts as an immunomodulator by exerting mitochondrial function in human T cells. Moreover, in vivo administration of H2 to pregnant mice regulated inflammatory responses and reduced PTB caused by T cell activation, which further supports the notion that H2 may contribute to prolonged gestation through its immunomodulatory effect. SIGNIFICANCE Measuring maternal H2-production could be a potential clinical tool in the management of PTB, and H2 may have positive impact on pregnancy maintenance.
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Affiliation(s)
- Chieko Aoki
- Department of Obstetrics and Gynecology, Japan
| | - Kenji Imai
- Department of Obstetrics and Gynecology, Japan.
| | - Teruyuki Mizutani
- Department of Obstetrics and Gynecology, Japan; Department of Immunology, Japan
| | | | - Rika Miki
- Laboratory of Bell Research Centre-Department of Obstetrics and Gynecology Collaborative Research, Bell Research Centre for Reproductive Health and Cancer, Department of Reproduction, Japan
| | - Yoshihiro Koya
- Laboratory of Bell Research Centre-Department of Obstetrics and Gynecology Collaborative Research, Bell Research Centre for Reproductive Health and Cancer, Department of Reproduction, Japan
| | | | | | | | | | - Taro Owaki
- Department of Obstetrics and Gynecology, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Japan; Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Peña-Ocaña BA, Hoshiko Y, Silva-Flores M, Maeda T, Pérez-Torres I, García-Contreras R, Gutiérrez-Sarmiento W, Hernández-Esquivel L, Marín-Hernández Á, Sánchez-Thomas R, Saavedra E, Rodríguez-Zavala JS, Jasso-Chávez R. Cultivation of gastrointestinal microbiota in a new growth system revealed dysbiosis and metabolic disruptions in carcinoma-bearing rats. Front Microbiol 2022; 13:949272. [PMID: 36118191 PMCID: PMC9479207 DOI: 10.3389/fmicb.2022.949272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
A challenge in the study of gastrointestinal microbiota (GITm) is the validation of the genomic data with metabolic studies of the microbial communities to understand how the microbial networks work during health and sickness. To gain insights into the metabolism of the GITm, feces from healthy and sick rats with cancer were inoculated in a defined synthetic medium directed for anaerobic prokaryote growth (INC-07 medium). Significant differences between cultures of healthy and sick individuals were found: 1) the consumption of the carbon source and the enzyme activity involved in their catabolism (e.g., sucrase, lactase, lipases, aminotransferases, and dehydrogenases); 2) higher excretion of acetic, propionic, isobutyric, butyric, valeric, and isovaleric acids; 3) methane production; 4) ability to form biofilms; and 5) up to 500 amplicon sequencing variants (ASVs) identified showed different diversity and abundance. Moreover, the bowel inflammation induced by cancer triggered oxidative stress, which correlated with deficient antioxidant machinery (e.g., NADPH-producing enzymes) determined in the GITm cultures from sick individuals in comparison with those from control individuals. Altogether, the data suggested that to preserve the microbial network between bacteria and methanogenic archaea, a complete oxidation of the carbon source may be essential for healthy microbiota. The correlation of 16S rRNA gene metabarcoding between cultures and feces, as well as metabolomic data found in cultures, suggest that INC-07 medium may be a useful tool to understand the metabolism of microbiota under gut conditions.
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Affiliation(s)
- Betsy Anaid Peña-Ocaña
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Yuki Hoshiko
- Division of Environment-Conscious Chemistry and Bioengineering, Department of Biological Functions Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Mayel Silva-Flores
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Toshinari Maeda
- Division of Environment-Conscious Chemistry and Bioengineering, Department of Biological Functions Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Israel Pérez-Torres
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wilbert Gutiérrez-Sarmiento
- Instituto Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Luz Hernández-Esquivel
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Rosina Sánchez-Thomas
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | | | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
- *Correspondence: Ricardo Jasso-Chávez
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Neyrinck AM, Rodriguez J, Zhang Z, Nazare JA, Bindels LB, Cani PD, Maquet V, Laville M, Bischoff SC, Walter J, Delzenne NM. Breath volatile metabolome reveals the impact of dietary fibres on the gut microbiota: Proof of concept in healthy volunteers. EBioMedicine 2022; 80:104051. [PMID: 35561452 PMCID: PMC9108873 DOI: 10.1016/j.ebiom.2022.104051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 01/06/2023] Open
Abstract
Background Current data suggest that dietary fibre (DF) interaction with the gut microbiota largely contributes to their physiological effects. The bacterial fermentation of DF leads to the production of metabolites, most of them are volatile. This study analyzed the breath volatile metabolites (BVM) profile in healthy individuals (n=15) prior and after a 3-week intervention with chitin-glucan (CG, 4.5 g/day), an insoluble fermentable DF. Methods The present exploratory study presents the original data related to the secondary outcomes, notably the analysis of BVM. BVM were analyzed throughout the test days -in fasting state and after standardized meals - using selected ion flow tube mass spectrometry (SIFT-MS). BVM production was correlated to the gut microbiota composition (Illumina sequencing, primary outcome), analyzed before and after the intervention. Findings The data reveal that the post-prandial state versus fasting state is a key determinant of BVM fingerprint. Correlation analyses with fecal microbiota spotlighted butyrate-producing bacteria, notably Faecalibacterium, as dominant bacteria involved in butyrate and other BVM expiration. CG intervention promotes interindividual variations of fasting BVM, and decreases or delays the expiration of most exhaled BVM in favor of H2 expiration, without any consequence on gastrointestinal tolerance. Interpretation Assessing BVM is a non-invasive methodology allowing to analyze the influence of DF intervention on the gut microbiota. Funding FiberTAG project was initiated from a European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL) and was supported by the Service Public de Wallonie (SPW-EER, convention 1610365, Belgium).
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Affiliation(s)
- Audrey M Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain (Université catholique de Louvain), avenue E. Mounier box B1.73.11, Brussels B-1200, Belgium
| | - Julie Rodriguez
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain (Université catholique de Louvain), avenue E. Mounier box B1.73.11, Brussels B-1200, Belgium
| | - Zhengxiao Zhang
- Department of Medicine, University of Alberta, Edmonton, Canada; College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Julie-Anne Nazare
- Rhône-Alpes Research Center for Human Nutrition, CarMeN Laboratory, Hospices Civils de Lyon, Université-Lyon, France
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain (Université catholique de Louvain), avenue E. Mounier box B1.73.11, Brussels B-1200, Belgium
| | - Patrice D Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain (Université catholique de Louvain), avenue E. Mounier box B1.73.11, Brussels B-1200, Belgium; WELBIO- Walloon Excellence in Life Sciences and Biotechnology, UCLouvain (Université catholique de Louvain), Brussels, Belgium
| | - Véronique Maquet
- KitoZyme, Parc Industriel des Hauts-Sart, Zone 2, Rue de Milmort 680, Herstal 4040, Belgium
| | - Martine Laville
- Rhône-Alpes Research Center for Human Nutrition, CarMeN Laboratory, Hospices Civils de Lyon, Université-Lyon, France
| | - Stephan C Bischoff
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Jens Walter
- Department of Medicine, APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain (Université catholique de Louvain), avenue E. Mounier box B1.73.11, Brussels B-1200, Belgium.
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Trischler R, Roth J, Sorbara MT, Schlegel X, Müller V. A functional Wood-Ljungdahl pathway devoid of a formate dehydrogenase in the gut acetogens Blautia wexlerae, Blautia luti and beyond. Environ Microbiol 2022; 24:3111-3123. [PMID: 35466558 DOI: 10.1111/1462-2920.16029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
Species of the genus Blautia are typical inhabitants of the human gut and considered as beneficial gut microbes. However, their role in the gut microbiome and their metabolic features are poorly understood. Blautia schinkii was described as an acetogenic bacterium, characterized by a functional Wood-Ljungdahl pathway (WLP) of acetogenesis from H2 + CO2 . Here we report that two relatives, Blautia luti and Blautia wexlerae do not grow on H2 + CO2 . Inspection of the genome sequence revealed all genes of the WLP except genes encoding a formate dehydrogenase and an electron-bifurcating hydrogenase. Enzyme assays confirmed this prediction. Accordingly, resting cells neither converted H2 + CO2 nor H2 + HCOOH + CO2 to acetate. Carbon monoxide is an intermediate of the WLP and substrate for many acetogens. B. luti and B. wexlerae had an active CO dehydrogenase and resting cells performed acetogenesis from HCOOH + CO2 + CO, demonstrating a functional WLP. Bioinformatic analyses revealed that many Blautia strains as well as other gut acetogens lack formate dehydrogenases and hydrogenases. Thus, the use of formate instead of H2 + CO2 as an interspecies hydrogen and electron carrier seems to be more common in the gut microbiome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Raphael Trischler
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Jennifer Roth
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Matthew T Sorbara
- Department Molecular and Cellular Biology, University of Guelph, Ontario, N1G 2W1, Canada
| | - Xenia Schlegel
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
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Lopez JG, Wingreen NS. Noisy metabolism can promote microbial cross-feeding. eLife 2022; 11:70694. [PMID: 35380535 PMCID: PMC8983042 DOI: 10.7554/elife.70694] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Cross-feeding, the exchange of nutrients between organisms, is ubiquitous in microbial communities. Despite its importance in natural and engineered microbial systems, our understanding of how inter-species cross-feeding arises is incomplete, with existing theories limited to specific scenarios. Here, we introduce a novel theory for the emergence of such cross-feeding, which we term noise-averaging cooperation (NAC). NAC is based on the idea that, due to their small size, bacteria are prone to noisy regulation of metabolism which limits their growth rate. To compensate, related bacteria can share metabolites with each other to ‘average out’ noise and improve their collective growth. According to the Black Queen Hypothesis, this metabolite sharing among kin, a form of ‘leakage’, then allows for the evolution of metabolic interdependencies among species including de novo speciation via gene deletions. We first characterize NAC in a simple ecological model of cell metabolism, showing that metabolite leakage can in principle substantially increase growth rate in a community context. Next, we develop a generalized framework for estimating the potential benefits of NAC among real bacteria. Using single-cell protein abundance data, we predict that bacteria suffer from substantial noise-driven growth inefficiencies, and may therefore benefit from NAC. We then discuss potential evolutionary pathways for the emergence of NAC. Finally, we review existing evidence for NAC and outline potential experimental approaches to detect NAC in microbial communities.
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Affiliation(s)
- Jaime G Lopez
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, United States
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McGuinness AJ, Davis JA, Dawson SL, Loughman A, Collier F, O’Hely M, Simpson CA, Green J, Marx W, Hair C, Guest G, Mohebbi M, Berk M, Stupart D, Watters D, Jacka FN. A systematic review of gut microbiota composition in observational studies of major depressive disorder, bipolar disorder and schizophrenia. Mol Psychiatry 2022; 27:1920-1935. [PMID: 35194166 PMCID: PMC9126816 DOI: 10.1038/s41380-022-01456-3] [Citation(s) in RCA: 158] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 02/07/2023]
Abstract
The emerging understanding of gut microbiota as 'metabolic machinery' influencing many aspects of physiology has gained substantial attention in the field of psychiatry. This is largely due to the many overlapping pathophysiological mechanisms associated with both the potential functionality of the gut microbiota and the biological mechanisms thought to be underpinning mental disorders. In this systematic review, we synthesised the current literature investigating differences in gut microbiota composition in people with the major psychiatric disorders, major depressive disorder (MDD), bipolar disorder (BD) and schizophrenia (SZ), compared to 'healthy' controls. We also explored gut microbiota composition across disorders in an attempt to elucidate potential commonalities in the microbial signatures associated with these mental disorders. Following the PRISMA guidelines, databases were searched from inception through to December 2021. We identified 44 studies (including a total of 2510 psychiatric cases and 2407 controls) that met inclusion criteria, of which 24 investigated gut microbiota composition in MDD, seven investigated gut microbiota composition in BD, and 15 investigated gut microbiota composition in SZ. Our syntheses provide no strong evidence for a difference in the number or distribution (α-diversity) of bacteria in those with a mental disorder compared to controls. However, studies were relatively consistent in reporting differences in overall community composition (β-diversity) in people with and without mental disorders. Our syntheses also identified specific bacterial taxa commonly associated with mental disorders, including lower levels of bacterial genera that produce short-chain fatty acids (e.g. butyrate), higher levels of lactic acid-producing bacteria, and higher levels of bacteria associated with glutamate and GABA metabolism. We also observed substantial heterogeneity across studies with regards to methodologies and reporting. Further prospective and experimental research using new tools and robust guidelines hold promise for improving our understanding of the role of the gut microbiota in mental and brain health and the development of interventions based on modification of gut microbiota.
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Affiliation(s)
- A. J. McGuinness
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia
| | - J. A. Davis
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia
| | - S. L. Dawson
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia ,grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia
| | - A. Loughman
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia
| | - F. Collier
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia
| | - M. O’Hely
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia ,grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia
| | - C. A. Simpson
- grid.1008.90000 0001 2179 088XMelbourne School of Psychological Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XMelbourne Neuropsychiatry Centre, Department of Medicine, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne and Melbourne Health, Melbourne, VIC Australia
| | - J. Green
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia ,grid.1002.30000 0004 1936 7857Monash Alfred Psychiatry Research Centre (MAPcr), Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Parkville, VIC Australia ,grid.466993.70000 0004 0436 2893Department of Psychiatry, Peninsula Health, Frankston, VIC Australia
| | - W. Marx
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia
| | - C. Hair
- grid.1021.20000 0001 0526 7079Deakin University, School of Medicine, Geelong, VIC Australia ,grid.414257.10000 0004 0540 0062Department of Gastroenterology, Barwon Health, Geelong, VIC Australia
| | - G. Guest
- grid.1021.20000 0001 0526 7079Deakin University, School of Medicine, Geelong, VIC Australia ,grid.415335.50000 0000 8560 4604Department of Surgery, University Hospital Geelong, Barwon Health, Geelong, VIC Australia
| | - M. Mohebbi
- grid.1021.20000 0001 0526 7079Biostatistics Unit, Faculty of Health, Deakin University, Melbourne, VIC Australia
| | - M. Berk
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia ,grid.1021.20000 0001 0526 7079Deakin University, School of Medicine, Geelong, VIC Australia ,grid.1008.90000 0001 2179 088XOrygen, The National Centre of Excellence in Youth Mental Health, Centre for Youth Mental Health, Florey Institute for Neuroscience and Mental Health and the Department of Psychiatry, The University of Melbourne, Melbourne, Australia
| | - D. Stupart
- grid.1021.20000 0001 0526 7079Deakin University, School of Medicine, Geelong, VIC Australia ,grid.415335.50000 0000 8560 4604Department of Surgery, University Hospital Geelong, Barwon Health, Geelong, VIC Australia
| | - D. Watters
- grid.1021.20000 0001 0526 7079Deakin University, School of Medicine, Geelong, VIC Australia ,grid.415335.50000 0000 8560 4604Department of Surgery, University Hospital Geelong, Barwon Health, Geelong, VIC Australia
| | - F. N. Jacka
- grid.1021.20000 0001 0526 7079The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Food & Mood Centre, School of Medicine and Barwon Health, Deakin University, Geelong, VIC Australia ,grid.1058.c0000 0000 9442 535XCentre for Adolescent Health, Murdoch Children’s Research Institute, Melbourne, VIC Australia ,grid.418393.40000 0001 0640 7766Black Dog Institute, Sydney, NSW Australia ,grid.1011.10000 0004 0474 1797College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, QLD Australia
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Daisley BA, Koenig D, Engelbrecht K, Doney L, Hards K, Al KF, Reid G, Burton JP. Emerging connections between gut microbiome bioenergetics and chronic metabolic diseases. Cell Rep 2021; 37:110087. [PMID: 34879270 DOI: 10.1016/j.celrep.2021.110087] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/25/2022] Open
Abstract
The conventional viewpoint of single-celled microbial metabolism fails to adequately depict energy flow at the systems level in host-adapted microbial communities. Emerging paradigms instead support that distinct microbiomes develop interconnected and interdependent electron transport chains that rely on cooperative production and sharing of bioenergetic machinery (i.e., directly involved in generating ATP) in the extracellular space. These communal resources represent an important subset of the microbial metabolome, designated here as the "pantryome" (i.e., pantry or external storage compartment), that critically supports microbiome function and can exert multifunctional effects on host physiology. We review these interactions as they relate to human health by detailing the genomic-based sharing potential of gut-derived bacterial and archaeal reference strains. Aromatic amino acids, metabolic cofactors (B vitamins), menaquinones (vitamin K2), hemes, and short-chain fatty acids (with specific emphasis on acetate as a central regulator of symbiosis) are discussed in depth regarding their role in microbiome-related metabolic diseases.
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Affiliation(s)
- Brendan A Daisley
- Department of Microbiology & Immunology, The University of Western Ontario, London, ON N6A 5C1, Canada; Canadian Centre for Human Microbiome and Probiotics Research, London, ON N6A 4V2, Canada
| | - David Koenig
- Kimberly Clark Corporation, Global Research and Engineering-Life Science, Neenah, WI, USA
| | - Kathleen Engelbrecht
- Kimberly Clark Corporation, Global Research and Engineering-Life Science, Neenah, WI, USA
| | - Liz Doney
- Kimberly Clark Corporation, Global Research and Engineering-Life Science, Neenah, WI, USA
| | - Kiel Hards
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
| | - Kait F Al
- Department of Microbiology & Immunology, The University of Western Ontario, London, ON N6A 5C1, Canada; Canadian Centre for Human Microbiome and Probiotics Research, London, ON N6A 4V2, Canada
| | - Gregor Reid
- Department of Microbiology & Immunology, The University of Western Ontario, London, ON N6A 5C1, Canada; Canadian Centre for Human Microbiome and Probiotics Research, London, ON N6A 4V2, Canada; Department of Surgery, Division of Urology, Schulich School of Medicine, London, ON N6A 5C1, Canada
| | - Jeremy P Burton
- Department of Microbiology & Immunology, The University of Western Ontario, London, ON N6A 5C1, Canada; Canadian Centre for Human Microbiome and Probiotics Research, London, ON N6A 4V2, Canada; Department of Surgery, Division of Urology, Schulich School of Medicine, London, ON N6A 5C1, Canada.
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45
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Zheng Y, Jiang X, Gao Y, Yuan L, Wang X, Wu S, Xia Y, Yao L, Yan J, Liu L, Wei Y, Song Z, Yu L, Chen Y. Microbial Profiles of Patients With Antipsychotic-Related Constipation Treated With Electroacupuncture. Front Med (Lausanne) 2021; 8:737713. [PMID: 34722577 PMCID: PMC8551555 DOI: 10.3389/fmed.2021.737713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
Antipsychotic-related constipation (APRC) is one of the most common side effects of taking antipsychotic medication. APRC can seriously impact patient quality of life and is potentially fatal, though the efficacy of current APRC treatments is low for most patients. In this study, we conducted a controlled, pilot randomized, sham-electroacupuncture (SEA) study to assess the efficacy of electroacupuncture (EA) in patients with APRC. We used 16S rRNA gene sequencing to assess the microbial profiles of these patients and analyze how EA treatments affected their bacteria. Methods: We treated 133 APRC patients with randomly assigned EA treatments or SEA treatments for 4 consecutive weeks, fully evaluating the patients 8 weeks after treatment. The participants, outcome assessors, and statistics were all blind to the EA and SEA treatments. Outcomes assessed included changes in spontaneous bowel movements (SBMs) and the frequency of rescue measures. We detected assessed the microbial diversity of stool specimens both before and after EA treatment using 16S rRNA gene sequencing. Results: Both EA and SEA treatments reduced the need for constipation rescue measures and did not have serious side effects. EA treatments were better than SEA treatments at increasing SBMs and reducing rescue measures. The diversity of gut microbiota changed after EA treatment. LEfSe analysis indicated changes in the genus (belonging to phylum Proteobacteria) of gut microbiota in patients following EA treatment. Conclusions: This study found that EA treatment is effective and safe for patients with APRC, and could be associated with changes in their microbial profiles. Further study, with larger sample sizes, is needed to explore the efficacy of EA intervention as a clinical treatment for APRC. Trial Registration: ChiCTR, ChiCTR-ONC-17010842, http://www.chictr.org.cn/showproj.aspx?proj=18420.
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Affiliation(s)
- Yuanjia Zheng
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiumin Jiang
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yacen Gao
- Rehabilitation Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lexin Yuan
- Department of Traditional Chinese Medicine, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China
| | - Xiaotong Wang
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shengwei Wu
- Department of Traditional Chinese Medicine, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China
| | - Yucen Xia
- Research Institute of Acupuncture and Moxibustion, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lin Yao
- Research Institute of Acupuncture and Moxibustion, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jinglan Yan
- Research Institute of Acupuncture and Moxibustion, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lanying Liu
- Department of Psychosomatics, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Yingdong Wei
- Medical Administration Division, Shenyang Anning Hospital, Shenyang, China
| | - Zhiqiang Song
- The Third People's Hospital of Qinghai Province, Xining, China
| | - Lin Yu
- Department of Traditional Chinese Medicine, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China
| | - Yongjun Chen
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China.,Research Institute of Acupuncture and Moxibustion, Shandong University of Traditional Chinese Medicine, Jinan, China.,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China
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46
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Abstract
The aim of this review is to provide an overview of the complex interactions between dietary fibre and the resident microbial community in the human gut. The microbiota influences both health maintenance and disease development. In the large intestine, the microbiota plays a crucial role in the degradation of dietary carbohydrates that remain undigested in the upper gut (non-digestible carbohydrates or fibre). Dietary fibre contains a variety of different types of carbohydrates, and its breakdown is facilitated by many different microbial enzymes. Some microbes, termed generalists, are able to degrade a range of different carbohydrates, whereas others are more specialised. Furthermore, the physicochemical characteristics of dietary fibre, such as whether it enters the gut in soluble or insoluble form, also likely influence which microbes can degrade it. A complex nutritional network therefore exists comprising primary degraders able to attack complex fibre and cross feeders that benefit from fibre breakdown intermediates or fermentation products. This leads predominately to the generation of the short-chain fatty acids (SCFA) acetate, propionate and butyrate, which exert various effects on host physiology, including the supply of energy, influencing glucose and lipid metabolism and anti-carcinogenic and anti-inflammatory actions. In order to effectively modulate the gut microbiota through diet, there is a need to better understand the complex competitive and cooperative interactions between gut microbes in dietary fibre breakdown, as well as how gut environmental factors and the physicochemical state of fibre originating from different types of diets influence microbial metabolism and ecology in the gut.
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47
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Small Intestinal Bacterial Overgrowth as Potential Therapeutic Target in Parkinson's Disease. Int J Mol Sci 2021; 22:ijms222111663. [PMID: 34769091 PMCID: PMC8584211 DOI: 10.3390/ijms222111663] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/17/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence suggests that the gut microbiota and the brain are closely connected via the so-called gut–brain axis. Small intestinal bacterial overgrowth (SIBO) is a gut dysbiosis in which the small intestine is abundantly colonized by bacteria that are typically found in the colon. Though not a disease, it may result in intestinal symptoms caused by the accumulation of microbial gases in the intestine. Intestinal inflammation, malabsorption and vitamin imbalances may also develop. SIBO can be eradicated by one or several courses of antibiotics but reappears if the predisposing condition persists. Parkinson’s disease (PD) is a common neurodegenerative proteinopathy for which disease modifying interventions are not available. Sporadic forms may start in the gut years before the development of clinical features. Increased gastrointestinal transit time is present in most people with PD early during the course of the disease, predisposing to gut dysbiosis, including SIBO. The role that gut dysbiosis may play in the etiopathogenesis of PD is not fully understood yet. Here, we discuss the possibility that SIBO could contribute to the progression of PD, by promoting or preventing neurodegeneration, thus being a potential target for treatments aiming at slowing down the progression of PD. The direct symptomatic impact of SIBO and its impact on symptomatic medication are also briefly discussed.
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48
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Jing YZ, Li SJ, Sun ZJ. Gas and gas-generating nanoplatforms in cancer therapy. J Mater Chem B 2021; 9:8541-8557. [PMID: 34608920 DOI: 10.1039/d1tb01661j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gas therapy is the usage of certain gases with special therapeutic effects for the treatment of diseases. Hydrogen (H2), nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H2S) acting as gas signalling molecules are representative gases in cancer therapy. They act directly on mitochondria or nuclei to lead to cell apoptosis. They can also alleviate immuno-suppression in the tumour microenvironment and promote phenotype conversion of tumour-associated macrophages. Moreover, the combination of gas therapy and other traditional therapy methods can reduce side effects and improve therapeutic efficacy. Here, we discuss the roles of NO, CO, H2S and H2 in cancer biology. Considering the rapidly developing nanotechnology, gas-generating nanoplatforms which can achieve targeted delivery and controlled release were also discussed. Finally, we highlight the current challenges and future opportunities of gas-based cancer therapy.
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Affiliation(s)
- Yuan-Zhe Jing
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine, Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, P. R. China.
| | - Shu-Jin Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine, Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, P. R. China.
| | - Zhi-Jun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine, Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, P. R. China. .,Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, P. R. China
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49
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Alsharairi NA. The Role of Short-Chain Fatty Acids in Mediating Very Low-Calorie Ketogenic Diet-Infant Gut Microbiota Relationships and Its Therapeutic Potential in Obesity. Nutrients 2021; 13:3702. [PMID: 34835958 PMCID: PMC8624546 DOI: 10.3390/nu13113702] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
As the very low-calorie ketogenic diet (VLCKD) gains increased interest as a therapeutic approach for many diseases, little is known about its therapeutic use in childhood obesity. Indeed, the role of VLCKD during pregnancy and lactation in influencing short chain fatty acid (SCFA)-producing bacteria and the potential mechanisms involved in the protective effects on obesity are still unclear. Infants are characterized by a diverse gut microbiota composition with higher abundance of SCFA-producing bacteria. Maternal VLCKD during pregnancy and lactation stimulates the growth of diverse species of SCFA-producing bacteria, which may induce epigenetic changes in infant obese gene expression and modulate adipose tissue inflammation in obesity. Therefore, this review aims to determine the mechanistic role of SCFAs in mediating VLCKD-infant gut microbiota relationships and its protective effects on obesity.
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Affiliation(s)
- Naser A Alsharairi
- Heart, Mind & Body Research Group, Griffith University, Gold Coast, QLD 4222, Australia
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50
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Berkhout MD, Plugge CM, Belzer C. How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding. Glycobiology 2021; 32:182-200. [PMID: 34939101 PMCID: PMC8966484 DOI: 10.1093/glycob/cwab105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 11/12/2022] Open
Abstract
The intestinal epithelium is protected from direct contact with gut microbes by a mucus layer. This mucus layer consists of secreted mucin glycoproteins. The outer mucus layer in the large intestine forms a niche that attracts specific gut microbiota members of which several gut commensals can degrade mucin. Mucin glycan degradation is a complex process that requires a broad range of glycan degrading enzymes, as mucin glycans are intricate and diverse molecules. Consequently, it is hypothesised that microbial mucin breakdown requires concerted action of various enzymes in a network of multiple resident microbes at the gut mucosa. This review investigates the evolutionary relationships of microbial CAZymes that are potentially involved in mucin glycan degradation and focuses on the role that microbial enzymes play in the degradation of gut mucin glycans in microbial cross-feeding and syntrophic interactions.
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Affiliation(s)
- Maryse D Berkhout
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
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