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Britton RA, Verdu EF, Di Rienzi SC, Reyes Muñoz A, Tarr PI, Preidis GA. Taking Microbiome Science to the Next Level: Recommendations to Advance the Emerging Field of Microbiome-Based Therapeutics and Diagnostics. Gastroenterology 2024:S0016-5085(24)05000-5. [PMID: 38815708 DOI: 10.1053/j.gastro.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024]
Affiliation(s)
- Robert A Britton
- Department of Molecular Virology and Microbiology and Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology and Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Phillip I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, and, Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri
| | - Geoffrey A Preidis
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
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Pereira H, Chakarov N, Hoffman JI, Rinaud T, Ottensmann M, Gladow KP, Tobias B, Caspers BA, Maraci Ö, Krüger O. Early-life factors shaping the gut microbiota of Common buzzard nestlings. Anim Microbiome 2024; 6:27. [PMID: 38745254 DOI: 10.1186/s42523-024-00313-8] [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: 01/19/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors. RESULTS We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition. CONCLUSION Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany.
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Kai-Philipp Gladow
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Busche Tobias
- Medical School East Westphalia-Lippe & Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, NRW, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
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Schütterle DM, Hegner R, Temovska M, Ortiz-Ardila AE, Angenent LT. Exclusive D-lactate-isomer production during a reactor-microbiome conversion of lactose-rich waste by controlling pH and temperature. WATER RESEARCH 2024; 250:121045. [PMID: 38159537 DOI: 10.1016/j.watres.2023.121045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Lactate is among the top-ten-biobased products. It occurs naturally as D- or L-isomer and as a racemic mixture (DL-lactate). Generally, lactate with a high optical purity is more valuable. In searching for suitable renewable feedstocks for lactate production, unutilized organic waste streams are increasingly coming into focus. Here, we investigated acid whey, which is a lactose-rich byproduct of yogurt production, that represents a considerable environmental footprint for the dairy industry. We investigated the steering of the lactate-isomer composition in a continuous and open culture system (HRT = 0.6 d) at different pH values (pH 5.0 vs. pH 6.5) and process temperatures (38°C to 50°C). The process startup was achieved by autoinoculation. At a pH of 5.0 and a temperature of 47°C-50°C, exclusive D-lactate production occurred because of the dominance of Lactobacillus spp. (> 95% of relative abundance). The highest volumetric D-lactate production rate of 722 ± 94.6 mmol C L-1 d-1 (0.90 ± 0.12 g L-1 h-1), yielding 0.93 ± 0.15 mmol C mmol C-1, was achieved at a pH of 5.0 and a temperature of 44°C (n = 18). At a pH of 6.5 and a temperature of 44°C, we found a mixture of DL-lactate (average D-to-L-lactate production rate ratio of 1.69 ± 0.90), which correlated with a high abundance of Streptococcus spp. and Enterococcus spp. However, exclusive L-lactate production could not be achieved. Our results show that for the continuous conversion of lactose-rich dairy waste streams, the pH was a critical process parameter to control the yield of lactate isomers by influencing the composition of the microbiota. In contrast, temperature adjustments allowed the improvement of bioprocess kinetics.
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Affiliation(s)
- Dorothea M Schütterle
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
| | - Richard Hegner
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
| | - Monika Temovska
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany; AG Angenent, Max Planck Institute for Biology, Max Planck Ring 5, Tübingen 72076, Germany
| | - Andrés E Ortiz-Ardila
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
| | - Largus T Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, Tübingen 72076, Germany; AG Angenent, Max Planck Institute for Biology, Max Planck Ring 5, Tübingen 72076, Germany; Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds vej 10D, Aarhus C 8000, Denmark; The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds vej 10C, Aarhus C 8000, Denmark; Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72074, Germany.
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Cosier DJ, Lambert K, Neale EP, Probst Y, Charlton K. The effect of oral synbiotics on the gut microbiota and inflammatory biomarkers in healthy adults: a systematic review and meta-analysis. Nutr Rev 2024:nuae002. [PMID: 38341803 DOI: 10.1093/nutrit/nuae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024] Open
Abstract
CONTEXT Prior research has explored the effect of synbiotics, the combination of probiotics and prebiotics, on the gut microbiota in clinical populations. However, evidence related to the effect of synbiotics on the gut microbiota in healthy adults has not been reviewed to date. OBJECTIVE A systematic review and meta-analysis was conducted to comprehensively investigate the effect of synbiotics on the gut microbiota and inflammatory markers in populations of healthy adults. DATA SOURCES Scopus, PubMed, Web of Science, ScienceDirect, MEDLINE, CINAHL, and The Cochrane Library were systematically searched to retrieve randomized controlled trials examining the primary outcome of gut microbiota or intestinal permeability changes after synbiotic consumption in healthy adults. Secondary outcomes of interest were short-chain fatty acids, inflammatory biomarkers, and gut microbiota diversity. DATA EXTRACTION Weighted (WMD) or standardized mean difference (SMD) outcome data were pooled in restricted maximum likelihood models using random effects. Twenty-seven articles reporting on 26 studies met the eligibility criteria (n = 1319). DATA ANALYSIS Meta-analyses of 16 studies showed synbiotics resulted in a significant increase in Lactobacillus cell count (SMD, 0.74; 95% confidence interval [CI], 0.15, 1.33; P = 0.01) and propionate concentration (SMD, 0.22; 95% CI, 0.02, 0.43; P = 0.03) compared with controls. A trend for an increase in Bifidobacterium relative abundance (WMD, 0.97; 95% CI, 0.42, 2.52; P = 0.10) and cell count (SMD, 0.82; 95% CI, 0.13, 1.88; P = 0.06) was seen. No significant differences in α-diversity, acetate, butyrate, zonulin, IL-6, CRP, or endotoxins were observed. CONCLUSION This review demonstrates that synbiotics modulate the gut microbiota by increasing Lactobacillus and propionate across various healthy adult populations, and may result in increased Bifidobacterium. Significant variations in synbiotic type, dose, and duration should be considered as limitations when applying findings to clinical practice. SYSTEMATIC REVIEW REGISTRATION PROSPERO no. CRD42021284033.
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Affiliation(s)
- Denelle J Cosier
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kelly Lambert
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Elizabeth P Neale
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yasmine Probst
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Karen Charlton
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
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Peled S, Freilich S, Hanani H, Kashi Y, Livney YD. Next-generation prebiotics: Maillard-conjugates of 2'-fucosyllactose and lactoferrin hydrolysates beneficially modulate gut microbiome composition and health promoting activity in a murine model. Food Res Int 2024; 177:113830. [PMID: 38225111 DOI: 10.1016/j.foodres.2023.113830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Current prebiotics are predominantly carbohydrates. However, great competition exists among gut microbes for the scarce protein in the colon, as most consumed protein is digested and absorbed in the small intestine. Herein we evaluated in-vivo novel next-generation prebiotics: protein-containing-prebiotics, for selectively-targeted delivery of protein to colonic probiotics, to boost their growth. This system is based on micellar-particles, composed of Maillard-glycoconjugates of 2'-Fucosyllactose (2'-FL, human-milk-oligosaccharide) shell, engulfing lactoferrin peptic-then-tryptic hydrolysate (LFH) core. This core-shell structure lowers protein-core digestibility, while the prebiotic glycans are hypothesized to serve as molecular-recognition ligands for selectively targeting probiotics. To study the efficacy of this novel prebiotic, we fed C57BL/6JRccHsd mice with either 2'-FL-LFH Maillard-glycoconjugates, unconjugated components (control), or saline (blank). Administration of 2'-FL-LFH significantly increased the levels of short-chain-fatty-acids (SCFAs)-producing bacterial families (Ruminococcaceae, Lachnospiraceae) and genus (Odoribacter) and the production of the health-related metabolites, SCFAs, compared to the unconjugated components and to saline. The SCFAs-producing genus Prevotella significantly increased upon 2'-FL-LFH consumption, compared to only moderate increase in the unconjugated components. Interestingly, the plasma-levels of inflammation-inducing lipopolysaccharides (LPS), which indicate increased gut-permeability, were significantly lower in the 2'-FL-LFH group compared to the unconjugated-components and the saline groups. We found that Maillard-glycoconjugates of 2'-FL-LFH can serve as novel protein-containing prebiotics, beneficially modulating gut microbial composition and its metabolic activity, thereby contributing to host health more effectively than the conventional carbohydrate-only prebiotics.
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Affiliation(s)
- Stav Peled
- Laboratory of Biopolymers for Food and Health, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Shay Freilich
- Laboratory of Applied Genomics, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Hila Hanani
- Laboratory of Applied Genomics, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Yechezkel Kashi
- Laboratory of Applied Genomics, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Yoav D Livney
- Laboratory of Biopolymers for Food and Health, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
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Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Microbial transmission in the social microbiome and host health and disease. Cell 2024; 187:17-43. [PMID: 38181740 PMCID: PMC10958648 DOI: 10.1016/j.cell.2023.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Cameron J A McInroy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Siobhán Harty
- Independent, Tandy Court, Spitalfields, Dublin, Ireland
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK; Department of Computing, University of Turku, Turku, Finland
| | - Neil G O Ibata
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mireia Valles-Colomer
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Katerina V-A Johnson
- Institute of Psychology, Leiden University, Leiden, the Netherlands; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph Henrich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Francesca S Gazzaniga
- Molecular Pathology Unit, Cancer Center, Massachusetts General Hospital Research Institute, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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Spragge F, Bakkeren E, Jahn MT, B N Araujo E, Pearson CF, Wang X, Pankhurst L, Cunrath O, Foster KR. Microbiome diversity protects against pathogens by nutrient blocking. Science 2023; 382:eadj3502. [PMID: 38096285 DOI: 10.1126/science.adj3502] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023]
Abstract
The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonization of two major bacterial pathogens, both in vitro and in gnotobiotic mice. Whereas single species alone had negligible effects, colonization resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explained these ecological patterns through the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Furthermore, we applied our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities.
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Affiliation(s)
- Frances Spragge
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Erik Bakkeren
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Martin T Jahn
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Claire F Pearson
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Xuedan Wang
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louise Pankhurst
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Olivier Cunrath
- CNRS, UMR7242, Biotechnology and Cell Signaling, University of Strasbourg, Illkirch, France
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
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González L, Paredes Sosa JL, Mosquito S, Filio Y, Romero PE, Ochoa TJ, Tsukayama P. Oral lactoferrin administration does not impact the diversity or composition of the infant gut microbiota in a Peruvian cohort. Microbiol Spectr 2023; 11:e0009623. [PMID: 37882571 PMCID: PMC10715004 DOI: 10.1128/spectrum.00096-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/05/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Previous studies have suggested that oral lactoferrin enhances diversity in the gut microbiota in infants while inhibiting the growth of opportunistic pathogens. However, the effect of lactoferrin on infant gut microbiota over time has yet to be thoroughly studied. Our study suggests that lactoferrin oral treatment in infants aged 12-18 months does not affect gut microbiome diversity and composition over time. To our knowledge, this is the first study to report the effect of lactoferrin on infant gut microbiome composition over time and helps elucidate its impact on infant health and its therapeutic potential.
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Affiliation(s)
- Luis González
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru
| | - Jose Luis Paredes Sosa
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Susan Mosquito
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Yesenia Filio
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pedro E. Romero
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Theresa J. Ochoa
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
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9
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy. Int J Mol Sci 2023; 24:15201. [PMID: 37894882 PMCID: PMC10607084 DOI: 10.3390/ijms242015201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Juan Carlos Rodríguez
- Microbiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, 03010 Alicante, Spain;
| | - María-Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Carmen Molina-Pardines
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Francisco Marco-Jiménez
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
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10
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Villatoro-Castañeda M, Forsburg ZR, Ortiz W, Fritts SR, Gabor CR, Carlos-Shanley C. Exposure to Roundup and Antibiotics Alters Gut Microbial Communities, Growth, and Behavior in Rana berlandieri Tadpoles. BIOLOGY 2023; 12:1171. [PMID: 37759571 PMCID: PMC10525943 DOI: 10.3390/biology12091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
The gut microbiome is important for digestion, host fitness, and defense against pathogens, which provides a tool for host health assessment. Amphibians and their microbiomes are highly susceptible to pollutants including antibiotics. We explored the role of an unmanipulated gut microbiome on tadpole fitness and phenotype by comparing tadpoles of Rana berlandieri in a control group (1) with tadpoles exposed to: (2) Roundup® (glyphosate active ingredient), (3) antibiotic cocktail (enrofloxacin, sulfamethazine, trimethoprim, streptomycin, and penicillin), and (4) a combination of Roundup and antibiotics. Tadpoles in the antibiotic and combination treatments had the smallest dorsal body area and were the least active compared to control and Roundup-exposed tadpoles, which were less active than control tadpoles. The gut microbial community significantly changed across treatments at the alpha, beta, and core bacterial levels. However, we did not find significant differences between the antibiotic- and combination-exposed tadpoles, suggesting that antibiotic alone was enough to suppress growth, change behavior, and alter the gut microbiome composition. Here, we demonstrate that the gut microbial communities of tadpoles are sensitive to environmental pollutants, namely Roundup and antibiotics, which may have consequences for host phenotype and fitness via altered behavior and growth.
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Affiliation(s)
- Melissa Villatoro-Castañeda
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Zachery R. Forsburg
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
- Archbold Biological Station, 123 Main Dr., Venus, FL 33960, USA
| | - Whitney Ortiz
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
- Department of Molecular Microbiology and Immunology, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| | - Sarah R. Fritts
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Caitlin R. Gabor
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Camila Carlos-Shanley
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
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11
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Zhu L. Editorial: Animal social behaviour and gut microbiome. Front Microbiol 2023; 14:1210717. [PMID: 37614609 PMCID: PMC10443586 DOI: 10.3389/fmicb.2023.1210717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023] Open
Affiliation(s)
- Lifeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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12
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Tap J, Lejzerowicz F, Cotillard A, Pichaud M, McDonald D, Song SJ, Knight R, Veiga P, Derrien M. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nat Commun 2023; 14:3310. [PMID: 37339957 DOI: 10.1038/s41467-023-38558-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/04/2023] [Indexed: 06/22/2023] Open
Abstract
The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches' tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | | | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Patrick Veiga
- Danone Nutricia Research, Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Muriel Derrien
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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13
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Del Chierico F, Marzano V, Scanu M, Reddel S, Dentici ML, Capolino R, Di Donato M, Spasari I, Fiscarelli EV, Digilio MC, Abreu MT, Dallapiccola B, Putignani L. Analysis of gut microbiota in patients with Williams-Beuren Syndrome reveals dysbiosis linked to clinical manifestations. Sci Rep 2023; 13:9797. [PMID: 37328513 PMCID: PMC10275996 DOI: 10.1038/s41598-023-36704-1] [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: 02/24/2023] [Accepted: 06/08/2023] [Indexed: 06/18/2023] Open
Abstract
Williams-Beuren syndrome (WBS) is a multisystem genetic disease caused by the deletion of a region of 1.5-1.8 Mb on chromosome 7q11.23. The elastin gene seems to account for several comorbidities and distinct clinical features such including cardiovascular disease, connective tissue abnormalities, growth retardation, and gastrointestinal (GI) symptoms. Increasing evidence points to alterations in gut microbiota composition as a primary or secondary cause of some GI or extra-intestinal characteristics. In this study, we performed the first exploratory analysis of gut microbiota in WBS patients compared to healthy subjects (CTRLs) using 16S rRNA amplicon sequencing, by investigating the gut dysbiosis in relation to diseases and comorbidities. We found that patients with WBS have significant dysbiosis compared to age-matched CTRLs, characterized by an increase in proinflammatory bacteria such as Pseudomonas, Gluconacetobacter and Eggerthella, and a reduction of anti-inflammatory bacteria including Akkermansia and Bifidobacterium. Microbial biomarkers associated with weight gain, GI symptoms and hypertension were identified. Gut microbiota profiling could represent a new tool that characterise intestinal dysbiosis to complement the clinical management of these patients. In particular, the administration of microbial-based treatments, alongside traditional therapies, could help in reducing or preventing the burden of these symptoms and improve the quality of life of these patients.
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Affiliation(s)
- Federica Del Chierico
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Valeria Marzano
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Matteo Scanu
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sofia Reddel
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division and Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Genetics and Rare Diseases Research Division and Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maddalena Di Donato
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Iolanda Spasari
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ersilia Vita Fiscarelli
- Research Unit of Diagnostical and Management Innovations, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division and Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Teresa Abreu
- Crohn's and Colitis Center, Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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14
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Li L, Wang T, Ning Z, Zhang X, Butcher J, Serrana JM, Simopoulos CMA, Mayne J, Stintzi A, Mack DR, Liu YY, Figeys D. Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics. Nat Commun 2023; 14:3428. [PMID: 37301875 PMCID: PMC10257714 DOI: 10.1038/s41467-023-39149-2] [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: 11/05/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.
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Affiliation(s)
- Leyuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Zhibin Ning
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Xu Zhang
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Joeselle M Serrana
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Caitlin M A Simopoulos
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - David R Mack
- Department of Paediatrics, Faculty of Medicine, University of Ottawa and Children's Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Daniel Figeys
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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15
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Kazarina A, Kuzmicka J, Bortkevica S, Zayakin P, Kimsis J, Igumnova V, Sadovska D, Freimane L, Kivrane A, Namina A, Capligina V, Poksane A, Ranka R. Oral microbiome variations related to ageing: possible implications beyond oral health. Arch Microbiol 2023; 205:116. [PMID: 36920536 PMCID: PMC10016173 DOI: 10.1007/s00203-023-03464-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
The global population is getting older due to a combination of longer life expectancy and declining birth rates. Growing evidence suggests that the oral microbiota composition and distribution may have a profound effect on how well we age. The purpose of this study was to investigate age-related oral microbiome variations of supragingival plaque and buccal mucosa samples in the general population in Latvia. Our results indicated significant difference between supragingival plaque bacterial profiles of three age groups (20-40; 40-60; 60 + years). Within supragingival plaque samples, age group 20-40 showed the highest bacterial diversity with a decline during the 40-60 age period and uprise again after the age of 60. Among other differences, the important oral commensal Neisseria had declined after the age of 40. Additionally, prevalence of two well-documented opportunistic pathogens Streptococcus anginosus and Gemella sanguinis gradually rose with age within our samples. Furthermore, supragingival plaque and buccal mucosa samples significantly differed in overall bacterial composition.
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Affiliation(s)
- Alisa Kazarina
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia.
| | | | - Santa Bortkevica
- Riga Stradins University, 16 Dzirciema Str., Riga, LV-1007, Latvia
| | - Pawel Zayakin
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Janis Kimsis
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Viktorija Igumnova
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Darja Sadovska
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Lauma Freimane
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Agnija Kivrane
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Agne Namina
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Valentina Capligina
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Alise Poksane
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
| | - Renate Ranka
- Laboratory of Molecular Biology, Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., Riga, LV-1067, Latvia
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16
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Moraes MM, Mendes TT, Borges L, Marques AL, Núñez-Espinosa C, Gonçalves DAP, Simões CB, Vieira TS, Ladeira RVP, Lourenço TGB, Ribeiro DV, Hatanaka E, Heller D, Arantes RME. A 7-Week Summer Camp in Antarctica Induces Fluctuations on Human Oral Microbiome, Pro-Inflammatory Markers and Metabolic Hormones Profile. Microorganisms 2023; 11:microorganisms11020339. [PMID: 36838304 PMCID: PMC9960157 DOI: 10.3390/microorganisms11020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/31/2023] Open
Abstract
Antarctic camps pose psychophysiological challenges related to isolated, confined, and extreme (ICE) conditions, including meals composed of sealed food. ICE conditions can influence the microbiome and inflammatory responses. Seven expeditioners took part in a 7-week Antarctic summer camp (Nelson Island) and were evaluated at Pre-Camp (i.e., at the beginning of the ship travel), Camp-Initial (i.e., 4th and 5th day in camp), Camp-Middle (i.e., 19th-20th, and 33rd-34th days), Camp-Final (i.e., 45th-46th day), and at the Post-Camp (on the ship). At the Pre-Camp, Camp-Initial, and Camp-Final, we assessed microbiome and inflammatory markers. Catecholamines were accessed Pre- and Post-Camp. Heart rate variability (HRV), leptin, thyroid stimulating hormone (TSH), and thyroxine (T4) were accessed at all time points. Students' t-tests or repeated-measures analysis of variance (one or two-way ANOVA) followed by Student-Newman-Keuls (post hoc) were used for parametric analysis. Kruskal-Wallis test was applied for non-parametric analysis. Microbiome analysis showed a predominance of Pseudomonadota (34.01%), Bacillota (29.82%), and Bacteroidota (18.54%), followed by Actinomycetota (5.85%), and Fusobacteria (5.74%). Staying in a long-term Antarctic camp resulted in microbiome fluctuations with a reduction in Pseudomonadota-a "microbial signature" of disease. However, the pro-inflammatory marker leptin and IL-8 tended to increase, and the angiogenic factor VEGF was reduced during camp. These results suggest that distinct Antarctic natural environments and behavioral factors modulate oral microbiome and inflammation.
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Affiliation(s)
- Michele M. Moraes
- Department of Pathology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Center for Newborn Screening and Genetics Diagnosis, Faculty of Medicine, Universidade Federal de Minas Gerais, NUPAD-FM/UFMG, Belo Horizonte 30130-100, MG, Brazil
| | - Thiago T. Mendes
- Department of Physical Education, Faculty of Education, Universidade Federal da Bahia, Salvador 40170-110, BA, Brazil
| | - Leandro Borges
- Interdisciplinary Program in Health Sciences, Universidade Cruzeiro do Sul, São Paulo 01506-000, SP, Brazil
| | - Alice L. Marques
- Post-Graduation Program in Social Sciences in Development, Culture and Society of the Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, RJ, Brazil
| | - Cristian Núñez-Espinosa
- School of Medicine, Universidad de Magallanes, Punta Arenas 6200000, Chile
- Austral Integrative Neurophysiology Group, Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6200000, Chile
- Interuniversity Center for Healthy Aging, Punta Arenas 6200000, Chile
| | - Dawit A. P. Gonçalves
- Exercise Physiology Laboratory, School of Physical Education, Physiotherapy and Occupational Therapy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Sports Training Center, School of Physical Education, Physiotherapy and Occupational Therapy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Carolina B. Simões
- Exercise Physiology Laboratory, School of Physical Education, Physiotherapy and Occupational Therapy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Sports Training Center, School of Physical Education, Physiotherapy and Occupational Therapy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Tales S. Vieira
- Exercise Physiology Laboratory, School of Physical Education, Physiotherapy and Occupational Therapy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Roberto V. P. Ladeira
- Center for Newborn Screening and Genetics Diagnosis, Faculty of Medicine, Universidade Federal de Minas Gerais, NUPAD-FM/UFMG, Belo Horizonte 30130-100, MG, Brazil
| | - Talita G. B. Lourenço
- Oral Microbiology Laboratory, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Danielle V. Ribeiro
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
- Post-Graduate Studies in Dentistry, Universidade Cruzeiro do Sul, São Paulo 430-0926, SP, Brazil
| | - Elaine Hatanaka
- Interdisciplinary Program in Health Sciences, Universidade Cruzeiro do Sul, São Paulo 01506-000, SP, Brazil
| | - Debora Heller
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
- Post-Graduate Studies in Dentistry, Universidade Cruzeiro do Sul, São Paulo 430-0926, SP, Brazil
- Department of Periodontology, School of Dentistry, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Rosa M. E. Arantes
- Department of Pathology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Center for Newborn Screening and Genetics Diagnosis, Faculty of Medicine, Universidade Federal de Minas Gerais, NUPAD-FM/UFMG, Belo Horizonte 30130-100, MG, Brazil
- Correspondence: ; Tel.: +55-(31)-999037400
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17
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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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18
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Johnson KVA, Watson KK, Dunbar RIM, Burnet PWJ. Sociability in a non-captive macaque population is associated with beneficial gut bacteria. Front Microbiol 2022; 13:1032495. [PMID: 36439813 PMCID: PMC9691693 DOI: 10.3389/fmicb.2022.1032495] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022] Open
Abstract
The relationship between social behaviour and the microbiome is known to be reciprocal. Research in wild animal populations, particularly in primate social groups, has revealed the role that social interactions play in microbial transmission, whilst studies in laboratory animals have demonstrated that the gut microbiome can affect multiple aspects of behaviour, including social behaviour. Here we explore behavioural variation in a non-captive animal population with respect to the abundance of specific bacterial genera. Social behaviour based on grooming interactions is assessed in a population of rhesus macaques (Macaca mulatta), and combined with gut microbiome data. We focus our analyses on microbiome genera previously linked to sociability and autistic behaviours in rodents and humans. We show in this macaque population that some of these genera are also related to an individual's propensity to engage in social interactions. Interestingly, we find that several of the genera positively related to sociability, such as Faecalibacterium, are well known for their beneficial effects on health and their anti-inflammatory properties. In contrast, the genus Streptococcus, which includes pathogenic species, is more abundant in less sociable macaques. Our results indicate that microorganisms whose abundance varies with individual social behaviour also have functional links to host immune status. Overall, these findings highlight the connections between social behaviour, microbiome composition, and health in an animal population.
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Affiliation(s)
- Katerina V.-A. Johnson
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom,Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom,*Correspondence: Katerina V.-A. Johnson,
| | - Karli K. Watson
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, CO, United States
| | - Robin I. M. Dunbar
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
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19
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Creedon AC, Dimidi E, Hung ES, Rossi M, Probert C, Grassby T, Miguens-Blanco J, Marchesi JR, Scott SM, Berry SE, Whelan K. The impact of almonds and almond processing on gastrointestinal physiology, luminal microbiology, and gastrointestinal symptoms: a randomized controlled trial and mastication study. Am J Clin Nutr 2022; 116:1790-1804. [PMID: 36130222 PMCID: PMC9761756 DOI: 10.1093/ajcn/nqac265] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/16/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Almonds contain lipid, fiber, and polyphenols and possess physicochemical properties that affect nutrient bioaccessibility, which are hypothesized to affect gut physiology and microbiota. OBJECTIVES To investigate the impact of whole almonds and ground almonds (almond flour) on fecal bifidobacteria (primary outcome), gut microbiota composition, and gut transit time. METHODS Healthy adults (n = 87) participated in a parallel, 3-arm randomized controlled trial. Participants received whole almonds (56 g/d), ground almonds (56 g/d), or an isocaloric control in place of habitual snacks for 4 wk. Gut microbiota composition and diversity (16S rRNA gene sequencing), SCFAs (GC), volatile organic compounds (GC-MS), gut transit time (wireless motility capsule), stool output and gut symptoms (7-d diary) were measured at baseline and endpoint. The impact of almond form on particle size distribution (PSD) and predicted lipid release was measured (n = 31). RESULTS Modified intention-to-treat analysis was performed on 79 participants. There were no significant differences in mean ± SD abundance of fecal bifidobacteria after consumption of whole almonds (8.7% ± 7.7%), ground almonds (7.8% ± 6.9%), or control (13.0% ± 10.2%; q = 0.613). Consumption of almonds (whole and ground pooled) resulted in higher mean ± SD butyrate (24.1 ± 15.0 μmol/g) than control (18.2 ± 9.1 μmol/g; P = 0.046). There was no effect of almonds on gut microbiota at the phylum level or diversity, gut transit time, stool consistency, or gut symptoms. Almond form (whole compared with ground) had no effect on study outcomes. Ground almonds resulted in significantly smaller PSD and higher mean ± SD predicted lipid release (10.4% ± 1.8%) than whole almonds (9.3% ± 2.0%; P = 0.017). CONCLUSIONS Almond consumption has limited impact on microbiota composition but increases butyrate in adults, suggesting positive alterations to microbiota functionality. Almonds can be incorporated into the diet to increase fiber consumption without gut symptoms.This trial was registered at clinicaltrials.gov as NCT03581812.
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Affiliation(s)
- Alice C Creedon
- Department of Nutritional Sciences, King's College London, London, United Kingdom
| | - Eirini Dimidi
- Department of Nutritional Sciences, King's College London, London, United Kingdom
| | | | - Megan Rossi
- Department of Nutritional Sciences, King's College London, London, United Kingdom
| | - Christopher Probert
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Terri Grassby
- Department of Nutritional Sciences, University of Surrey, Guildford, United Kingdom
| | | | - Julian R Marchesi
- Division of Digestive Diseases, Imperial College London, London, United Kingdom
| | - S Mark Scott
- Department of Neuroscience, Surgery and Trauma, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, United Kingdom
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20
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Avalos-Fernandez M, Alin T, Métayer C, Thiébaut R, Enaud R, Delhaes L. The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis. Respir Res 2022; 23:214. [PMID: 35999634 PMCID: PMC9396807 DOI: 10.1186/s12931-022-02132-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/17/2022] [Indexed: 11/26/2022] Open
Abstract
Background While there seems to be a consensus that a decrease in gut microbiome diversity is related to a decline in health status, the associations between respiratory microbiome diversity and chronic lung disease remain a matter of debate. We provide a systematic review and meta-analysis of studies examining lung microbiota alpha-diversity in patients with asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF) or bronchiectasis (NCFB), in which a control group based on disease status or healthy subjects is provided for comparison. Results We reviewed 351 articles on title and abstract, of which 27 met our inclusion criteria for systematic review. Data from 24 of these studies were used in the meta-analysis. We observed a trend that CF patients have a less diverse respiratory microbiota than healthy individuals. However, substantial heterogeneity was present and detailed using random-effects models, which limits the comparison between studies. Conclusions Knowledge on respiratory microbiota is under construction, and for the moment, it seems that alpha-diversity measurements are not enough documented to fully understand the link between microbiota and health, excepted in CF context which represents the most studied chronic respiratory disease with consistent published data to link alpha-diversity and lung function. Whether differences in respiratory microbiota profiles have an impact on chronic respiratory disease symptoms and/or evolution deserves further exploration. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02132-4.
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Affiliation(s)
- Marta Avalos-Fernandez
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France. .,SISTM team Inria BSO, F-33405, Talence, France.
| | - Thibaud Alin
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France
| | - Clémence Métayer
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France
| | - Rodolphe Thiébaut
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France.,Pole of Public Health, University Hospital of Bordeaux, F-33000, Bordeaux, France
| | - Raphaël Enaud
- Cystic fibrosis centre (CRCM), Paediatrics Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,Parasitology-Mycology Department, University Hospital of Bordeaux, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Cystic fibrosis centre (CRCM), Paediatrics Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,Parasitology-Mycology Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,University of Bordeaux, Bordeaux Cardio-Thoracic Research Center, U1045, INSERM, F-33000, Bordeaux, France
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21
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Jung JH, Kim SE, Suk KT, Kim DJ. Gut microbiota-modulating agents in alcoholic liver disease: Links between host metabolism and gut microbiota. Front Med (Lausanne) 2022; 9:913842. [PMID: 35935787 PMCID: PMC9354621 DOI: 10.3389/fmed.2022.913842] [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: 04/06/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Alcoholic liver disease (ALD) involves a wide spectrum of diseases, including asymptomatic hepatic steatosis, alcoholic hepatitis, hepatic fibrosis, and cirrhosis, which leads to morbidity and mortality and is responsible for 0.9% of global deaths. Alcohol consumption induces bacterial translocation and alteration of the gut microbiota composition. These changes in gut microbiota aggravate hepatic inflammation and fibrosis. Alteration of the gut microbiota leads to a weakened gut barrier and changes host immunity and metabolic function, especially related to bile acid metabolism. Modulation and treatment for the gut microbiota in ALD has been studied using probiotics, prebiotics, synbiotics, and fecal microbial transplantation with meaningful results. In this review, we focused on the interaction between alcohol and gut dysbiosis in ALD. Additionally, treatment approaches for gut dysbiosis, such as abstinence, diet, pro-, pre-, and synbiotics, antibiotics, and fecal microbial transplantation, are covered here under ALD. However, further research through human clinical trials is warranted to evaluate the appropriate gut microbiota-modulating agents for each condition related to ALD.
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Affiliation(s)
- Jang Han Jung
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, South Korea
| | - Sung-Eun Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, South Korea
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Ki Tae Suk
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, South Korea
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Dong Joon Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, South Korea
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
- *Correspondence: Dong Joon Kim,
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22
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Principal Amalgamation Analysis for Microbiome Data. Genes (Basel) 2022; 13:genes13071139. [PMID: 35885922 PMCID: PMC9318429 DOI: 10.3390/genes13071139] [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: 05/03/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 12/02/2022] Open
Abstract
In recent years microbiome studies have become increasingly prevalent and large-scale. Through high-throughput sequencing technologies and well-established analytical pipelines, relative abundance data of operational taxonomic units and their associated taxonomic structures are routinely produced. Since such data can be extremely sparse and high dimensional, there is often a genuine need for dimension reduction to facilitate data visualization and downstream statistical analysis. We propose Principal Amalgamation Analysis (PAA), a novel amalgamation-based and taxonomy-guided dimension reduction paradigm for microbiome data. Our approach aims to aggregate the compositions into a smaller number of principal compositions, guided by the available taxonomic structure, by minimizing a properly measured loss of information. The choice of the loss function is flexible and can be based on familiar diversity indices for preserving either within-sample or between-sample diversity in the data. To enable scalable computation, we develop a hierarchical PAA algorithm to trace the entire trajectory of successive simple amalgamations. Visualization tools including dendrogram, scree plot, and ordination plot are developed. The effectiveness of PAA is demonstrated using gut microbiome data from a preterm infant study and an HIV infection study.
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23
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Raabis SM, Holschbach CL, Skarlupka JH, Suen G, Ollivett TL. Assessing the effects of experimental bacterial challenge with Pasteurella multocida and ampicillin on the respiratory microbiota of pre-weaned Holstein calves. Vet Microbiol 2022; 269:109428. [PMID: 35427993 PMCID: PMC11215343 DOI: 10.1016/j.vetmic.2022.109428] [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: 07/02/2021] [Revised: 03/08/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
The association between changes in the respiratory microbiota and Bovine Respiratory Disease (BRD) in dairy calves is not well understood. We investigated characteristics of the nasopharyngeal (NP) microbiota associated with BRD following Pasteurella multocida infection. We also evaluated the effect of ampicillin on the respiratory microbiota. Calves (n = 30) were inoculated with P. multocida and randomly allocated into an antibiotic group (AMP; n = 17) or placebo group (PLAC; n = 11) when lung lesions developed. Deep NP swabs (DNPS) were collected before and after challenge. Monitoring was performed daily until euthanasia at day 14. Swabs and tissue samples were collected for analysis. The V4 hypervariable region of the 16 S rRNA gene was amplified and sequenced on an Illumina MiSeq. Increased species abundance in the pre-challenge DNPS was associated with a decrease in cumulative respiratory disease over 14 days post-infection. While NP beta diversity was affected by infection, antibiotic therapy showed no effect on the alpha and beta diversity nor the relative abundance (RA) of genera in the NP tonsil, lymph node and lung microbiota. Antibiotic therapy was associated with an increased RA of NP Pasteurella spp. and a decreased RA of NP Prevotella spp. Common taxa among all samples included GIT-associated bacteria, which suggests a possible link between the GIT microbiota and respiratory microbiota in dairy calves.
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Affiliation(s)
- Sarah M Raabis
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Chelsea L Holschbach
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Joseph H Skarlupka
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Theresa L Ollivett
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, United States.
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24
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Ding X, Jin F, Xu J, Zhang S, Chen D, Hu B, Hong Y. The impact of aquaculture system on the microbiome and gut metabolome of juvenile Chinese softshell turtle ( Pelodiscus sinensis). IMETA 2022; 1:e17. [PMID: 38868566 PMCID: PMC10989827 DOI: 10.1002/imt2.17] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2024]
Abstract
The commercial aquatic animal microbiome may markedly affect the successful host's farming in various aquaculture systems. However, very little was known about it. Here, two different aquaculture systems, the rice-fish culture (RFC) and intensive pond culture (IPC) systems, were compared to deconstruct the skin, oral, and gut microbiome, as well as the gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis). Higher alpha-diversity and functional redundancy of P. sinensis microbial community were found in the RFC than those of the IPC. The aquaculture systems have the strongest influence on the gut microbiome, followed by the skin microbiome, and finally the oral microbiome. Source-tracking analysis showed that the RFC's microbial community originated from more unknown sources than that of the IPC across all body regions. Strikingly, the RFC's oral and skin microbiome exhibited a significantly higher proportion of generalists and broader habitat niche breadth than those of the IPC, but not the gut. Null model analysis revealed that the RFC's oral and skin microbial community assembly was governed by a significantly greater proportion of deterministic processes than that of the IPC, but not the gut. We further identified the key gene and microbial contribution to five significantly changed gut metabolites, 2-oxoglutarate, N-acetyl-d-mannosamine, cis-4-hydroxy-d-proline, nicotinamide, and l-alanine, which were significantly correlated with important categories of microbe-mediated processes, including the amino acid metabolism, GABAergic synapse, ABC transporters, biosynthesis of unsaturated fatty acids, as well as citrate cycle. Moreover, different aquaculture systems have a significant impact on the hepatic lipid metabolism and body shape of P. sinensis. Our results provide new insight into the influence of aquaculture systems on the microbial community structure feature and assembly mechanism in an aquatic animal, also highlighting the key microbiome and gene contributions to the metabolite variation in the gut microbiome-metabolome association.
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Affiliation(s)
- Xia Ding
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Feng Jin
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Jiawang Xu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Shulei Zhang
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Dongxu Chen
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Beijuan Hu
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
| | - Yijiang Hong
- School of Life SciencesNanchang UniversityNanchangJiangxiChina
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25
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Theofilou VI, Alfaifi A, Montelongo-Jauregui D, Pettas E, Georgaki M, Nikitakis NG, Jabra-Rizk MA, Sultan AS. The oral mycobiome: Oral epithelial dysplasia and oral squamous cell carcinoma. J Oral Pathol Med 2022; 51:413-420. [PMID: 35347760 DOI: 10.1111/jop.13295] [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: 12/18/2021] [Revised: 02/16/2022] [Accepted: 03/20/2022] [Indexed: 12/16/2022]
Abstract
Fungi, a diverse group of eukaryotic organisms, play distinct roles in health and disease. Recent advances in the field of mycobiology have enabled the characterization of the "human mycobiome." The human mycobiome has extensively been studied in various disease models. However, to date, the role of the oral mycobiome in oral carcinogenesis has yet to be elucidated. Candida albicans, the most common oral colonizer, has been speculated to display tumorigenic effects; however, the literature lacks consistent documentation from mechanistic studies on whether oral mycobiota act as drivers, facilitators, or passive colonizers of oral premalignancy and cancer. This review article provides an overview of existing hypothesis-driven mechanistic models that outline the complex interplay between the oral mycobiome and oral epithelial dysplasia as well as their potential clinical implications.
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Affiliation(s)
- Vasileios Ionas Theofilou
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, Maryland, USA.,Department of Oral Medicine & Pathology and Hospital Dentistry, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Areej Alfaifi
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, Maryland, USA.,Department of Restorative and Prosthetic Dental Sciences, College of Dentistry King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Daniel Montelongo-Jauregui
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Efstathios Pettas
- Department of Oral Medicine & Pathology and Hospital Dentistry, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Georgaki
- Department of Oral Medicine & Pathology and Hospital Dentistry, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos G Nikitakis
- Department of Oral Medicine & Pathology and Hospital Dentistry, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Mary-Ann Jabra-Rizk
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, Maryland, USA.,Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Ahmed S Sultan
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, Maryland, USA.,Program in Oncology, University of Maryland Greenebaum Cancer Center, Baltimore, Maryland, USA
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26
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Peng X, Huang Y, Wang G, He Y, Hu L, Fang Z, Lin Y, Xu S, Feng B, Li J, Tang J, Hua L, Jiang X, Zhuo Y, Che L, Wu D. Maternal Long-Term Intake of Inulin Improves Fetal Development through Gut Microbiota and Related Metabolites in a Rat Model. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1840-1851. [PMID: 35129337 DOI: 10.1021/acs.jafc.1c07284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Adequate dietary fiber intake during gestation is critical for maternal-fetal health. This experiment aims to uncover the impacts of maternal long-term intake of inulin on fetal development and its underlying mechanism. Eighty female Sprague-Dawley rats were randomly assigned to two groups receiving either a fiber-free diet or an inulin diet (inulin) for three parities. On the 19th day of pregnancy in the third parity, blood, intestinal, placental, and colonic digesta samples were collected. Results showed that maternal intake of inulin significantly decreased the within-litter birth weight variation in parities 2 and 3. Inulin intake modified the gut microbiome profiles and elevated the colonic contents of short chain fatty acids (propionate and butyrate). Inulin decreased the serotonin (5-HT) concentration in the colon, whereas it increased the 5-HT concentrations in serum and placenta and the number of 5-HT+ enterochromaffin cells in the colon. The protein expression of melatonin-synthesizing enzyme (arylalkylamine N-acetyltransferase) and the melatonin concentration in the placenta were also increased by inulin. Inulin improved the placental redox status and nutrient transport. These findings indicated that maternal long-term intake of inulin improves fetal development by altering the intestinal microbiota and related metabolites in rats.
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Affiliation(s)
- Xie Peng
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yingyan Huang
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guixiang Wang
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ying He
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang Hu
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhengfeng Fang
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Lin
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengyu Xu
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Feng
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jian Li
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiayong Tang
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lun Hua
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuemei Jiang
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Zhuo
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lianqiang Che
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - De Wu
- Key Laboratory for Animal Disease Resistant Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China
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27
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Leclaire S, Pineaux M, Blanchard P, White J, Hatch SA. Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird. Mol Ecol 2022; 32:2115-2133. [PMID: 35152516 DOI: 10.1111/mec.16398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
Abstract
The microbiota is suggested to be a fundamental contributor to host reproduction and survival, but associations between microbiota and fitness are rare, especially for wild animals. Here, we tested the association between microbiota and two proxies of breeding performance in multiple body sites of the black-legged kittiwake, a seabird species. First we found that, in females, nonbreeders (i.e., birds that did not lay eggs) hosted different microbiota composition to that of breeders in neck and flank feathers, in the choanae, in the outer-bill and in the cloacae, but not in preen feathers and tracheae. These differences in microbiota might reflect variations in age or individual quality between breeders and nonbreeders. Second, we found that better female breeders (i.e., with higher body condition, earlier laying date, heavier eggs, larger clutch, and higher hatching success) had lower abundance of several Corynebacteriaceae in cloaca than poorer female breeders, suggesting that these bacteria might be pathogenic. Third, in females, better breeders had different microbiota composition and lower microbiota diversity in feathers, especially in preen feathers. They had also reduced dispersion in microbiota composition across body sites. These results might suggest that good breeding females are able to control their feather microbiota-potentially through preen secretions-more tightly than poor breeding females. We did not find strong evidence for an association between reproductive outcome and microbiota in males. Our results are consistent with the hypothesis that natural variation in the microbiota is associated with differences in host fitness in wild animals, but the causal relationships remain to be investigated.
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Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Maxime Pineaux
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Pierrick Blanchard
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Joël White
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
- ENSFEA Castanet‐Tolosan France
| | - Scott A Hatch
- Institute for Seabird Research and Conservation Anchorage AK 99516 USA
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28
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Abstract
Objective: Hormone therapy (HT) is used to treat menopause-related conditions and symptoms. The small intestine plays key roles in metabolic and endocrine function, but the effects of HT on the small intestinal microbiome are unknown. Here, we characterize duodenal microbiome differences, and the effects of HT, in postmenopausal women. Methods: Female participants undergoing esophagogastroduodenoscopy who were postmenopausal and taking HT (HT+), postmenopausal but not taking HT (HT−), or of reproductive age and not taking exogenous hormones (RA), were identified and matched for body mass index (±3 kg/m2). DNAs were isolated from duodenal aspirates obtained during upper endoscopy. V3 and V4 libraries were used for 16S rRNA sequencing. Serum hormone levels were analyzed by Luminex FlexMap. Results: The core duodenal microbiome was different in HT− participants (n = 12) when compared with RA participants (n = 10), but more similar in HT+ (n = 13) and RA participants. HT− participants had increased Proteobacteria taxa, leading to greater microbial dysbiosis compared with HT+ participants, and had decreased prevalence of Bacteroidetes, which was associated with higher fasting glucose levels, lower duodenal microbial diversity, and lower testosterone levels. HT+ participants had significantly higher estradiol (P = 0.04) and progesterone (P = 0.04), and lower fasting glucose (P = 0.03), than HT− participants, and had increased relative abundance of Prevotella (P = 0.01), and decreased Escherichia (P = 1.12E-7), Klebsiella (P = 5.93E-7), and Lactobacillus (P = 0.02), all associated with lower cardiovascular disease risks. Conclusions: These findings support previous studies suggesting that HT may have beneficial effects following menopause, and although preliminary, may also support a beneficial effect of HT on the duodenal microbiome.
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29
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Fernández J, Fernández-Sanjurjo M, Iglesias-Gutiérrez E, Martínez-Camblor P, Villar CJ, Tomás-Zapico C, Fernández-García B, Lombó F. Resistance and Endurance Exercise Training Induce Differential Changes in Gut Microbiota Composition in Murine Models. Front Physiol 2022; 12:748854. [PMID: 35002754 PMCID: PMC8739997 DOI: 10.3389/fphys.2021.748854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/01/2021] [Indexed: 11/27/2022] Open
Abstract
Background: The effect of resistance training on gut microbiota composition has not been explored, despite the evidence about endurance exercise. The aim of this study was to compare the effect of resistance and endurance training on gut microbiota composition in mice. Methods: Cecal samples were collected from 26 C57BL/6N mice, divided into three groups: sedentary (CTL), endurance training on a treadmill (END), and resistance training on a vertical ladder (RES). After 2 weeks of adaption, mice were trained for 4 weeks, 5 days/week. Maximal endurance and resistance capacity test were performed before and after training. Genomic DNA was extracted and 16S Ribosomal RNA sequenced for metagenomics analysis. The percentages for each phylum, class, order, family, or genus/species were obtained using an open-source bioinformatics pipeline. Results: END showed higher diversity and evenness. Significant differences among groups in microbiota composition were only observed at genera and species level. END showed a significantly higher relative abundance of Desulfovibrio and Desulfovibrio sp., while Clostridium and C. cocleatum where higher for RES. Trained mice showed significantly lower relative abundance of Ruminococcus gnavus and higher of the genus Parabacteroides compared to CTL. We explored the relationship between relative taxa abundance and maximal endurance and resistance capacities after the training period. Lachnospiraceae and Lactobacillaceae families were negatively associated with endurance performance, while several taxa, including Prevotellaceae family, Prevotella genus, and Akkermansia muciniphila, were positively correlated. About resistance performance, Desulfovibrio sp. was negatively correlated, while Alistipes showed a positive correlation. Conclusion: Resistance and endurance training differentially modify gut microbiota composition in mice, under a high-controlled environment. Interestingly, taxa associated with anti- and proinflammatory responses presented the same pattern after both models of exercise. Furthermore, the abundance of several taxa was differently related to maximal endurance or resistance performance, most of them did not respond to training.
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Affiliation(s)
- Javier Fernández
- Department of Functional Biology, Microbiology, University of Oviedo, Oviedo, Spain.,Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - Manuel Fernández-Sanjurjo
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.,Department of Functional Biology, Physiology, University of Oviedo, Oviedo, Spain
| | - Eduardo Iglesias-Gutiérrez
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.,Department of Functional Biology, Physiology, University of Oviedo, Oviedo, Spain
| | - Pablo Martínez-Camblor
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Claudio J Villar
- Department of Functional Biology, Microbiology, University of Oviedo, Oviedo, Spain.,Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - Cristina Tomás-Zapico
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.,Department of Functional Biology, Physiology, University of Oviedo, Oviedo, Spain
| | - Benjamin Fernández-García
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.,Department of Morphology and Cell Biology, Anatomy, University of Oviedo, Oviedo, Spain
| | - Felipe Lombó
- Department of Functional Biology, Microbiology, University of Oviedo, Oviedo, Spain.,Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
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30
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Xu Y, Nash K, Acharjee A, Gkoutos GV. CACONET: a novel classification framework for microbial correlation networks. Bioinformatics 2022; 38:1639-1647. [PMID: 34983063 PMCID: PMC8896646 DOI: 10.1093/bioinformatics/btab879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/15/2021] [Accepted: 12/30/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Existing microbiome-based disease prediction relies on the ability of machine learning methods to differentiate disease from healthy subjects based on the observed taxa abundance across samples. Despite numerous microbes have been implicated as potential biomarkers, challenges remain due to not only the statistical nature of microbiome data but also the lack of understanding of microbial interactions which can be indicative of the disease. RESULTS We propose CACONET (classification of Compositional-Aware COrrelation NETworks), a computational framework that learns to classify microbial correlation networks and extracts potential signature interactions, taking as input taxa relative abundance across samples and their health status. By using Bayesian compositional-aware correlation inference, a collection of posterior correlation networks can be drawn and used for graph-level classification, thus incorporating uncertainty in the estimates. CACONET then employs a deep learning approach for graph classification, achieving excellent performance metrics by exploiting the correlation structure. We test the framework on both simulated data and a large real-world dataset pertaining to microbiome samples of colorectal cancer (CRC) and healthy subjects, and identify potential network substructure characteristic of CRC microbiota. CACONET is customizable and can be adapted to further improve its utility. AVAILABILITY AND IMPLEMENTATION CACONET is available at https://github.com/yuanwxu/corr-net-classify. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuanwei Xu
- To whom correspondence should be addressed.
| | - Katrina Nash
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Animesh Acharjee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK,NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham B15 2TT, UK,Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK,MRC Health Data Research UK (HDR), Midlands Site B15 2TT, UK
| | - Georgios V Gkoutos
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK,NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham B15 2TT, UK,Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK,MRC Health Data Research UK (HDR), Midlands Site B15 2TT, UK
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31
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Worsley SF, Davies CS, Mannarelli ME, Hutchings MI, Komdeur J, Burke T, Dugdale HL, Richardson DS. Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population. Anim Microbiome 2021; 3:84. [PMID: 34930493 PMCID: PMC8685825 DOI: 10.1186/s42523-021-00149-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/28/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The vertebrate gut microbiome (GM) can vary substantially across individuals within the same natural population. Although there is evidence linking the GM to health in captive animals, very little is known about the consequences of GM variation for host fitness in the wild. Here, we explore the relationship between faecal microbiome diversity, body condition, and survival using data from the long-term study of a discrete natural population of the Seychelles warbler (Acrocephalus sechellensis) on Cousin Island. To our knowledge, this is the first time that GM differences associated with survival have been fully characterised for a natural vertebrate species, across multiple age groups and breeding seasons. RESULTS We identified substantial variation in GM community structure among sampled individuals, which was partially explained by breeding season (5% of the variance), and host age class (up to 1% of the variance). We also identified significant differences in GM community membership between adult birds that survived, versus those that had died by the following breeding season. Individuals that died carried increased abundances of taxa that are known to be opportunistic pathogens, including several ASVs in the genus Mycobacterium. However, there was no association between GM alpha diversity (the diversity of bacterial taxa within a sample) and survival to the next breeding season, or with individual body condition. Additionally, we found no association between GM community membership and individual body condition. CONCLUSIONS These results demonstrate that components of the vertebrate GM can be associated with host fitness in the wild. However, further research is needed to establish whether changes in bacterial abundance contribute to, or are only correlated with, differential survival; this will add to our understanding of the importance of the GM in the evolution of host species living in natural populations.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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Toribio-Mateas MA, Bester A, Klimenko N. Impact of Plant-Based Meat Alternatives on the Gut Microbiota of Consumers: A Real-World Study. Foods 2021; 10:2040. [PMID: 34574149 PMCID: PMC8465665 DOI: 10.3390/foods10092040] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
Eating less meat is increasingly seen as a healthier, more ethical option. This is leading to growing numbers of flexitarian consumers looking for plant-based meat alternatives (PBMAs) to replace at least some of the animal meat they consume. Popular PBMA products amongst flexitarians, including plant-based mince, burgers, sausages and meatballs, are often perceived as low-quality, ultra-processed foods. However, we argue that the mere industrial processing of ingredients of plant origin does not make a PBMA product ultra-processed by default. To test our hypothesis, we conducted a randomised controlled trial to assess the changes to the gut microbiota of a group of 20 participants who replaced several meat-containing meals per week with meals cooked with PBMA products and compared these changes to those experienced by a size-matched control. Stool samples were subjected to 16S rRNA sequencing. The resulting raw data was analysed in a compositionality-aware manner, using a range of innovative bioinformatic methods. Noteworthy changes included an increase in butyrate metabolising potential-chiefly in the 4-aminobutyrate/succinate and glutarate pathways-and in the joint abundance of butyrate-producing taxa in the intervention group compared to control. We also observed a decrease in the Tenericutes phylum in the intervention group and an increase in the control group. Based on our findings, we concluded that the occasional replacement of animal meat with PBMA products seen in flexitarian dietary patterns can promote positive changes in the gut microbiome of consumers.
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Affiliation(s)
- Miguel A. Toribio-Mateas
- School of Applied Sciences, London South Bank University, London SE1 0AA, UK;
- School of Health and Education, Middlesex University, London SE1 0AA, UK
| | - Adri Bester
- School of Applied Sciences, London South Bank University, London SE1 0AA, UK;
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
- Research and Development Department, Knomics LLC, Skolkovo Innovation Center, 121205 Moscow, Russia
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Goolam Mahomed T, Peters R, Pretorius G, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome. BMC Microbiol 2021; 21:228. [PMID: 34407769 PMCID: PMC8371770 DOI: 10.1186/s12866-021-02288-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/29/2021] [Indexed: 12/23/2022] Open
Abstract
Background Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. Methods Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. Results Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. Conclusions It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02288-x.
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Affiliation(s)
- T Goolam Mahomed
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rph Peters
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,CAPHRI School for Public Health & Primary Care, Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | | | - V Ueckermann
- Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Tshwane, South Africa
| | - M M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. .,Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Tshwane, South Africa.
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35
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Martínez-Cuesta MC, Del Campo R, Garriga-García M, Peláez C, Requena T. Taxonomic Characterization and Short-Chain Fatty Acids Production of the Obese Microbiota. Front Cell Infect Microbiol 2021; 11:598093. [PMID: 34222034 PMCID: PMC8242951 DOI: 10.3389/fcimb.2021.598093] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Intestinal microbiota seems to play a key role in obesity. The impact of the composition and/or functionality of the obesity-associated microbiota have yet to be fully characterized. This work assessed the significance of the taxonomic composition and/or metabolic activity of obese- microbiota by massive 16S rRNA gene sequencing of the fecal microbiome of obese and normoweight individuals. The obese metabolic activity was also assessed by in vitro incubation of obese and normoweight microbiotas in nutritive mediums with different energy content. We found that the microbiome richness and diversity of the two groups did not differ significantly, except for Chao1 index, significantly higher in normoweight individuals. At phylum level, neither the abundance of Firmicutes or Bacteroidetes nor their ratio was associated with the body mass index. Besides, the relative proportions in Collinsella, Clostridium XIVa, and Catenibacterium were significantly enriched in obese participants, while Alistipes, Clostridium sensu stricto, Romboutsia, and Oscillibacter were significantly diminished. In regard to metabolic activity, short-chain fatty acids content was significant higher in obese individuals, with acetate being the most abundant followed by propionate and butyrate. Acetate and butyrate production was also higher when incubating obese microbiota in mediums mimicking diets with different energy content; interestingly, a reduced capability of propionate production was associated to the obese microbiome. In spite of the large interindividual variability, the obese phenotype seems to be defined more by the abundance and/or the absence of distinct communities of microorganism rather than by the presence of a specific population.
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Affiliation(s)
- M Carmen Martínez-Cuesta
- Department of Food Biotechnology and Microbiology, Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), Madrid, Spain
| | - Rosa Del Campo
- Microbiology Department, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | - Carmen Peláez
- Department of Food Biotechnology and Microbiology, Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), Madrid, Spain
| | - Teresa Requena
- Department of Food Biotechnology and Microbiology, Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), Madrid, Spain
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Reframing Nutritional Microbiota Studies To Reflect an Inherent Metabolic Flexibility of the Human Gut: a Narrative Review Focusing on High-Fat Diets. mBio 2021; 12:mBio.00579-21. [PMID: 33849977 PMCID: PMC8092254 DOI: 10.1128/mbio.00579-21] [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] [Indexed: 02/07/2023] Open
Abstract
There is a broad consensus in nutritional-microbiota research that high-fat (HF) diets are harmful to human health, at least in part through their modulation of the gut microbiota. However, various studies also support the inherent flexibility of the human gut and our microbiota’s ability to adapt to a variety of food sources, suggesting a more nuanced picture. There is a broad consensus in nutritional-microbiota research that high-fat (HF) diets are harmful to human health, at least in part through their modulation of the gut microbiota. However, various studies also support the inherent flexibility of the human gut and our microbiota’s ability to adapt to a variety of food sources, suggesting a more nuanced picture. In this article, we first discuss some problems facing basic translational research and provide a different framework for thinking about diet and gut health in terms of metabolic flexibility. We then offer evidence that well-formulated HF diets, such as ketogenic diets, may provide healthful alternative fuel sources for the human gut. We place this in the context of cancer research, where this concern over HF diets is also expressed, and consider various potential objections concerning the effects of lipopolysaccharides, trimethylamine-N-oxide, and secondary bile acids on human gut health. We end by providing some general suggestions for how to improve research and clinical practice with respect to the gut microbiota when considering the framework of metabolic flexibility.
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37
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Kong X, Liu J, Liu K, Koh M, Tian R, Hobbie C, Fong M, Chen Q, Zhao M, Budjan C, Kong J. Altered Autonomic Functions and Gut Microbiome in Individuals with Autism Spectrum Disorder (ASD): Implications for Assisting ASD Screening and Diagnosis. J Autism Dev Disord 2021; 51:144-157. [PMID: 32410097 DOI: 10.1007/s10803-020-04524-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorder (ASD) is a complex neurological and developmental disorder, and a growing body of literature suggests the presence of autonomic nervous system (ANS) dysfunction in individuals with ASD. ANS is part of the "gut brain axis", which consists of an intricate interplay between the gut microbiome, mucosal immune system, enteric nervous system, ANS, and central processes receiving input from the vagus nerve. Measurements of the gut microbiome and the autonomic indices can serve as non-invasive markers of the status of the gut-brain axis in ASD. To our knowledge, no previous studies have explored the relationship between ANS and gut microbiome in individuals with ASD. Furthermore, while previous studies investigated the use of autonomic indices and gut microbiome independently as markers of ASD-related comorbidities, such as anxiety, cardiovascular issues, and gastrointestinal dysfunction, the use of combined autonomic indices and gut microbiome factors to classify ASD and control subjects has not been explored. In this study, we characterized autonomic function of a group of individuals with ASD in comparison to their paired, first-degree relative controls. Second, we explored the ASD gut-brain-axis through the relationship between gut microbiome markers and autonomic indices, as well as the correlation between the gut-brain-axis and clinical presentation of ASD. Lastly, this study explores the predictive capability of gut-brain-axis biomarkers (including autonomic and microbiome indices) in subtyping ASD cases, serving as a starting point to investigate the possibility of assisting in ASD screening and diagnosis that still heavily relies on psychological testing, which may be based on highly subjective standards.
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Affiliation(s)
- Xuejun Kong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA. .,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Jun Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Kevin Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Madelyn Koh
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Ruiyi Tian
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Clara Hobbie
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Michelle Fong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Qiuyi Chen
- Bentley University, 175 Forest St, Waltham, MA, 02452, USA
| | - Minxuan Zhao
- Bentley University, 175 Forest St, Waltham, MA, 02452, USA
| | - Christoph Budjan
- Dana Faber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Jian Kong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street Charlestown, Boston, MA, 02129, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
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Loftus M, Hassouneh SAD, Yooseph S. Bacterial community structure alterations within the colorectal cancer gut microbiome. BMC Microbiol 2021; 21:98. [PMID: 33789570 PMCID: PMC8011136 DOI: 10.1186/s12866-021-02153-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/16/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome. RESULTS By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome. CONCLUSIONS We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.
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Affiliation(s)
- Mark Loftus
- Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, 32816, FL, USA
| | - Sayf Al-Deen Hassouneh
- Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, 32816, FL, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, 32816, USA.
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Raabis SM, Quick AE, Skarlupka JH, Suen G, Ollivett TL. The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung lesions. J Dairy Sci 2021; 104:3386-3402. [PMID: 33455760 PMCID: PMC11232363 DOI: 10.3168/jds.2020-19096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/17/2020] [Indexed: 12/18/2022]
Abstract
The primary objective of this cross-sectional study was to identify associations between the diversity and composition of the nasopharyngeal (NP) microbiota and pneumonia status, as diagnosed by ultrasonography (US), in preweaned dairy calves. Characteristics of the NP microbiota were compared between calves with and without pneumonia, as diagnosed by US. Secondary objectives were to compare the composition of the NP microbiota between calves by age, clinical respiratory score (CRS), and previous antibiotic therapy. Holstein heifer calves (n = 50) from a southern Wisconsin dairy were enrolled at either 3 or 6 wk of age; 4 calves were sampled at both time points. Antibiotic treatment history was also collected for the 30 d before enrollment. For the purpose of this study, pneumonia was defined as having lobar pneumonia, as diagnosed by US, in at least 1 lung lobe. Following examination by CRS and US, a deep nasopharyngeal swab was obtained for 16S rRNA amplicon sequencing. Alpha diversity was reduced in calves that were CRS positive, and beta diversity tended to be different in calves previously treated with antibiotics and in calves that were CRS positive. Microbial diversity was not different between calves with and without pneumonia. The most dominant genus identified was Mycoplasma spp.; however, there was no association between relative abundance (RA) and pneumonia status. The median RA of Mycoplasma spp. was increased by 25 (95% confidence interval, CI: 3, 40) in calves at 3 wk of age compared with 6 wk of age. The median RA of Pasteurella spp. was increased by 1.5 (95% CI: 0.1, 3) in calves with pneumonia, as diagnosed by US, compared with calves without pneumonia. Additionally, Pasteurella spp. was increased by 2.3 (95% CI: 0, 9) in CRS-positive calves compared with CRS-negative calves. The median RA of Psychrobacter spp. was increased by 2 (95% CI: 0, 12) and median RA of Chryseobacterium spp. was increased by 0.15 (95% CI: 0, 2) in calves that were not treated previously with antibiotics compared with calves previously treated with antibiotics.
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Affiliation(s)
- S M Raabis
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison 53706
| | - A E Quick
- Department of Animal and Dairy Science, University of Wisconsin, Madison 53706
| | - J H Skarlupka
- Department of Bacteriology, University of Wisconsin, Madison 53706
| | - G Suen
- Department of Bacteriology, University of Wisconsin, Madison 53706
| | - T L Ollivett
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison 53706.
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Sasaki K, Sasaki D, Tsuge Y, Morita M, Kondo A. Enhanced methane production from cellulose using a two-stage process involving a bioelectrochemical system and a fixed film reactor. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:7. [PMID: 33407783 PMCID: PMC7789537 DOI: 10.1186/s13068-020-01866-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND It is desirable to improve the anaerobic digestion processes of recalcitrant materials, such as cellulose. Enhancement of methane (CH4) production from organic molecules was previously accomplished through coupling a bioelectrochemical system (BES); however, scaling-up BES-based production is difficult. Here, we developed a two-stage process consisting of a BES using low-cost and low-reactive carbon sheets as the cathode and anode, and a fixed film reactor (FFR) containing conductive material, i.e., carbon fiber textiles (CFTs) (:BES → FFR). By controlling the cathodic current at 2.7 μA/cm2 without abiotic H2 production, the three-electrode BES system was operated to mimic a microbial electrolysis cell. RESULTS The thermophilic BES (inlet pH: 6.1) and FFR (inlet pH: 7.5) were operated using hydraulic retention times (HRTs) of 2.5 and 4.2 days, respectively, corresponding to a cellulose load of 3555.6 mg-carbon (C)/(L day). The BES → FFR process achieved a higher CH4 yield (37.5%) with 52.8 vol% CH4 in the product gas compared to the non-bioelectrochemical system (NBES) → FFR process, which showed a CH4 yield of 22.1% with 46.8 vol% CH4. The CH4 production rate (67.5 mM/day) obtained with the BER → FFR process was much higher than that obtained using electrochemical methanogenesis (0.27 mM/day). Application of the electrochemical system or CFTs improved the yields of CH4 with the NBES → FFR or BES → non-fixed film reactor process, respectively. Meta 16S rRNA sequencing revealed that putative cellulolytic bacteria (identified as Clostridium species) were present in the BES and NBES, and followed (BES→ and NBES→) FFR. Notably, H2-consuming methanogens, Methanobacterium sp. and Methanosarcina sp., showed increased relative abundances in the suspended fraction and attached fraction of (BES→) FFR, respectively, compared to that of (NBES→) FFR, although these methanogens were observed at trace levels in the BES and NBES. CONCLUSIONS These results indicate that bioelectrochemical preprocessing at a low current effectively induces interspecies H2 transfer in the FFR with conductive material. Sufficient electrochemical preprocessing was observed using a relatively short HRT. This type of two-stage process, BES → FFR, is useful for stabilization and improvement of the biogas (CH4) production from cellulosic material, and our results imply that the two-stage system developed here may be useful with other recalcitrant materials.
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Affiliation(s)
- Kengo Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Daisuke Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Yota Tsuge
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Masahiko Morita
- Environment Chemistry Sector, Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Abiko-shi, Chiba-ken, 270-1194, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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Cheaib B, Seghouani H, Llewellyn M, Vandal-Lenghan K, Mercier PL, Derome N. The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance. Anim Microbiome 2021; 3:3. [PMID: 33499999 PMCID: PMC7934398 DOI: 10.1186/s42523-020-00063-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/13/2020] [Indexed: 12/25/2022] Open
Abstract
Background Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial habitats, free-living (water), and host-associated (skin and gut) were experimentally exposed to either a constant or gradual selection regime exerted by two sublethal cadmium chloride dosages (CdCl2). Yellow Perch (Perca flavescens) was used as a piscivorous ecotoxicological model. Using 16S rDNA gene based metataxonomics, quantitative diversity metrics of water, skin and gut microbial communities were characterized along with development and across experimental conditions. Results After 30 days, constant and gradual selection regimes drove a significant alpha diversity increase for both skin and gut microbiota. In the skin, pervasive negative correlations between taxa in both selection regimes in addition to the taxonomic convergence with the environmental bacterial community, suggest a loss of colonisation resistance resulting in the dysbiosis of yellow perch microbiota. Furthermore, the network connectivity in gut microbiome was exclusively maintained by rare (low abundance) OTUs, while most abundant OTUs were mainly composed of opportunistic invaders such as Mycoplasma and other genera related to fish pathogens such as Flavobacterium. Finally, the mathematical modelling of community assembly using both non-linear least squares models (NLS) based estimates of migration rates and normalized stochasticity ratios (NST) based beta-diversity distances suggested neutral processes drove by taxonomic drift in host and water communities for almost all treatments. The NLS models predicted higher demographic stochasticity in the cadmium-free host and water microbiomes, however, NST models suggested higher ecological stochasticity under perturbations. Conclusions Neutral models agree that water and host-microbiota assembly promoted by rare taxa have evolved predominantly under neutral processes with potential involvement of deterministic forces sourced from host filtering and cadmium selection. The early signals of perturbations in the skin microbiome revealed antagonistic interactions by a preponderance of negative correlations in the co-abundance networks. Our findings enhance our understanding of community assembly host-associated and free-living under anthropogenic selective pressure.
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Affiliation(s)
- Bachar Cheaib
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada. .,Institute of Biodiversity, Animal Health and Comparative Medicine (BACHM), Glasgow, University of Glasgow, Glasgow, UK. .,School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Hamza Seghouani
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Martin Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine (BACHM), Glasgow, University of Glasgow, Glasgow, UK
| | - Katherine Vandal-Lenghan
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
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Henn MR, O’Brien EJ, Diao L, Feagan BG, Sandborn WJ, Huttenhower C, Wortman JR, McGovern BH, Wang-Weigand S, Lichter DI, Chafee M, Ford CB, Bernardo P, Zhao P, Simmons S, Tomlinson AD, Cook DN, Pomerantz RJ, Misra BK, Auninš JG, Trucksis M. A Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis. Gastroenterology 2021; 160:115-127.e30. [PMID: 32763240 PMCID: PMC7402096 DOI: 10.1053/j.gastro.2020.07.048] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Firmicutes bacteria produce metabolites that maintain the intestinal barrier and mucosal immunity. Firmicutes are reduced in the intestinal microbiota of patients with ulcerative colitis (UC). In a phase 1b trial of patients with UC, we evaluated the safety and efficacy of SER-287, an oral formulation of Firmicutes spores, and the effects of vancomycin preconditioning on expansion (engraftment) of SER-287 species in the colon. METHODS We conducted a double-blind trial of SER-287 in 58 adults with active mild-to-moderate UC (modified Mayo scores 4-10, endoscopic subscores ≥1). Participants received 6 days of preconditioning with oral vancomycin (125 mg, 4 times daily) or placebo followed by 8 weeks of oral SER-287 or placebo. Patients were randomly assigned (2:3:3:3) to groups that received placebo followed by either placebo or SER-287 once weekly, or vancomycin followed by SER-287 once weekly, or SER-287 once daily. Clinical end points included safety and clinical remission (modified Mayo score ≤2; endoscopic subscores 0 or 1). Microbiome end points included SER-287 engraftment (dose species detected in stool after but not before SER-287 administration). Engraftment of SER-287 and changes in microbiome composition and associated metabolites were measured by analyses of stool specimens collected at baseline, after preconditioning, and during and 4 weeks after administration of SER-287 or placebo. RESULTS Proportions of patients with adverse events did not differ significantly among groups. A higher proportion of patients in the vancomycin/SER-287 daily group (40%) achieved clinical remission at week 8 than patients in the placebo/placebo group (0%), placebo/SER-287 weekly group (13.3%), or vancomycin/SER-287 weekly group (17.7%) (P = .024 for vancomycin/SER-287 daily vs placebo/placebo). By day 7, higher numbers of SER-287 dose species were detected in stool samples from all SER-287 groups compared with the placebo group (P < .05), but this difference was not maintained beyond day 7 in the placebo/SER-287 weekly group. In the vancomycin groups, a greater number of dose species were detected in stool collected on day 10 and all subsequent time points through 4 weeks post dosing compared with the placebo group (P < .05). A higher number of SER-287 dose species were detected in stool samples on days 7 and 10 from subjects who received daily vs weekly SER-287 doses (P < .05). Changes in fecal microbiome composition and metabolites were associated with both vancomycin/SER-287 groups. CONCLUSIONS In this small phase 1b trial of limited duration, the safety and tolerability of SER-287 were similar to placebo. SER-287 after vancomycin was significantly more effective than placebo for induction of remission in patients with active mild to moderate UC. Engraftment of dose species was facilitated by vancomycin preconditioning and daily dosing of SER-287. ClinicalTrials.gov ID NCT02618187.
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Affiliation(s)
- Matthew R. Henn
- Seres Therapeutics, Cambridge, Massachusetts,Correspondence Address correspondence to: Matthew R. Henn, PhD, Seres Therapeutics, 200 Sidney Street, Cambridge, Massachusetts 02139. fax: (617) 649-2963
| | | | - Liyang Diao
- Seres Therapeutics, Cambridge, Massachusetts
| | | | | | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts; 5Borland Groover Clinic, Jacksonville, FL
| | | | | | | | | | | | | | | | - Peng Zhao
- Seres Therapeutics, Cambridge, Massachusetts
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Brandon-Mong GJ, Shaw GTW, Chen WH, Chen CC, Wang D. A network approach to investigating the key microbes and stability of gut microbial communities in a mouse neuropathic pain model. BMC Microbiol 2020; 20:295. [PMID: 32998681 PMCID: PMC7525972 DOI: 10.1186/s12866-020-01981-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Neuropathic pain is an abnormally increased sensitivity to pain, especially from mechanical or thermal stimuli. To date, the current pharmacological treatments for neuropathic pain are still unsatisfactory. The gut microbiota reportedly plays important roles in inducing neuropathic pain, so probiotics have also been used to treat it. However, the underlying questions around the interactions in and stability of the gut microbiota in a spared nerve injury-induced neuropathic pain model and the key microbes (i.e., the microbes that play critical roles) involved have not been answered. We collected 66 fecal samples over 2 weeks (three mice and 11 time points in spared nerve injury-induced neuropathic pain and Sham groups). The 16S rRNA gene was polymerase chain reaction amplified, sequenced on a MiSeq platform, and analyzed using a MOTHUR- UPARSE pipeline. Results Here we show that spared nerve injury-induced neuropathic pain alters gut microbial diversity in mice. We successfully constructed reliable microbial interaction networks using the Metagenomic Microbial Interaction Simulator (MetaMIS) and analyzed these networks based on 177,147 simulations. Interestingly, at a higher resolution, our results showed that spared nerve injury-induced neuropathic pain altered both the stability of the microbial community and the key microbes in a gut micro-ecosystem. Oscillospira, which was classified as a low-abundance and core microbe, was identified as the key microbe in the Sham group, whereas Staphylococcus, classified as a rare and non-core microbe, was identified as the key microbe in the spared nerve injury-induced neuropathic pain group. Conclusions In summary, our results provide novel experimental evidence that spared nerve injury-induced neuropathic pain reshapes gut microbial diversity, and alters the stability and key microbes in the gut.
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Affiliation(s)
- Guo-Jie Brandon-Mong
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Grace Tzun-Wen Shaw
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Wei-Hsin Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chien-Chang Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan. .,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.
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Microbial transmission in animal social networks and the social microbiome. Nat Ecol Evol 2020; 4:1020-1035. [DOI: 10.1038/s41559-020-1220-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/11/2020] [Indexed: 12/15/2022]
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Duar RM, Henrick BM, Casaburi G, Frese SA. Integrating the Ecosystem Services Framework to Define Dysbiosis of the Breastfed Infant Gut: The Role of B. infantis and Human Milk Oligosaccharides. Front Nutr 2020; 7:33. [PMID: 32346537 PMCID: PMC7171047 DOI: 10.3389/fnut.2020.00033] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/05/2020] [Indexed: 12/17/2022] Open
Abstract
Mounting evidence supports a connection between the composition of the infant gut microbiome and long-term health. In fact, aberrant microbiome compositions during key developmental windows in early life are associated with increased disease risk; therefore, making pertinent modifications to the microbiome during infancy offers significant promise to improve human health. There is growing support for integrating the concept of ecosystem services (the provision of benefits from ecosystems to humans) in linking specific microbiome functions to human well-being. This framework is widely applied in conservation efforts of macro-ecosystems and offers a systematic approach to guide restoration actions aimed to recover critical ecological functions. The aim of this work is to apply the ecosystem services framework to integrate recent studies demonstrating stable alteration of the gut microbiome of breastfed infants when Bifidobacterium longum subsp. infantis EVC001, a gut symbiont capable of efficiently utilizing human milk oligosaccharides into organic acids that are beneficial for the infant and lower intestinal pH, is reintroduced. Additionally, using examples from the literature we illustrate how the absence of B. infantis results in diminished ecosystem services, which may be associated with health consequences related to immune and metabolic disorders. Finally, we propose a model by which infant gut dysbiosis can be defined as a reduction in ecosystem services supplied to the host by the gut microbiome rather than merely changes in diversity or taxonomic composition. Given the increased interest in targeted microbiome modification therapies to decrease acute and chronic disease risk, the model presented here provides a framework to assess the effectiveness of such strategies from a host-centered perspective.
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Affiliation(s)
| | - Bethany M Henrick
- Evolve BioSystems, Inc., Davis, CA, United States.,Department of Food Science and Technology, University of Nebraska, Lincoln, NE, United States
| | | | - Steven A Frese
- Evolve BioSystems, Inc., Davis, CA, United States.,Department of Food Science and Technology, University of Nebraska, Lincoln, NE, United States
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Abstract
Investigation of gut microbiome composition and diversity with respect to human personality. Analyses targeted bacterial genera linked to behaviour in animal and human psychiatric studies. Bacterial genera were modelled (using negative binomial regression) with respect to personality. Genera linked to autism are also related to social behaviour in the general population. Sociability is associated with higher diversity, and anxiety and stress with reduced diversity.
The gut microbiome has a measurable impact on the brain, influencing stress, anxiety, depressive symptoms and social behaviour. This microbiome–gut–brain axis may be mediated by various mechanisms including neural, immune and endocrine signalling. To date, the majority of research has been conducted in animal models, while the limited number of human studies has focused on psychiatric conditions. Here the composition and diversity of the gut microbiome is investigated with respect to human personality. Using regression models to control for possible confounding factors, the abundances of specific bacterial genera are shown to be significantly predicted by personality traits. Diversity analyses of the gut microbiome reveal that people with larger social networks tend to have a more diverse microbiome, suggesting that social interactions may shape the microbial community of the human gut. In contrast, anxiety and stress are linked to reduced diversity and an altered microbiome composition. Together, these results add a new dimension to our understanding of personality and reveal that the microbiome–gut–brain axis may also be relevant to behavioural variation in the general population as well as to cases of psychiatric disorders.
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Kenison EK, Hernández-Gómez O, Williams RN. A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders. CONSERVATION PHYSIOLOGY 2020; 8:coaa040. [PMID: 32431814 PMCID: PMC7221235 DOI: 10.1093/conphys/coaa040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 12/01/2019] [Accepted: 04/12/2020] [Indexed: 05/20/2023]
Abstract
Captive environments are maintained in hygienic ways that lack free-flowing microbes found in animals' natural environments. As a result, captive animals often have depauperate host-associated microbial communities compared to conspecifics in the wild and may have increased disease susceptibility and reduced immune function. Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have suffered precipitous population declines over the past few decades. To bolster populations, eastern hellbenders are reared in captivity before being translocated to the wild. However, the absence of natural microbial reservoirs within the captive environment diminishes the diversity of skin-associated bacteria on hellbender skin and may negatively influence their ability to defend against pathogenic species once they are released into the wild. To prepare hellbenders for natural bacteria found in riverine environments, we devised a novel bioaugmentation method to increase the diversity of skin microbial communities within a captive setting. We exposed juvenile hellbenders to increasing amounts of river water over 5 weeks before translocating them to the river. We genetically identified and phylogenetically compared bacteria collected from skin swabs and river water for alpha (community richness) and beta (community composition) diversity estimates. We found that hellbenders exposed to undiluted river water in captivity had higher alpha diversity and distinct differentiation in the community composition on their skin, compared to hellbenders only exposed to well water. We also found strong evidence that hellbender skin microbiota is host-specific rather than environmentally driven and is colonized by rare environmental operational taxonomic units in river water. This technique may increase hellbender translocation success as increasing microbial diversity is often correlated with elevated disease resistance. Future work is necessary to refine our methods, investigate the relationship between microbial diversity and hellbender health and understand how this bioaugmentation technique influences hellbenders' survival following translocation from captivity into the wild.
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Affiliation(s)
- Erin K Kenison
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN 47907, USA
- Idaho Fish and Wildlife Office, U.S. Fish and Wildlife Service, 1387 S. Vinnell Way, Boise, ID 83706, USA
- Corresponding author: Idaho Fish and Wildlife Office, U.S. Fish and Wildlife Service, Boise, ID 83706, USA. Tel: (208) 685-6965.
| | - Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN 47907, USA
- Department of Natural Sciences and Mathematics, Dominican University of California, 50 Acacia Ave., San Rafael, CA 94901, USA
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN 47907, USA
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Santos JG, Alves BC, Hammes TO, Dall'Alba V. Dietary interventions, intestinal microenvironment, and obesity: a systematic review. Nutr Rev 2019; 77:601-613. [PMID: 31188447 DOI: 10.1093/nutrit/nuz022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CONTEXT Obesity has been linked to the intestinal microenvironment. Diet plays an important role in obesity and has been associated with microbiota. OBJECTIVE This systematic review sought to evaluate the scientific evidence on the effect of dietary modification, including supplementation with prebiotics and probiotics, on microbiota diversity in obesity. DATA SOURCES A systematic search was performed in the MEDLINE and EMBASE databases. Studies were considered eligible if they were clinical trials evaluating dietary intervention and microbiota, body weight, or clinical parameters in obesity. DATA EXTRACTION Data were extracted by 2 independent reviewers. RESULTS From 168 articles identified, 20 were included (n = 931 participants). Increased phyla abundance after food interventions was the main finding in relation to microbiota. Regarding the impact of interventions, increased insulin sensitivity, reduced levels of inflammatory markers, and reduced body mass index were shown in several studies. CONCLUSIONS Interventions that modulate microbiota, especially prebiotics, show encouraging results in treating obesity, improving insulin levels, inflammatory markers, and body mass index. Because the studies included in this review were heterogeneous, it is difficult to achieve conclusive and definitive results.
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Affiliation(s)
- Johnny G Santos
- Graduate Program in Food, Nutrition and Health, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Bruna C Alves
- Graduate Program: Sciences of Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Thais O Hammes
- Nutrition and Dietetics Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil. V. Dall'Alba is with Department of Nutrition, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Valesca Dall'Alba
- Graduate Program in Food, Nutrition and Health, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Graduate Program: Sciences of Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Nutrition and Dietetics Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil. V. Dall'Alba is with Department of Nutrition, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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49
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Brüssow H. Problems with the concept of gut microbiota dysbiosis. Microb Biotechnol 2019; 13:423-434. [PMID: 31448542 PMCID: PMC7017827 DOI: 10.1111/1751-7915.13479] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/11/2022] Open
Abstract
The human microbiome research is with the notable exception of fecal transplantation still mostly in a descriptive phase. Part of the difficulty for translating research into medical interventions is due to the large compositional complexity of the microbiome resulting in datasets that need sophisticated statistical methods for their analysis and do not lend to industrial applications. Another part of the difficulty might be due to logical flaws in terminology particularly concerning ‘dysbiosis’ that avoids circular conclusions and is based on sound ecological and evolutionary reasoning. Many case–control studies are underpowered necessitating more meta‐analyses that sort out consistent from spurious dysbiosis–disease associations. We also need for the microbiome a transition from statistical associations to causal relationships with diseases that fulfil a set of modified Koch's postulates for commensals. Disturbingly, the most sophisticated statistical analyses explain only a small percentage of the variance in the microbiome. Microbe–microbe interactions irrelevant to the host and stochastic processes might play a greater role than anticipated. To satisfy the concept of Karl Popper about conjectures and refutations in the scientific process, we should also conduct more experiments that try to refute the role of the commensal gut microbiota for human health and disease.
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Affiliation(s)
- Harald Brüssow
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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50
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Barone M, Turroni S, Rampelli S, Soverini M, D’Amico F, Biagi E, Brigidi P, Troiani E, Candela M. Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context. PLoS One 2019; 14:e0220619. [PMID: 31393934 PMCID: PMC6687155 DOI: 10.1371/journal.pone.0220619] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more “ancestral” configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods–albeit with the exclusion of grains and pulses–along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.
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Affiliation(s)
- Monica Barone
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- * E-mail:
| | - Simone Rampelli
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Matteo Soverini
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Federica D’Amico
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Elena Biagi
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Emidio Troiani
- Primary Care Unit and Territorial Health, Social Security Institute, Cailungo, Republic of San Marino
| | - Marco Candela
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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