201
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Prenatal and postnatal contributions of the maternal microbiome on offspring programming. Front Neuroendocrinol 2019; 55:100797. [PMID: 31574280 DOI: 10.1016/j.yfrne.2019.100797] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/15/2019] [Accepted: 09/27/2019] [Indexed: 12/20/2022]
Abstract
The maternal microbiota is positioned to regulate the development of offspring immunity, metabolism, as well as brain function and behavior. The mechanisms by which maternal microbial signals drive these processes are beginning to be elucidated. In this review, we provide a brief overview on the importance of the microbiome in brain function and behavior, define the maternal vaginal and gut microbiota as distinct influences on offspring development, and outline current concepts in microbial origins of offspring health outcomes. We propose that the maternal microbiota influences prenatal and early postnatal offspring development and health outcomes through two overlapping processes. First, during pregnancy maternal gut microbiota provide metabolites and substrates essential for fetal growth through metabolic provisioning, driving expansion and maturation of central and peripheral immune cells, and formation of neural circuits. Second, vertical transmission of maternal microbiota during birth and in the early postnatal window elicits a potent immunostimulatory effect in offspring that induces metabolic and developmental transcriptional programs, primes the immune system for subsequent microbial exposure, and provides substrates for brain metabolism. Finally, we explore the possibility that environmental factors, such as malnutrition, stress and infection, may exert programmatic effects by disrupting the functional contributions of the maternal microbiome during prenatal and postnatal development to influence offspring outcomes across the lifespan.
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202
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Carlström CI, Field CM, Bortfeld-Miller M, Müller B, Sunagawa S, Vorholt JA. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat Ecol Evol 2019; 3:1445-1454. [PMID: 31558832 PMCID: PMC6774761 DOI: 10.1038/s41559-019-0994-z] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/21/2019] [Indexed: 12/12/2022]
Abstract
Multicellular organisms including plants are colonised by microorganisms, some of which are beneficial to growth and health. The assembly rules for establishing the plant microbiota are not well understood, and neither is the extent to which their members interact. We conducted drop-out and late introduction experiments by inoculating Arabidopsis thaliana with synthetic communities from a resource of 62 native bacterial strains to test how arrival order shapes community structure. As a read-out we tracked the relative abundance of all strains in the phyllosphere of individual plants. Our results showed that community assembly is historically contingent and subject to priority effects. Missing strains could, to various degrees, invade an already established microbiota, which was itself resistant and remained largely unaffected by latecomers. Additionally, our results indicate that individual Proteobacteria (Sphingomonas, Rhizobium) and Actinobacteria (Microbacterium, Rhodococcus) strains have the greatest potential to affect community structure as keystone species.
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Affiliation(s)
| | | | | | - Barbara Müller
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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203
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Greiling TM, Dehner C, Chen X, Hughes K, Iñiguez AJ, Boccitto M, Ruiz DZ, Renfroe SC, Vieira SM, Ruff WE, Sim S, Kriegel C, Glanternik J, Chen X, Girardi M, Degnan P, Costenbader KH, Goodman AL, Wolin SL, Kriegel MA. Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus. Sci Transl Med 2019; 10:10/434/eaan2306. [PMID: 29593104 DOI: 10.1126/scitranslmed.aan2306] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 11/17/2017] [Accepted: 01/19/2018] [Indexed: 12/14/2022]
Abstract
The earliest autoantibodies in lupus are directed against the RNA binding autoantigen Ro60, but the triggers against this evolutionarily conserved antigen remain elusive. We identified Ro60 orthologs in a subset of human skin, oral, and gut commensal bacterial species and confirmed the presence of these orthologs in patients with lupus and healthy controls. Thus, we hypothesized that commensal Ro60 orthologs may trigger autoimmunity via cross-reactivity in genetically susceptible individuals. Sera from human anti-Ro60-positive lupus patients immunoprecipitated commensal Ro60 ribonucleoproteins. Human Ro60 autoantigen-specific CD4 memory T cell clones from lupus patients were activated by skin and mucosal Ro60-containing bacteria, supporting T cell cross-reactivity in humans. Further, germ-free mice spontaneously initiated anti-human Ro60 T and B cell responses and developed glomerular immune complex deposits after monocolonization with a Ro60 ortholog-containing gut commensal, linking anti-Ro60 commensal responses in vivo with the production of human Ro60 autoantibodies and signs of autoimmunity. Together, these data support that colonization with autoantigen ortholog-producing commensal species may initiate and sustain chronic autoimmunity in genetically predisposed individuals. The concept of commensal ortholog cross-reactivity may apply more broadly to autoimmune diseases and lead to novel treatment approaches aimed at defined commensal species.
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Affiliation(s)
- Teri M Greiling
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA.,Department of Dermatology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carina Dehner
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xinguo Chen
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Kevin Hughes
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alonso J Iñiguez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Marco Boccitto
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Daniel Zegarra Ruiz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Stephen C Renfroe
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Silvio M Vieira
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - William E Ruff
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Soyeong Sim
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm SE-171 77, Sweden.,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Christina Kriegel
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Julia Glanternik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xindi Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Michael Girardi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Patrick Degnan
- Department of Microbial Pathogenesis and Yale Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Karen H Costenbader
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Yale Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sandra L Wolin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA. .,Bioscience, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Kriegel
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA. .,Section of Rheumatology, Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
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204
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A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nat Med 2019; 25:1442-1452. [PMID: 31477907 DOI: 10.1038/s41591-019-0559-3] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/23/2019] [Indexed: 12/18/2022]
Abstract
Our understanding of how the gut microbiome interacts with its human host has been restrained by limited access to longitudinal datasets to examine stability and dynamics, and by having only a few isolates to test mechanistic hypotheses. Here, we present the Broad Institute-OpenBiome Microbiome Library (BIO-ML), a comprehensive collection of 7,758 gut bacterial isolates paired with 3,632 genome sequences and longitudinal multi-omics data. We show that microbial species maintain stable population sizes within and across humans and that commonly used 'omics' survey methods are more reliable when using averages over multiple days of sampling. Variation of gut metabolites within people over time is associated with amino acid levels, and differences across people are associated with differences in bile acids. Finally, we show that genomic diversification can be used to infer eco-evolutionary dynamics and in vivo selection pressures for strains within individuals. The BIO-ML is a unique resource designed to enable hypothesis-driven microbiome research.
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205
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Wang S, Martins R, Sullivan MC, Friedman ES, Misic AM, El-Fahmawi A, De Martinis ECP, O'Brien K, Chen Y, Bradley C, Zhang G, Berry ASF, Hunter CA, Baldassano RN, Rondeau MP, Beiting DP. Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. MICROBIOME 2019; 7:126. [PMID: 31472697 PMCID: PMC6717631 DOI: 10.1186/s40168-019-0740-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/19/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The microbiome has been implicated in the initiation and persistence of inflammatory bowel disease. Despite the fact that diet is one of the most potent modulators of microbiome composition and function and that dietary intervention is the first-line therapy for treating pediatric Crohn's disease, the relationships between diet-induced remission, enteropathy, and microbiome are poorly understood. Here, we leverage a naturally-occurring canine model of chronic inflammatory enteropathy that exhibits robust remission following nutritional therapy, to perform a longitudinal study that integrates clinical monitoring, 16S rRNA gene amplicon sequencing, metagenomic sequencing, metabolomic profiling, and whole genome sequencing to investigate the relationship between therapeutic diet, microbiome, and disease. RESULTS We show that remission induced by a hydrolyzed protein diet is accompanied by alterations in microbial community structure marked by decreased abundance of pathobionts (e.g., Escherichia coli and Clostridium perfringens), reduced severity of dysbiosis, and increased levels of the secondary bile acids, lithocholic and deoxycholic acid. Physiologic levels of these bile acids inhibited the growth of E. coli and C. perfringens isolates, in vitro. Metagenomic analysis and whole genome sequencing identified the bile acid producer Clostridium hiranonis as elevated after dietary therapy and a likely source of secondary bile acids during remission. When C. hiranonis was administered to mice, levels of deoxycholic acid were preserved and pathology associated with DSS colitis was ameliorated. Finally, a closely related bile acid producer, Clostridium scindens, was associated with diet-induced remission in human pediatric Crohn's disease. CONCLUSIONS These data highlight that remission induced by a hydrolyzed protein diet is associated with improved microbiota structure, an expansion of bile acid-producing clostridia, and increased levels of secondary bile acids. Our observations from clinical studies of exclusive enteral nutrition in human Crohn's disease, along with our in vitro inhibition assays and in vivo studies in mice, suggest that this may be a conserved response to diet therapy with the potential to ameliorate disease. These findings provide insight into diet-induced remission of gastrointestinal disease and could help guide the rational design of more effective therapeutic diets.
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Affiliation(s)
- Shuai Wang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rene Martins
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Megan C Sullivan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elliot S Friedman
- Division of Gastroenterology, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ana M Misic
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ayah El-Fahmawi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Kevin O'Brien
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ying Chen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Charles Bradley
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Grace Zhang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexander S F Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert N Baldassano
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mark P Rondeau
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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206
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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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207
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Siebert JC, Neff CP, Schneider JM, Regner EH, Ohri N, Kuhn KA, Palmer BE, Lozupone CA, Görg C. VOLARE: visual analysis of disease-associated microbiome-immune system interplay. BMC Bioinformatics 2019; 20:432. [PMID: 31429723 PMCID: PMC6701114 DOI: 10.1186/s12859-019-3021-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/06/2019] [Indexed: 02/08/2023] Open
Abstract
Background Relationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the likely relationships. “Omic” methodologies such as 16S ribosomal RNA (rRNA) sequencing and time-of-flight mass cytometry (CyTOF) immunophenotyping generate data that support generation of hypotheses, with the potential to identify additional relationships at a level of granularity ripe for further experimentation. Pairwise linear regressions between microbial and host immune features provide one approach for quantifying relationships between “omes”, and the differences in these relationships across study cohorts or arms. This approach yields a top table of candidate results. However, the top table alone lacks the detail that domain experts such as microbiologists and immunologists need to vet candidate results for follow-up experiments. Results To support this vetting, we developed VOLARE (Visualization Of LineAr Regression Elements), a web application that integrates a searchable top table, small in-line graphs illustrating the fitted models, a network summarizing the top table, and on-demand detailed regression plots showing full sample-level detail. We applied VOLARE to three case studies—microbiome:cytokine data from fecal samples in human immunodeficiency virus (HIV), microbiome:cytokine data in inflammatory bowel disease and spondyloarthritis, and microbiome:immune cell data from gut biopsies in HIV. We present both patient-specific phenomena and relationships that differ by disease state. We also analyzed interaction data from system logs to characterize usage scenarios. This log analysis revealed that users frequently generated detailed regression plots, suggesting that this detail aids the vetting of results. Conclusions Systematically integrating microbe:immune cell readouts through pairwise linear regressions and presenting the top table in an interactive environment supports the vetting of results for scientific relevance. VOLARE allows domain experts to control the analysis of their results, screening dozens of candidate relationships with ease. This interactive environment transcends the limitations of a static top table. Electronic supplementary material The online version of this article (10.1186/s12859-019-3021-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janet C Siebert
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. .,CytoAnalytics, Denver, CO, 80113, USA.
| | - Charles Preston Neff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jennifer M Schneider
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Emilie H Regner
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Neha Ohri
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kristine A Kuhn
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Brent E Palmer
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Catherine A Lozupone
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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208
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Kang Y, Li Y, Du Y, Guo L, Chen M, Huang X, Yang F, Hong J, Kong X. Konjaku flour reduces obesity in mice by modulating the composition of the gut microbiota. Int J Obes (Lond) 2019; 43:1631-1643. [PMID: 30242233 DOI: 10.1038/s41366-018-0187-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/23/2018] [Accepted: 07/02/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Changes in the intestinal flora composition is referred to as dysbiosis, which is related to obesity development, thus supporting the potential roles of nutrients acting on intestinal flora to exert salutary effects on energetic metabolism of host. Dietary fiber has been known to affect the composition of intestinal flora. The aim of the present study was to investigate the functional effects of konjac flour (KF) on obesity control in respect to improving inflammation, metabolism, and intestinal barrier function, and the possible association of the effects with intestinal flora composition changes. METHODS Mice (n = 30) were randomly divided into control group (n = 10), high-fat-diet (HFD) group (n = 10), and KF intervention group (n = 10), followed by feeding for 12 weeks and with adding a KF daily supplementation for the treatment group. Body weight, fat accumulation, inflammation, and energetic metabolism markers in multiple tissues and the gut microbiota of the mice were examined at the end of the experiment. RESULTS The KF supplementation significantly reduced the gains in weight, fat mass, as well as adipocyte size of HFD mice and lowered the serum TC, leptin (LEP), thiobarbituric acid-reacting substance (TBARS), IL-6, and lipopolysaccharide (LPS) levels in HFD mice. KF also upregulated the expression of intestinal mucosa protein gene Intection and tight junction ZO-1 in HFD mice, as well as upregulate the expression of energy metabolism genes PPARα and CPT-1 as well as the fat metabolism gene HLS in livers and fat tissues, and downregulate that of fat synthesis gene PPARγ (p < 0.05). The KF treatment increases the α-diversity and change the β-diversity of the intestinal microflora in HFD mice and boosted the abundances of some obesity-related beneficial microorganisms (such as Megasphaera elsdenii) in the intestinal microflora of HFD mice, while reduced those of harmful microorganisms (such as Alistipes, Alloprevotella, Bacteroides acidifaciens, and Parabacteroides goldsteinii). The abundance of Alistipes was positively correlated with weight, fat mass, serum TC, TG, LEP, IL-6, and LPS contents as well as PPARγ gene expression; while notably and negatively related to the expression of CPT-1 and HLS genes (p < 0.01). KF remarkably increased the abundance of Aerococcaceae, while reduced that of Alistipes finegoldii (p < 0.01). CONCLUSIONS Supplementation with KF achieves favorable effects on treating obesity, improving inflammatory response, metabolism, and intestinal barrier function, by regulating intestinal microfloral structure in HFD-fed mice.
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Affiliation(s)
- Yongbo Kang
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China
- Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, Yunnan, China
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yu Li
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China
- Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yuhui Du
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China
- Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Liqiong Guo
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China
- Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Minghui Chen
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China
- Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xinwei Huang
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China
- Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Fang Yang
- Nutrition Department, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jingan Hong
- Nutrition Department, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xiangyang Kong
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China.
- Genetics and Pharmacogenomics Laboratory, Kunming University of Science and Technology, Kunming, Yunnan, China.
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209
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Ai C, Jiang P, Liu Y, Duan M, Sun X, Luo T, Jiang G, Song S. The specific use of alginate from Laminaria japonica by Bacteroides species determined its modulation of the Bacteroides community. Food Funct 2019; 10:4304-4314. [PMID: 31270523 DOI: 10.1039/c9fo00289h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Accumulating studies showed that the beneficial actions of polysaccharides were closely associated with an improvement of the gut microbiota, but mechanisms that link polysaccharides and gut microbiota alterations are ill defined. Alginate from Laminaria japonica (LJP-A) can avoid being digested by the upper digestive tract and reach the colon where it can improve the gut microbiota community. LJP-A increased the relative abundance of some Bacteroidaceae members, e.g. Bacteroides species. The distribution of Bacteroides species in the gut is specific to the individual, and the specific use of LJP-A by Bacteroides species can determine LJP-A-induced alterations of the intestinal Bacteroides community, in which carbon source-based syntrophic interactions occur in Bacteroides species of the human gut microbial ecosystem. Compared to other species, Bacteroides finegoldii responded more positively to LJP-A intervention, and its properties may have a close connection with the bioactivities of LJP-A. This study provides a rationale for personalized treatment with dietary polysaccharides that were optimally fermented within a particular individual.
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Affiliation(s)
- Chunqing Ai
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, P. R. China.
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210
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Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ. Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet. Cell Host Microbe 2019; 26:265-272.e4. [PMID: 31324413 DOI: 10.1016/j.chom.2019.06.013] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/22/2019] [Accepted: 06/23/2019] [Indexed: 02/08/2023]
Abstract
Multiple research groups have shown that diet impacts the gut microbiome; however, variability in experimental design and quantitative assessment have made it challenging to assess the degree to which similar diets have reproducible effects across studies. Through an unbiased subject-level meta-analysis framework, we re-analyzed 27 dietary studies including 1,101 samples from rodents and humans. We demonstrate that a high-fat diet (HFD) reproducibly changes gut microbial community structure. Finer taxonomic analysis revealed that the most reproducible signals of a HFD are Lactococcus species, which we experimentally demonstrate to be common dietary contaminants. Additionally, a machine-learning approach defined a signature that predicts the dietary intake of mice and demonstrated that phylogenetic and gene-centric transformations of this model can be translated to humans. Together, these results demonstrate the utility of microbiome meta-analyses in identifying robust and reproducible features for mechanistic studies in preclinical models.
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Affiliation(s)
- Jordan E Bisanz
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Vaibhav Upadhyay
- Department of Internal Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jessie A Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kimberly Ly
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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211
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Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL, Cheng J, Chen RY, Subramanian S, Cowardin CA, Meier MF, O'Donnell D, Talcott M, Spears LD, Semenkovich CF, Henrissat B, Giannone RJ, Hettich RL, Ilkayeva O, Muehlbauer M, Newgard CB, Sawyer C, Head RD, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Hossain MI, Islam M, Choudhury N, Sarker SA, Huq S, Mahmud I, Mostafa I, Mahfuz M, Barratt MJ, Ahmed T, Gordon JI. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. Science 2019; 365:eaau4732. [PMID: 31296738 PMCID: PMC6683325 DOI: 10.1126/science.aau4732] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 04/24/2019] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
To examine the contributions of impaired gut microbial community development to childhood undernutrition, we combined metabolomic and proteomic analyses of plasma samples with metagenomic analyses of fecal samples to characterize the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned, after standard treatment, to moderate acute malnutrition (MAM) with persistent microbiota immaturity. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes targeting weaning-phase bacterial taxa underrepresented in SAM and MAM microbiota were characterized in gnotobiotic mice and gnotobiotic piglets colonized with age- and growth-discriminatory bacteria. A randomized, double-blind controlled feeding study identified a lead MDCF that changes the abundances of targeted bacteria and increases plasma biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function in children with MAM.
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Affiliation(s)
- Jeanette L Gehrig
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Siddarth Venkatesh
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vanderlene L Kung
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sathish Subramanian
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carrie A Cowardin
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martin F Meier
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David O'Donnell
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael Talcott
- Division of Comparative Medicine, Washington University, St. Louis, MO 63110, USA
| | - Larry D Spears
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Clay F Semenkovich
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, 13288 Marseille cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher Sawyer
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Genome Technology Access Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Genome Technology Access Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Aleksandr A Arzamasov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Md Iqbal Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Munirul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Nuzhat Choudhury
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Sayeeda Huq
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Imteaz Mahmud
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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212
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Ruff WE, Dehner C, Kim WJ, Pagovich O, Aguiar CL, Yu AT, Roth AS, Vieira SM, Kriegel C, Adeniyi O, Mulla MJ, Abrahams VM, Kwok WW, Nussinov R, Erkan D, Goodman AL, Kriegel MA. Pathogenic Autoreactive T and B Cells Cross-React with Mimotopes Expressed by a Common Human Gut Commensal to Trigger Autoimmunity. Cell Host Microbe 2019; 26:100-113.e8. [PMID: 31227334 PMCID: PMC8194364 DOI: 10.1016/j.chom.2019.05.003] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 04/08/2019] [Accepted: 05/08/2019] [Indexed: 12/21/2022]
Abstract
Given the immense antigenic load present in the microbiome, we hypothesized that microbiota mimotopes can be a persistent trigger in human autoimmunity via cross-reactivity. Using antiphospholipid syndrome (APS) as a model, we demonstrate cross-reactivity between non-orthologous mimotopes expressed by a common human gut commensal, Roseburia intestinalis (R. int), and T and B cell autoepitopes in the APS autoantigen β2-glycoprotein I (β2GPI). Autoantigen-reactive CD4+ memory T cell clones and an APS-derived, pathogenic monoclonal antibody cross-reacted with R. int mimotopes. Core-sequence-dependent anti-R. int mimotope IgG titers were significantly elevated in APS patients and correlated with anti-β2GPI IgG autoantibodies. R. int immunization of mice induced β2GPI-specific lymphocytes and autoantibodies. Oral gavage of susceptible mice with R. int induced anti-human β2GPI autoantibodies and autoimmune pathologies. Together, these data support a role for non-orthologous commensal-host cross-reactivity in the development and persistence of autoimmunity in APS, which may apply more broadly to human autoimmune disease.
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Affiliation(s)
- William E Ruff
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Carina Dehner
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Woo J Kim
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Odelya Pagovich
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Cassyanne L Aguiar
- Barbara Volcker Center for Women and Rheumatic Diseases, Hospital for Special Surgery, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrew T Yu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Alexander S Roth
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Christina Kriegel
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Olamide Adeniyi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Melissa J Mulla
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA
| | - Vikki M Abrahams
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Doruk Erkan
- Barbara Volcker Center for Women and Rheumatic Diseases, Hospital for Special Surgery, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrew L Goodman
- Microbial Sciences Institute, Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
| | - Martin A Kriegel
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Medicine, Section of Rheumatology, Yale School of Medicine, New Haven, CT 06510, USA.
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213
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Centanni M, Carnachan SM, Bell TJ, Daines AM, Hinkley SFR, Tannock GW, Sims IM. Utilization of Complex Pectic Polysaccharides from New Zealand Plants ( Tetragonia tetragonioides and Corynocarpus laevigatus) by Gut Bacteroides Species. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7755-7764. [PMID: 31251611 DOI: 10.1021/acs.jafc.9b02429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pectic polysaccharides from New Zealand (NZ) spinach (Tetragonia tetragonioides) and karaka berries (Corynocarpus laevigatus) were extracted and analyzed. NZ spinach polysaccharides comprised mostly homogalacturonan (64.4%) and rhamnogalacturonan I (5.8%), with side chains of arabinan (8.1%), galactan (2.2%), and type II arabinogalactan (7.1%); karaka berry polysaccharides comprised homogalacturonan (21.8%) and rhamnogalacturonan I (10.0%), with greater proportions of side chains (arabinan, 15.6%; galactan, 23.8%; and type II arabinogalactan, 19.3%). Screening of gut commensal Bacteroides showed that six were able to grow on the NZ spinach extract, while five were able to grow on the karaka berry extract. Analysis of the polysaccharides remaining after fermentation, by size-exclusion chromatography and constituent sugar analysis, showed that the Bacteroides species that grew on these two substrates showed preferences for the different pectic polysaccharide types. Our data suggest that, to completely degrade and utilize the complex pectin structures found in plants, members of Bacteroides and other bowel bacteria work as metabolic consortia.
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Affiliation(s)
| | - Susan M Carnachan
- Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Road , Lower Hutt 5040 , New Zealand
| | - Tracey J Bell
- Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Road , Lower Hutt 5040 , New Zealand
| | - Alison M Daines
- Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Road , Lower Hutt 5040 , New Zealand
| | - Simon F R Hinkley
- Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Road , Lower Hutt 5040 , New Zealand
| | - Gerald W Tannock
- Riddet Institute Centre of Research Excellence , Palmerston North 4442 , New Zealand
| | - Ian M Sims
- Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Road , Lower Hutt 5040 , New Zealand
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214
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Ravcheev DA, Moussu L, Smajic S, Thiele I. Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome. Front Genet 2019; 10:636. [PMID: 31333721 PMCID: PMC6620236 DOI: 10.3389/fgene.2019.00636] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/18/2019] [Indexed: 12/16/2022] Open
Abstract
Bacterial microcompartments are self-assembling subcellular structures surrounded by a semipermeable protein shell and found only in bacteria, but not archaea or eukaryotes. The general functions of the bacterial microcompartments are to concentrate enzymes, metabolites, and cofactors for multistep pathways; maintain the cofactor ratio; protect the cell from toxic metabolic intermediates; and protect the encapsulated pathway from unwanted side reactions. The bacterial microcompartments were suggested to play a significant role in organisms of the human gut microbiome, especially for various pathogens. Here, we used a comparative genomics approach to analyze the bacterial microcompartments in 646 individual genomes of organisms commonly found in the human gut microbiome. The bacterial microcompartments were found in 150 (23.2%) analyzed genomes. These microcompartments include previously known ones for the utilization of ethanolamine, 1,2-propanediol, choline, and fucose/rhamnose. Moreover, we reconstructed two novel pathways associated with the bacterial microcompartments. These pathways are catabolic pathways for the utilization of 1-amino-2-propanol/1-amino-2-propanone and xanthine. Remarkably, the xanthine utilization pathway does not demonstrate similarity to previously known microcompartment-associated pathways. Thus, we describe a novel type of bacterial microcompartment.
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Affiliation(s)
- Dmitry A Ravcheev
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lubin Moussu
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Semra Smajic
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
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215
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Zhao H, Gao D, Gao X. Rhubarb ameliorates cognitive dysfunction in a rat model of Alzheimer's disease through regulation of the intestinal microbiome. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2019. [DOI: 10.1016/j.jtcms.2019.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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216
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Lu X, Liu J, Zhang N, Fu Y, Zhang Z, Li Y, Wang W, Li Y, Shen P, Cao Y. Ripened Pu-erh Tea Extract Protects Mice from Obesity by Modulating Gut Microbiota Composition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6978-6994. [PMID: 31070363 DOI: 10.1021/acs.jafc.8b04909] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ripened Pu-erh tea extract contributes to reducing weight gain and fat accumulation; however, the role of gut microbiota on the antiobesity effect of ripened Pu-erh tea extract in obese mice remains unclear. This study aims to explore the role of alterations in gut microbes mediated by ripened Pu-erh tea extract in obese mice through 16S rRNA sequencing and a fecal transplant trial. Our results suggested that drinking water containing ripened Pu-erh tea extract could decrease weight gain, fat accumulation, adipose inflammation, the Firmicutes-to-Bacteroidetes ratio, and metabolic endotoxemia while, in the meantime, improving the intestinal barrier integrity in obese mice. Moreover, the fecal transplant trial indicated that feces from the donor mice treated with ripened Pu-erh tea extract could significantly modulate weight and metabolic syndrome in the recipient mice. Thus, our results indicated that gut microbiota can mediate the function of ripened Pu-erh tea extract against obesity; additionally, ripened Pu-erh tea extract can potentially prevent individuals from being obese through rebalancing the gut microbiota.
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Affiliation(s)
- Xiaojie Lu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Jiuxi Liu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Naisheng Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Yunhe Fu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Zecai Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Yanxin Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Wenqing Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Yanyi Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Peng Shen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
| | - Yongguo Cao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
- Key Laboratory for Zoonosis Research, Ministry of Education, College of Veterinary Medicine , Jilin University , Changchun , 130062 , People's Republic of China
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217
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Zhang W, Zhu S. Gut metabolites: make orphans adopted. PRECISION CLINICAL MEDICINE 2019; 2:87-89. [PMID: 35692448 PMCID: PMC8985774 DOI: 10.1093/pcmedi/pbz012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/17/2019] [Indexed: 12/28/2022] Open
Abstract
A commentary on “A forward chemical genetic screen reveals gut microbiota metabolites that modulate host physiology”.
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Affiliation(s)
- Weiqiao Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shu Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
- School of Data Science, University of Science and Technology of China, Hefei, China
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218
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Liu S, Qin P, Wang J. High-Fat Diet Alters the Intestinal Microbiota in Streptozotocin-Induced Type 2 Diabetic Mice. Microorganisms 2019; 7:microorganisms7060176. [PMID: 31208113 PMCID: PMC6617241 DOI: 10.3390/microorganisms7060176] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/04/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
Intestinal microbiota is closely associated with various metabolic diseases such as type 2 diabetes (T2D), and microbiota is definitely affected by diet. However, more work is required to gain detailed information about gut metagenome and their associated impact with diet in T2D patients. We used a streptozotocin-high-fat diet (HFD) to induce a T2D mouse model and investigated the effect of standard chow diet and HFD on the composition and function of gut microbiota. We found that a HFD could worsen the diabetes status compared with a standard diet. 16S rRNA gene sequencing revealed that a HFD caused a large disturbance to the microbial structure and was linked to an increased ratio of Firmicutes to Bacteroidetes. A HFD increased the bacteria of the Ruminococcaceae and Erysipelotrichaceae family and decreased the bacteria of S24-7 and Rikenellaceae. Meanwhile, a HFD decreased the abundance of Parabacteroidesdistasonis and Eubacteriumdolichum, both of which have previously been reported to alleviate obesity and metabolic dysfunctions. Moreover, PICRUSt-predicted KEGG pathways related to membrane transport, lipid metabolism, and xenobiotics biodegradation and metabolism were significantly elevated in HFD-fed T2D mice. Our results provide insights into dietary and nutritional approaches for improving host metabolism and ameliorating T2D.
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Affiliation(s)
- Sheng Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Panpan Qin
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
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219
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Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature 2019; 570:462-467. [PMID: 31158845 PMCID: PMC6597290 DOI: 10.1038/s41586-019-1291-3] [Citation(s) in RCA: 605] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 05/22/2019] [Indexed: 02/08/2023]
Abstract
Individuals vary widely in their responses to medicinal drugs, which can be dangerous and expensive owing to treatment delays and adverse effects. Although increasing evidence implicates the gut microbiome in this variability, the molecular mechanisms involved remain largely unknown. Here we show, by measuring the ability of 76 human gut bacteria from diverse clades to metabolize 271 orally administered drugs, that many drugs are chemically modified by microorganisms. We combined high-throughput genetic analyses with mass spectrometry to systematically identify microbial gene products that metabolize drugs. These microbiome-encoded enzymes can directly and substantially affect intestinal and systemic drug metabolism in mice, and can explain the drug-metabolizing activities of human gut bacteria and communities on the basis of their genomic contents. These causal links between the gene content and metabolic activities of the microbiota connect interpersonal variability in microbiomes to interpersonal differences in drug metabolism, which has implications for medical therapy and drug development across multiple disease indications.
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Affiliation(s)
- Michael Zimmermann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Maria Zimmermann-Kogadeeva
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Rebekka Wegmann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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220
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Microbiota: Overview and Implication in Immunotherapy-Based Cancer Treatments. Int J Mol Sci 2019; 20:ijms20112699. [PMID: 31159348 PMCID: PMC6600175 DOI: 10.3390/ijms20112699] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/17/2019] [Accepted: 05/26/2019] [Indexed: 12/12/2022] Open
Abstract
During the last few years, the gut microbiota has gained increasing attention as a consequence of its emerging role as a modulator of the immune system. With the advent of the era of checkpoint inhibitors immunotherapy and adoptive cell transfer (ACT) in oncology, these findings became of primary relevance in light of experimental data that suggested the microbiota involvement as a plausible predictor of a good or poor response. These remarks justify the efforts to pinpoint the specific actions of the microbiota and to identify new strategies to favorably edit its composition.
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221
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Sun J, Qi C, Zhu H, Zhou Q, Xiao H, Le G, Chen D, Yu R. IgA-Targeted Lactobacillus jensenii Modulated Gut Barrier and Microbiota in High-Fat Diet-Fed Mice. Front Microbiol 2019; 10:1179. [PMID: 31178854 PMCID: PMC6542990 DOI: 10.3389/fmicb.2019.01179] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
IgA-coated Lactobacillus live in the mucous layer of the human or mammalian intestine in close proximity to epithelial cells. They act as potential probiotics for functional food development, but their physiological regulation has not yet been studied. We isolated IgA-targeted (Lactobacillus jensenii IgA21) and lumen lactic acid bacterial strains (Pediococcus acidilactici FS1) from the fecal microbiota of a healthy woman. C57BL/6 mice were fed a normal (CON) or high fat diet (HFD) for 6 weeks and then treated with IgA21 or FS1 for 4 weeks. HFD caused dyslipidemia, mucosal barrier damage, and intestinal microbiota abnormalities. Only IgA21 significantly inhibited dyslipidemia and gut barrier damage. This was related to significant up-regulation of mucin-2, PIgR mRNA expression, and colonic butyrate production (P < 0.05 vs. HFD). Unlike IgA21, FS1 caused a more pronounced gut dybiosis than did HFD, and, in particular, it induced a significant decrease in the Bacteroidales S24-7 group and an increase in Desulfovibrionaceae (P < 0.05 vs. CON). In conclusion, IgA-coated and non-coated lactic acid bacteria of gut have been demonstrated to differentially affect the intestinal barrier and serum lipids. This indicates that IgA-bound bacteria possess the potential to more easily interact with the host gut to regulate homeostasis.
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Affiliation(s)
- Jin Sun
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Ce Qi
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hualing Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qin Zhou
- The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Guowei Le
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Daozhen Chen
- The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Renqiang Yu
- The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
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Yousi F, Kainan C, Junnan Z, Chuanxing X, Lina F, Bangzhou Z, Jianlin R, Baishan F. Evaluation of the effects of four media on human intestinal microbiota culture in vitro. AMB Express 2019; 9:69. [PMID: 31123874 PMCID: PMC6533344 DOI: 10.1186/s13568-019-0790-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/06/2019] [Indexed: 02/08/2023] Open
Abstract
The human intestinal microbiota has an important role in the maintenance of human health and disease pathogenesis. The aim of this research was to investigate the impact of four media on human intestinal microbiota metabolite and composition changes, we performed in vitro batch culture using intestinal microbiota samples from three fecal microbiota transplantation (FMT) donors. After 48 h culture, gut microbiota medium (GMM) had the highest production of acetic acid (73.00 ± 7.56 mM) and propionic acid (16.79 ± 1.59 mM), bacterial growth media (BGM) had the highest production of butyric acid (13.39 ± 0.56 mM). In addition, brain heart infusion (BHI) promoted (p < 0.05) the growth of Bacteroidetes, especially Bacteroides after 48 h, GMM resulted in a significant increase (p < 0.05) in Actinobacteria and increased the beneficial genus Bifidobacterium, fastidious anaerobe broth (FAB) increased Firmicutes population, and BGM promoted the growth of Escherichia-Shigella and Akkermansia. The results suggest that four media had different effects on the human intestinal microbiota metabolism and composition in vitro. These results may facilitate the culture of bacteria from the human intestinal microbiota.
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223
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Chen H, Nwe PK, Yang Y, Rosen CE, Bielecka AA, Kuchroo M, Cline GW, Kruse AC, Ring AM, Crawford JM, Palm NW. A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology. Cell 2019; 177:1217-1231.e18. [PMID: 31006530 PMCID: PMC6536006 DOI: 10.1016/j.cell.2019.03.036] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/11/2019] [Accepted: 03/16/2019] [Indexed: 01/11/2023]
Abstract
The intestinal microbiota produces tens of thousands of metabolites. Here, we used host sensing of small molecules by G-protein coupled receptors (GPCRs) as a lens to illuminate bioactive microbial metabolites that impact host physiology. We screened 144 human gut bacteria against the non-olfactory GPCRome and identified dozens of bacteria that activated both well-characterized and orphan GPCRs, including strains that converted dietary histidine into histamine and shaped colonic motility; a prolific producer of the essential amino acid L-Phe, which we identified as an agonist for GPR56 and GPR97; and a species that converted L-Phe into the potent psychoactive trace amine phenethylamine, which crosses the blood-brain barrier and triggers lethal phenethylamine poisoning after monoamine oxidase inhibitor administration. These studies establish an orthogonal approach for parsing the microbiota metabolome and uncover multiple biologically relevant host-microbiota metabolome interactions.
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Affiliation(s)
- Haiwei Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Phu-Khat Nwe
- Chemical Biology Institute and Department of Chemistry, Yale University, West Haven and New Haven, CT, USA
| | - Yi Yang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Connor E Rosen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Agata A Bielecka
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Manik Kuchroo
- Yale University School of Medicine, New Haven, CT, USA
| | - Gary W Cline
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Aaron M Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jason M Crawford
- Chemical Biology Institute and Department of Chemistry, Yale University, West Haven and New Haven, CT, USA; Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Noah W Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat Biomed Eng 2019; 3:520-531. [PMID: 31086325 PMCID: PMC6658209 DOI: 10.1038/s41551-019-0397-0] [Citation(s) in RCA: 427] [Impact Index Per Article: 85.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/04/2019] [Indexed: 02/06/2023]
Abstract
The diverse bacterial populations that comprise the commensal microbiome of the human intestine play a central role in health and disease. A method that sustains complex microbial communities in direct contact with living human intestinal cells and their overlying mucus layer in vitro would thus enable investigations of host–microbiome interactions. Here, we show the extended co-culture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota, enabled by a microfluidic intestine-on-a-chip that permits the control and real-time assessment of physiologically relevant oxygen gradients. When compared to aerobic co-culture conditions, the establishment of a transluminal hypoxia gradient in the chip increased intestinal barrier function and sustained a physiologically relevant level of microbial diversity, consisting of over 200 unique operational taxonomic units from 11 different genera, and of an abundance of obligate anaerobic bacteria with ratios of Firmicutes and Bacteroidetes similar to those observed in human faeces. The intestine-on-a-chip may serve as a discovery tool for the development of microbiome-related therapeutics, probiotics and nutraceuticals.
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225
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Walker MM, Talley NJ, Keely S. Follow up on atopy and the gastrointestinal tract - a review of a common association 2018. Expert Rev Gastroenterol Hepatol 2019; 13:437-445. [PMID: 30900475 DOI: 10.1080/17474124.2019.1596025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Primary atopic disorders can be classified as heritable genetic disorders presenting with deregulated pathogenic allergic effector responses irrespective of sensitization. In the last decade, there are parallel rises in the burden of atopic and gastrointestinal (GI) diseases. Areas covered: There is increasing recognition of an association between atopy and GI disease through immune dysregulation, the microbiome and shared genetic pathways. Since the first article on atopy and the GI tract in 2014 in this journal, many more studies have shed light on the shared pathways in these diseases, particularly in the field of eosinophilic GI disease, functional GI disorders, and inflammatory bowel disease. Expert opinion: Understanding the links with common mechanisms in atopy and GI diseases that may lead to better targeting of treatment through manipulation of immune mechanisms, the microbiome, genetics, food allergens and specific GI diseases such as inflammatory bowel disease, functional GI disorders.
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Affiliation(s)
- Marjorie M Walker
- a Faculty of Medicine & Health University of Newcastle , School of Medicine & Public Health , Callaghan , NSW , Australia.,b School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine , University of Newcastle , Newcastle , NSW , Australia.,c Priority Research Centre for Digestive Health and Neurogastroenterology , University of Newcastle , Newcastle , NSW , Australia
| | - Nicholas J Talley
- c Priority Research Centre for Digestive Health and Neurogastroenterology , University of Newcastle , Newcastle , NSW , Australia.,d Priority Research Centre for Digestive Health & Neurogastroenterology , Hunter Medical Research Institute, New Lambton Heights , Newcastle , NSW , Australia
| | - Simon Keely
- b School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine , University of Newcastle , Newcastle , NSW , Australia.,c Priority Research Centre for Digestive Health and Neurogastroenterology , University of Newcastle , Newcastle , NSW , Australia.,d Priority Research Centre for Digestive Health & Neurogastroenterology , Hunter Medical Research Institute, New Lambton Heights , Newcastle , NSW , Australia
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Dubourg G, Baron S, Cadoret F, Couderc C, Fournier PE, Lagier JC, Raoult D. From Culturomics to Clinical Microbiology and Forward. Emerg Infect Dis 2019; 24:1683-1690. [PMID: 30124405 PMCID: PMC6106433 DOI: 10.3201/eid2409.170995] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Culturomics has permitted discovery of hundreds of new bacterial species isolated from the human microbiome. Profiles generated by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry have been added to the mass spectrometer database used in clinical microbiology laboratories. We retrospectively collected raw data from MALDI-TOF mass spectrometry used routinely in our laboratory in Marseille, France, during January 2012-March 2018 and analyzed 16S rDNA sequencing results from misidentified strains. During the study period, 744 species were identified from clinical specimens, of which 21 were species first isolated from culturomics. This collection involved 105 clinical specimens, accounting for 98 patients. In 64 cases, isolation of the bacteria was considered clinically relevant. MALDI-TOF mass spectrometry was able to identify the species in 95.2% of the 105 specimens. While contributing to the extension of the bacterial repertoire associated with humans, culturomics studies also enlarge the spectrum of prokaryotes involved in infectious diseases.
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227
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Fessler J, Matson V, Gajewski TF. Exploring the emerging role of the microbiome in cancer immunotherapy. J Immunother Cancer 2019; 7:108. [PMID: 30995949 PMCID: PMC6471869 DOI: 10.1186/s40425-019-0574-4] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/22/2019] [Indexed: 12/24/2022] Open
Abstract
The activity of the commensal microbiota significantly impacts human health and has been linked to the development of many diseases, including cancer. Gnotobiotic animal models have shown that the microbiota has many effects on host physiology, including on the development and regulation of immune responses. More recently, evidence has indicated that the microbiota can more specifically influence the outcome of cancer immunotherapy. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes have shown promise in mouse studies. Ongoing endeavors are translating these pre-clinical findings to early stage clinical testing. In this review we summarize 1) basic methodologies and considerations for studies of host-microbiota interactions; 2) experimental evidence towards a causal link between gut microbiota composition and immunotherapeutic efficacy; 3) possible mechanisms governing the microbiota-mediated impact on immunotherapy efficacy. Moving forward, there is need for a deeper understanding of the underlying biological mechanisms that link specific bacterial strains to host immunity. Integrating microbiome effects with other tumor and host factors regulating immunotherapy responsiveness versus resistance could facilitate optimization of therapeutic outcomes.
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Affiliation(s)
- Jessica Fessler
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Vyara Matson
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Thomas F Gajewski
- Department of Pathology, The University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S. Maryland Ave., MC2115, Chicago, IL, 60637, USA.
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228
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Crook N, Ferreiro A, Gasparrini AJ, Pesesky MW, Gibson MK, Wang B, Sun X, Condiotte Z, Dobrowolski S, Peterson D, Dantas G. Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut. Cell Host Microbe 2019; 25:499-512.e8. [PMID: 30926240 PMCID: PMC6487504 DOI: 10.1016/j.chom.2019.02.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/06/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022]
Abstract
Probiotics are living microorganisms that are increasingly used as gastrointestinal therapeutics by virtue of their innate or engineered genetic function. Unlike abiotic therapeutics, probiotics can replicate in their intended site, subjecting their genomes and therapeutic properties to natural selection. We exposed the candidate probiotic E. coli Nissle (EcN) to the mouse gastrointestinal tract over several weeks, systematically altering the diet and background microbiota complexity. In-transit EcN accumulates genetic mutations that modulate carbohydrate utilization, stress response, and adhesion to gain competitive fitness, while previous exposure to antibiotics reveals an acquisition of resistance. We then leveraged these insights to generate an EcN strain that shows therapeutic efficacy in a mouse model of phenylketonuria and found that it was genetically stable over 1 week, thereby validating EcN's utility as a chassis for engineering. Collectively, we demonstrate a generalizable pipeline that can be applied to other probiotics to better understand their safety and engineering potential.
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Affiliation(s)
- Nathan Crook
- Equal Contribution
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA
| | - Aura Ferreiro
- Equal Contribution
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Andrew J. Gasparrini
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: VL55, 55 Cambridge Pwky, Cambridge, MA 02142, USA
| | - Mitchell W. Pesesky
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Molly K. Gibson
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Flagship Pioneering, 55 Cambridge Pkwy, Cambridge, MA 02142, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zevin Condiotte
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Present address: Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen Dobrowolski
- Department of Pathology, Children’s Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Daniel Peterson
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Present address: Eli Lilly & Company, 307 East McCarty Street, Indianapolis, IN 46225, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Lead Contact: Gautam Dantas, Ph.D. ()
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229
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Raymond F, Boissinot M, Ouameur AA, Déraspe M, Plante PL, Kpanou SR, Bérubé È, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J. Culture-enriched human gut microbiomes reveal core and accessory resistance genes. MICROBIOME 2019; 7:56. [PMID: 30953542 PMCID: PMC6451232 DOI: 10.1186/s40168-019-0669-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/20/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer. RESULTS Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements. CONCLUSION Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.
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Affiliation(s)
- Frédéric Raymond
- École de nutrition, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec City, Canada.
- Institut sur la nutrition et les aliments fonctionnels, Québec, Canada.
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Amin Ahmed Ouameur
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Maxime Déraspe
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
| | - Pier-Luc Plante
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
| | - Sewagnouin Rogia Kpanou
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
| | - Ève Bérubé
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Ann Huletsky
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Paul H Roy
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Département de Microbiologie, Infectiologie et d'Immunologie, Faculté de Médecine, Université Laval, Québec City, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Département de Microbiologie, Infectiologie et d'Immunologie, Faculté de Médecine, Université Laval, Québec City, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
- Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec City, Canada
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Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose. Appl Environ Microbiol 2019; 85:AEM.03018-18. [PMID: 30709823 DOI: 10.1128/aem.03018-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/30/2019] [Indexed: 12/13/2022] Open
Abstract
Few characteristics are more important to a bacterium than the substrates it consumes. It is hard to identify what substrates are consumed by bacteria in natural communities, however, because most bacteria have not been cultured. In this study, we developed a method that uses fluorescent substrate analogs, cell sorting, and DNA sequencing to identify substrates taken up by bacteria. We deployed this method using 2[N-(7-nitrobenz-2-oxa-1,2-diaxol-4-yl)amino]-2-deoxyglucose (2-NBDG), a fluorescent glucose analog, and bacteria of the bovine rumen. This method revealed over 40 different bacteria (amplicon sequence variants [ASVs]) from the rumen that take up glucose. Nearly half of these ASVs represent previously uncultured bacteria. We attempted to grow these ASVs on agar media, and we confirmed that nearly two-thirds resisted culture. In coculture experiments, the fluorescent label of 2-NBDG was not transferred to nontarget bacteria by cross-feeding. Because it is not affected by cross-feeding, our method has an advantage over stable isotope probing. Though we focus on glucose, many substrates can be labeled with the fluorophore NBD. Our method represents a new paradigm for identifying substrates used by uncultured bacteria. It will help delineate the niche of bacteria in their environment.IMPORTANCE We introduce a method for identifying what substrates are consumed by bacteria in natural communities. Our method offers significant improvement over existing methods for studying this characteristic. Our method uses a fluorescently labeled substrate which clearly labels target bacteria (glucose consumers in our case). Previous methods use isotope-labeled substrates, which are notorious for off-target labeling (due to cross-feeding of labeled metabolites). Our method can be deployed with a variety of substrates and microbial communities. It represents a major advance in connecting bacteria to the substrates they take up.
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Rodríguez Amor D, Dal Bello M. Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities. Life (Basel) 2019; 9:E22. [PMID: 30813538 PMCID: PMC6462982 DOI: 10.3390/life9010022] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 12/25/2022] Open
Abstract
Microbial cooperation pervades ecological scales, from single-species populations to host-associated microbiomes. Understanding the mechanisms promoting the stability of cooperation against potential threats by cheaters is a major question that only recently has been approached experimentally. Synthetic biology has helped to uncover some of these basic mechanisms, which were to some extent anticipated by theoretical predictions. Moreover, synthetic cooperation is a promising lead towards the engineering of novel functions and enhanced productivity of microbial communities. Here, we review recent progress on engineered cooperation in microbial ecosystems. We focus on bottom-up approaches that help to better understand cooperation at the population level, progressively addressing the challenges of tackling higher degrees of complexity: spatial structure, multispecies communities, and host-associated microbiomes. We envisage cooperation as a key ingredient in engineering complex microbial ecosystems.
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Affiliation(s)
- Daniel Rodríguez Amor
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Martina Dal Bello
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Beneficial effects of Enterococcus faecalis in hypercholesterolemic mice on cholesterol transportation and gut microbiota. Appl Microbiol Biotechnol 2019; 103:3181-3191. [DOI: 10.1007/s00253-019-09681-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 01/22/2023]
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234
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Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Science 2019; 363:363/6427/eaat9931. [PMID: 30733391 DOI: 10.1126/science.aat9931] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 11/02/2018] [Accepted: 12/20/2018] [Indexed: 12/24/2022]
Abstract
The gut microbiota is implicated in the metabolism of many medical drugs, with consequences for interpersonal variation in drug efficacy and toxicity. However, quantifying microbial contributions to drug metabolism is challenging, particularly in cases where host and microbiome perform the same metabolic transformation. We combined gut commensal genetics with gnotobiotics to measure brivudine drug metabolism across tissues in mice that vary in a single microbiome-encoded enzyme. Informed by these measurements, we built a pharmacokinetic model that quantitatively predicts microbiome contributions to systemic drug and metabolite exposure, as a function of bioavailability, host and microbial drug-metabolizing activity, drug and metabolite absorption, and intestinal transit kinetics. Clonazepam studies illustrate how this approach disentangles microbiome contributions to metabolism of drugs subject to multiple metabolic routes and transformations.
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Affiliation(s)
- Michael Zimmermann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Maria Zimmermann-Kogadeeva
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Rebekka Wegmann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
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235
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A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat Biotechnol 2019; 37:186-192. [PMID: 30718869 PMCID: PMC6785715 DOI: 10.1038/s41587-018-0009-7] [Citation(s) in RCA: 311] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 12/13/2018] [Indexed: 12/12/2022]
Abstract
Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota. A large bacterial strain collection and genome sequences will boost gut microbiome research.
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236
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Gershuni VM, Friedman ES. The Microbiome-Host Interaction as a Potential Driver of Anastomotic Leak. Curr Gastroenterol Rep 2019; 21:4. [PMID: 30684121 DOI: 10.1007/s11894-019-0668-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The goal of this paper is to review current literature on the gut microbiome within the context of host response to surgery and subsequent risk of developing complications, particularly anastomotic leak. We provide background on the relationship between host and gut microbiota with description of the role of the intestinal mucus layer as an important regulator of host health. RECENT FINDINGS Despite improvements in surgical technique and adherence to the tenets of creating a tension-free anastomosis with adequate blood flow, the surgical community has been unable to decrease rates of anastomotic leak using the current paradigm. Rather than adhere to empirical strategies of decontamination, it is imperative to focus on the interaction between the human host and the gut microbiota that live within us. The gut microbiome has been found to play a potential role in development of post-operative complications, including but not limited to anastomotic leak. Evidence suggests that peri-operative interventions may have a role in instigating or mitigating the impact of the gut microbiota via disruption of the protective mucus layer, use of multiple medications, and activation of virulence factors. The microbiome plays a potential role in the development of surgical complications and can be modulated by peri-operative interventions. As such, further research into this relationship is urgently needed.
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Affiliation(s)
- Victoria M Gershuni
- Department of Surgery, Perelman School of Medicine, Hospital of the University of Pennsylvania, 3400 Spruce Street, 4 Maloney, Philadelphia, PA, 19104, USA. .,Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Elliot S Friedman
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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237
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Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, Llewellyn SR, Hira S, Johnson C, Rabinowitz KM, Barkan R, Dotan I, Hirten RP, Fu SC, Luo Y, Yang N, Luong T, Labrias PR, Lira S, Peter I, Grinspan A, Clemente JC, Kosoy R, Kim-Schulze S, Qin X, Castillo A, Hurley A, Atreja A, Rogers J, Fasihuddin F, Saliaj M, Nolan A, Reyes-Mercedes P, Rodriguez C, Aly S, Santa-Cruz K, Peters L, Suárez-Fariñas M, Huang R, Hao K, Zhu J, Zhang B, Losic B, Irizar H, Song WM, Di Narzo A, Wang W, Cohen BL, DiMaio C, Greenwald D, Itzkowitz S, Lucas A, Marion J, Maser E, Ungaro R, Naymagon S, Novak J, Shah B, Ullman T, Rubin P, George J, Legnani P, Telesco SE, Friedman JR, Brodmerkel C, Plevy S, Cho JH, Colombel JF, Schadt EE, Argmann C, Dubinsky M, Kasarskis A, Sands B, Faith JJ. Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife 2019; 8:e40553. [PMID: 30666957 PMCID: PMC6342524 DOI: 10.7554/elife.40553] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn's disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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238
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Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel JF, Dubinsky MC, Faith JJ. Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt + Regulatory T Cells and Exacerbate Colitis in Mice. Immunity 2019; 50:212-224.e4. [PMID: 30650377 PMCID: PMC6512335 DOI: 10.1016/j.immuni.2018.12.015] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/03/2018] [Accepted: 12/13/2018] [Indexed: 12/13/2022]
Abstract
Microbiota are thought to influence the development and progression of inflammatory bowel disease (IBD), but determining generalizable effects of microbiota on IBD etiology requires larger-scale functional analyses. We colonized germ-free mice with intestinal microbiotas from 30 healthy and IBD donors and determined the homeostatic intestinal T cell response to each microbiota. Compared to microbiotas from healthy donors, transfer of IBD microbiotas into germ-free mice increased numbers of intestinal Th17 cells and Th2 cells and decreased numbers of RORγt+ Treg cells. Colonization with IBD microbiotas exacerbated disease in a model where colitis is induced upon transfer of naive T cells into Rag1-/- mice. The proportions of Th17 and RORγt+ Treg cells induced by each microbiota were predictive of human disease status and accounted for disease severity in the Rag1-/- colitis model. Thus, an impact on intestinal Th17 and RORγt+ Treg cell compartments emerges as a unifying feature of IBD microbiotas, suggesting a general mechanism for microbial contribution to IBD pathogenesis.
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Affiliation(s)
- Graham J Britton
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilaria Mogno
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia H Vennaro
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean R Llewellyn
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruby Ng
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihua Li
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arthur Mortha
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anuk Das
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Namita Singh
- Pediatric Gastroenterology and Inflammatory Bowel Disease, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Braun
- UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jose C Clemente
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce E Sands
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C Dubinsky
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Pediatric Gastroenterology and Hepatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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239
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Perofsky AC, Lewis RJ, Meyers LA. Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals. THE ISME JOURNAL 2019; 13:50-63. [PMID: 30108305 PMCID: PMC6299109 DOI: 10.1038/s41396-018-0251-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/03/2018] [Accepted: 07/19/2018] [Indexed: 12/14/2022]
Abstract
The gut microbiomes of mammals appear to mirror their hosts' phylogeny, suggesting host-driven microbial community assembly. Yet, much of this evidence stems from comparative studies of distinct wild or captive populations that lack data for disentangling the relative influences of shared phylogeny and environment. Here, we present phylogenetic and multivariate analyses of gut microbiomes from six sympatric (i.e., co-occurring) mammal species inhabiting a 1-km2 area in western Madagascar-three lemur and three non-primate species-that consider genetic, dietary, and ecological predictors of microbiome functionality and composition. Host evolutionary history, indeed, appears to shape gut microbial patterns among both closely and distantly related species. However, we also find that diet-reliance on leaves versus fruit-is the best predictor of microbiome similarity among closely related lemur species, and that host substrate use-ground versus tree-constrains horizontal transmission via incidental contact with feces, with arboreal species harboring far more distinct communities than those of their terrestrial and semi-terrestrial counterparts.
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Affiliation(s)
- Amanda C Perofsky
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Rebecca J Lewis
- Department of Anthropology, The University of Texas at Austin, Austin, TX, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Santa Fe Institute, Santa Fe, NM, USA
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240
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Zegarra-Ruiz DF, El Beidaq A, Iñiguez AJ, Lubrano Di Ricco M, Manfredo Vieira S, Ruff WE, Mubiru D, Fine RL, Sterpka J, Greiling TM, Dehner C, Kriegel MA. A Diet-Sensitive Commensal Lactobacillus Strain Mediates TLR7-Dependent Systemic Autoimmunity. Cell Host Microbe 2018; 25:113-127.e6. [PMID: 30581114 DOI: 10.1016/j.chom.2018.11.009] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/27/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022]
Abstract
Western lifestyle is linked to autoimmune and metabolic diseases, driven by changes in diet and gut microbiota composition. Using Toll-like receptor 7 (TLR7)-dependent mouse models of systemic lupus erythematosus (SLE), we dissect dietary effects on the gut microbiota and find that Lactobacillus reuteri can drive autoimmunity but is ameliorated by dietary resistant starch (RS). Culture of internal organs and 16S rDNA sequencing revealed TLR7-dependent translocation of L. reuteri in mice and fecal enrichment of Lactobacillus in a subset of SLE patients. L. reuteri colonization worsened autoimmune manifestations under specific-pathogen-free and gnotobiotic conditions, notably increasing plasmacytoid dendritic cells (pDCs) and interferon signaling. However, RS suppressed the abundance and translocation of L. reuteri via short-chain fatty acids, which inhibited its growth. Additionally, RS decreased pDCs, interferon pathways, organ involvement, and mortality. Thus, RS exerts beneficial effects in lupus-prone hosts through suppressing a pathobiont that promotes interferon pathways implicated in the pathogenesis of human autoimmunity.
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MESH Headings
- Animals
- Autoimmunity
- Clostridiaceae
- DNA, Ribosomal/genetics
- Dendritic Cells/metabolism
- Diet
- Diet Therapy
- Disease Models, Animal
- Fatty Acids, Volatile/antagonists & inhibitors
- Fatty Acids, Volatile/metabolism
- Feces/microbiology
- Female
- Gastrointestinal Microbiome
- Germ-Free Life
- Glomerulonephritis/pathology
- Humans
- Hypersensitivity
- Interferon Type I/metabolism
- Kidney/pathology
- Lactobacillus/drug effects
- Lactobacillus/genetics
- Lactobacillus/pathogenicity
- Limosilactobacillus reuteri
- Lupus Erythematosus, Systemic/microbiology
- Lupus Erythematosus, Systemic/mortality
- Lupus Erythematosus, Systemic/pathology
- Membrane Glycoproteins/metabolism
- Mice
- Mice, Inbred C57BL
- RNA, Ribosomal, 16S/genetics
- Starch
- Survival Rate
- Toll-Like Receptor 7/metabolism
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Affiliation(s)
- Daniel F Zegarra-Ruiz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Asmaa El Beidaq
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Alonso J Iñiguez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | | | - Silvio Manfredo Vieira
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - William E Ruff
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Derek Mubiru
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Rebecca L Fine
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - John Sterpka
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Teri M Greiling
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Carina Dehner
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Martin A Kriegel
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA.
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241
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GABA-modulating bacteria of the human gut microbiota. Nat Microbiol 2018; 4:396-403. [PMID: 30531975 PMCID: PMC6384127 DOI: 10.1038/s41564-018-0307-3] [Citation(s) in RCA: 556] [Impact Index Per Article: 92.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022]
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242
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Del Fiol FS, Balcão VM, Barberato-Fillho S, Lopes LC, Bergamaschi CC. Obesity: A New Adverse Effect of Antibiotics? Front Pharmacol 2018; 9:1408. [PMID: 30559670 PMCID: PMC6287021 DOI: 10.3389/fphar.2018.01408] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Since the introduction of antibiotics, they have been used freely, with their prescription occurring almost always when they were not necessary. The other major form of contact between humans and antibiotics, now unintentionally, is with the large amount of these drugs in the environment and in our food. The relationship between antibiotic use and the development of obesity has become increasingly evident and apparent in humans, with some authors clearly establishing the relationship between the large-scale use of antibiotics in the past 70 years and the “epidemic” of obesity that has occurred in parallel, almost as an adverse epidemiological effect. In the research effort entertained herein, a correlation between the use and abuse of antibiotics and the onset of obesity was investigated.
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Affiliation(s)
- Fernando S Del Fiol
- Seriema - Evidence Service for Monitoring and Evaluation, University of Sorocaba, Sorocaba, Brazil
| | - Victor M Balcão
- PhageLab - Laboratory of Biofilms and Bacteriophages of UNISO, i(bs)2 - Intelligent Biosensing and Biomolecule Stabilization Research Group, University of Sorocaba, Sorocaba, Brazil
| | - Silvio Barberato-Fillho
- Seriema - Evidence Service for Monitoring and Evaluation, University of Sorocaba, Sorocaba, Brazil
| | - Luciane C Lopes
- Seriema - Evidence Service for Monitoring and Evaluation, University of Sorocaba, Sorocaba, Brazil
| | - Cristiane C Bergamaschi
- Seriema - Evidence Service for Monitoring and Evaluation, University of Sorocaba, Sorocaba, Brazil
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243
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Ho L, Zhao D, Ono K, Ruan K, Mogno I, Tsuji M, Carry E, Brathwaite J, Sims S, Frolinger T, Westfall S, Mazzola P, Wu Q, Hao K, Lloyd TE, Simon JE, Faith J, Pasinetti GM. Heterogeneity in gut microbiota drive polyphenol metabolism that influences α-synuclein misfolding and toxicity. J Nutr Biochem 2018; 64:170-181. [PMID: 30530257 DOI: 10.1016/j.jnutbio.2018.10.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 09/19/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022]
Abstract
The intestinal microbiota actively converts dietary flavanols into phenolic acids, some of which are bioavailable in vivo and may promote resilience to select neurological disorders by interfering with key pathologic mechanisms. Since every person harbors a unique set of gut bacteria, we investigated the influence of the gut microbiota's interpersonal heterogeneity on the production and bioavailability of flavonoid metabolites that may interfere with the misfolding of alpha (α)-synuclein, a process that plays a central role in Parkinson's disease and other α-synucleinopathies. We generated two experimental groups of humanized gnotobiotic mice with compositionally diverse gut bacteria and orally treated the mice with a flavanol-rich preparation (FRP). The two gnotobiotic mouse groups exhibited distinct differences in the generation and bioavailability of FRP-derived microbial phenolic acid metabolites that have bioactivity towards interfering with α-synuclein misfolding or inflammation. We also demonstrated that these bioactive phenolic acids are effective in modulating the development and progression of motor dysfunction in a Drosophila model of α-synucleinopathy. Lastly, through in vitro bacterial fermentation studies, we identified select bacteria that are capable of supporting the generation of these bioavailable and bioactive phenolic acids. Outcomes from our studies provide a better understanding of how interpersonal heterogeneity in the gut microbiota differentially modulates the efficacy of dietary flavanols to protect against select pathologic mechanisms. Collectively, our findings provide the basis for future developments of probiotic, prebiotic, or synbiotic approaches for modulating the onset and/or progression of α-synucleinopathies and other neurological disorders involving protein misfolding and/or inflammation.
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Affiliation(s)
- Lap Ho
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029; Geriatric Research, Education and Clinical Center, James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA 10468
| | - Danyue Zhao
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA 08901
| | - Kenjiro Ono
- Department of Internal Medicine, Division of Neurology, Showa University School of Medicine, Tokyo, Japan
| | - Kai Ruan
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, USA, MD 21205
| | - Ilaria Mogno
- Precision Immunology Institute and Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029
| | - Mayumi Tsuji
- Department of Pharmacology, Showa University School of Medicine, Tokyo, Japan
| | - Eileen Carry
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Piscataway, NJ, USA 08854
| | - Justin Brathwaite
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029
| | - Steven Sims
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029
| | - Tal Frolinger
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029
| | - Susan Westfall
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029
| | - Paolo Mazzola
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029
| | - Qingli Wu
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA 08901
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, USA, MD 21205; Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, USA, MD 21205
| | - James E Simon
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA 08901
| | - Jeremiah Faith
- Precision Immunology Institute and Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029
| | - Giulio M Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, NY, New York, USA 10029; Geriatric Research, Education and Clinical Center, James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA 10468.
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244
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Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model. Nat Microbiol 2018; 3:1461-1471. [PMID: 30397344 PMCID: PMC6280189 DOI: 10.1038/s41564-018-0272-x] [Citation(s) in RCA: 299] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
Abstract
Humans with metabolic and inflammatory diseases frequently harbour lower levels of butyrate-producing bacteria in their gut. However, it is not known whether variation in the levels of these organisms is causally linked with disease development and whether diet modifies the impact of these bacteria on health. Here we show that a prominent gut-associated butyrate-producing bacterial genus (Roseburia) is inversely correlated with atherosclerotic lesion development in a genetically diverse mouse population. We use germ-free apolipoprotein E-deficient mice colonized with synthetic microbial communities that differ in their capacity to generate butyrate to demonstrate that Roseburia intestinalis interacts with dietary plant polysaccharides to: impact gene expression in the intestine, directing metabolism away from glycolysis and toward fatty acid utilization; lower systemic inflammation; and ameliorate atherosclerosis. Furthermore, intestinal administration of butyrate reduces endotoxaemia and atherosclerosis development. Together, our results illustrate how modifiable diet-by-microbiota interactions impact cardiovascular disease, and suggest that interventions aimed at increasing the representation of butyrate-producing bacteria may provide protection against atherosclerosis.
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245
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Wang H, Zhang X, Wang S, Li H, Lu Z, Shi J, Xu Z. Mannan-oligosaccharide modulates the obesity and gut microbiota in high-fat diet-fed mice. Food Funct 2018; 9:3916-3929. [PMID: 29974116 DOI: 10.1039/c8fo00209f] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The gut microbiota is considered to be associated with high-fat diet (HFD)-induced obesity and metabolic syndrome (MS). Mannan-oligosaccharide (MOS) is widely used as a natural additive, and its effect on promoting fat metabolism has been reported. Here, we performed a 11-week study on C57BL/6J mice fed a high-fat diet (HFD) with/without MOS supplementation, and the results showed that MOS could attenuate high-fat diet induced metabolic syndrome, including slower body weight gain, lowered serum lipids and reduced insulin resistance. Next generation sequencing (NGS) of the gut microbiota indicated that MOS modulated the overall structure of the gut microbiome, which was highly correlated with MS parameters. Specifically, the intake of MOS decreased the Firmicutes/Bacteroidetes ratio and could reverse the changes in the relative abundance of several species caused by HFD, including Akkermansia muciniphila, Bacteroides acidifaciens, Lactobacillus gasseri and Bifidobacterium pseudolongum. Thus, MOS has the potential to be used as a new prebiotic for regulating the gut microbiota and helping in attenuating metabolic disorders.
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Affiliation(s)
- Hongshan Wang
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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246
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Honey bees as models for gut microbiota research. Lab Anim (NY) 2018; 47:317-325. [PMID: 30353179 DOI: 10.1038/s41684-018-0173-x] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
Abstract
The gut microbiota of the honey bee (Apis mellifera) offers several advantages as an experimental system for addressing how gut communities affect their hosts and for exploring the processes that determine gut community composition and dynamics. A small number of bacterial species dominate the honey bee gut community. These species are restricted to bee guts and can be grown axenically and genetically manipulated. Large numbers of microbiota-free hosts can be economically reared and then inoculated with single isolates or defined communities to examine colonization patterns and effects on host phenotypes. Honey bees have been studied extensively, due to their importance as agricultural pollinators and as models for sociality. Because of this history of bee research, the physiology, development, and behavior of honey bees is relatively well understood, and established behavioral and phenotypic assays are available. To date, studies on the honey bee gut microbiota show that it affects host nutrition, weight gain, endocrine signaling, immune function, and pathogen resistance, while perturbation of the microbiota can lead to reduced host fitness. As in humans, the microbiota is concentrated in the distal part of the gut, where it contributes to digestion and fermentation of plant cell wall components. Much like the human gut microbiota, many bee gut bacteria are specific to the bee gut and can be directly transmitted between individuals through social interaction. Although simpler than the human gut microbiota, the bee gut community presents opportunities to understand the processes that govern the assembly of specialized gut communities as well as the routes through which gut communities impact host biology.
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247
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Cadena AM, Ma Y, Ding T, Bryant M, Maiello P, Geber A, Lin PL, Flynn JL, Ghedin E. Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure. MICROBIOME 2018; 6:180. [PMID: 30301469 PMCID: PMC6178261 DOI: 10.1186/s40168-018-0560-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/20/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND The specific interactions of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and the lung microbiota in infection are entirely unexplored. Studies in cancer and other infectious diseases suggest that there are important exchanges occurring between host and microbiota that influence the immunological landscape. This can result in alterations in immune regulation and inflammation both locally and systemically. To assess whether Mtb infection modifies the lung microbiome, and identify changes in microbial abundance and diversity as a function of pulmonary inflammation, we compared infected and uninfected lung lobe washes collected serially from 26 macaques by bronchoalveolar lavage over the course of infection. RESULTS We found that Mtb induced an initial increase in lung microbial diversity at 1 month post infection that normalized by 5 months of infection across all macaques. Several core genera showed global shifts from baseline and throughout infection. Moreover, we identified several specific taxa normally associated with the oral microbiome that increased in relative abundance in the lung following Mtb infection, including SR1, Aggregatibacter, Leptotrichia, Prevotella, and Campylobacter. On an individual macaque level, we found significant heterogeneity in both the magnitude and duration of change within the lung microbial community that was unrelated to lung inflammation and lobe involvement as seen by positron emission tomography/computed tomography (PET/CT) imaging. By comparing microbial interaction networks pre- and post-infection using the predictive algorithm SPIEC-EASI, we observe that extra connections are gained by Actinomycetales, the order containing Mtb, in spite of an overall reduction in the number of interactions of the whole community post-infection, implicating Mtb-driven ecological reorganization within the lung. CONCLUSIONS This study is the first to probe the dynamic interplay between Mtb and host microbiota longitudinally and in the macaque lung. Our findings suggest that Mtb can alter the microbial landscape of infected lung lobes and that these interactions induce dysbiosis that can disrupt oral-airway boundaries, shift overall lung diversity, and modulate specific microbial relationships. We also provide evidence that this effect is heterogeneous across different macaques. Overall, however, the changes to the airway microbiota after Mtb infection were surprisingly modest, despite a range of Mtb-induced pulmonary inflammation in this cohort of macaques.
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Affiliation(s)
- Anthony M Cadena
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Present address: Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yixuan Ma
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - Tao Ding
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - MacKenzie Bryant
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Present address: Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Adam Geber
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - Philana Ling Lin
- Department of Pediatrics, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA.
- College of Global Public Health, New York University, New York, NY, USA.
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248
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Zhang C, Jiao S, Wang ZA, Du Y. Exploring Effects of Chitosan Oligosaccharides on Mice Gut Microbiota in in vitro Fermentation and Animal Model. Front Microbiol 2018; 9:2388. [PMID: 30356845 PMCID: PMC6190755 DOI: 10.3389/fmicb.2018.02388] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/18/2018] [Indexed: 01/15/2023] Open
Abstract
Chitosan oligosaccharides (COS) have shown positive effects on host gut health and influence on intestinal microbial community. However, the bioactivity and mechanism of COS on gut microbiota is still poorly understood. Here, we presented systematic studies of COS on mice fecal/gut microbiota. During in vitro fermentation of COS by mice gut microbiota, total bacterial population significantly decreased after 8-h COS treatment but was returned to the normal level after extended incubation. Consumption of COS and production of SCFAs suggested that COS were utilized by the microbe, although the consumption of chitosan pentasaccharides was obviously slower than others. COS treatments on mice fecal samples caused the decrease of potential pathogenic genera Escherichia/Shigella and the increase of genus Parabacteroides. In vivo animal study indicated that COS reduced population of probiotic genera Lactobacillus, Bifidobacterium and harmful genus Desulfovibrio, and increased abundance of genus Akkermansia. Phylum Proteobacteria was significantly inhibited by COS both in the animal model and in vitro fermentation. Our findings suggested that COS could reform the community structure of gut microbiota. The relationship among COS, gut microbiota and host health deserve further study.
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Affiliation(s)
- Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Siming Jiao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zhuo A Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
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249
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Derakhshani H, Fehr KB, Sepehri S, Francoz D, De Buck J, Barkema HW, Plaizier JC, Khafipour E. Invited review: Microbiota of the bovine udder: Contributing factors and potential implications for udder health and mastitis susceptibility. J Dairy Sci 2018; 101:10605-10625. [PMID: 30292553 DOI: 10.3168/jds.2018-14860] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/05/2018] [Indexed: 12/13/2022]
Abstract
Various body sites of vertebrates provide stable and nutrient-rich ecosystems for a diverse range of commensal, opportunistic, and pathogenic microorganisms to thrive. The collective genomes of these microbial symbionts (the microbiome) provide host animals with several advantages, including metabolism of indigestible carbohydrates, biosynthesis of vitamins, and modulation of innate and adaptive immune systems. In the context of the bovine udder, however, the relationship between cow and microbes has been traditionally viewed strictly from the perspective of host-pathogen interactions, with intramammary infections by mastitis pathogens triggering inflammatory responses (i.e., mastitis) that are often detrimental to mammary tissues and cow physiology. This traditional view has been challenged by recent metagenomic studies indicating that mammary secretions of clinically healthy quarters can harbor genomic markers of diverse bacterial groups, the vast majority of which have not been associated with mastitis. These observations have given rise to the concept of "commensal mammary microbiota," the ecological properties of which can have important implications for understanding the pathogenesis of mastitis and offer opportunities for development of novel prophylactic or therapeutic products (or both) as alternatives to antimicrobials. Studies conducted to date have suggested that an optimum diversity of mammary microbiota is associated with immune homeostasis, whereas the microbiota of mastitic quarters, or those with a history of mastitis, are considerably less diverse. Whether disruption of the diversity of udder microbiota (dysbiosis) has a role in determining mastitis susceptibility remains unknown. Moreover, little is known about contributions of various biotic and abiotic factors in shaping overall diversity of udder microbiota. This review summarizes current understanding of the microbiota within various niches of the udder and highlights the need to view the microbiota of the teat apex, teat canal, and mammary secretions as interconnected niches of a highly dynamic microbial ecosystem. In addition, host-associated factors, including physiological and anatomical parameters, as well as genetic traits that may affect the udder microbiota are briefly discussed. Finally, current understanding of the effect of antimicrobials on the composition of intramammary microbiota is discussed, highlighting the resilience of udder microbiota to exogenous perturbants.
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Affiliation(s)
- Hooman Derakhshani
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada
| | - Kelsey B Fehr
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada
| | - Shadi Sepehri
- Children Hospital Research Institute of Manitoba, Winnipeg, MB, R3E 3P4 Canada
| | - David Francoz
- Département de Sciences Cliniques, Faculté de Médecine Vétérinaire, Université de Montréal, Montréal, QC, J2S 2M2 Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1 Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1 Canada
| | - Jan C Plaizier
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9 Canada.
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250
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Seekatz AM, Theriot CM, Rao K, Chang YM, Freeman AE, Kao JY, Young VB. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection. Anaerobe 2018; 53:64-73. [PMID: 29654837 PMCID: PMC6185828 DOI: 10.1016/j.anaerobe.2018.04.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 02/06/2023]
Abstract
A significant proportion of individuals develop recurrent Clostridium difficile infection (CDI) following initial disease. Fecal microbiota transplantation (FMT), a highly effective treatment method for recurrent CDI, has been demonstrated to induce microbiota recovery. One of the proposed functions associated with restoration of colonization resistance against C. difficile has been recovery of bile acid metabolism. In this study, we aimed to assess recovery of short chain fatty acids (SCFAs) in addition to bile acids alongside microbial community structure in six patients with recurrent CDI following treatment with FMT over time. Using 16S rRNA gene-based sequencing, we observed marked similarity of the microbiota between recipients following FMT (n = 6, sampling up to 6 months post-FMT) and their respective donors. Sustained increases in the levels of the SCFAs butyrate, acetate, and propionate were observed post-FMT, and variable recovery over time was observed in the secondary bile acids deoxycholate and lithocholate. To correlate these changes with specific microbial taxa at an individual level, we applied a generalized estimating equation approach to model metabolite concentrations with the presence of specific members of the microbiota. Metabolites that increased following FMT were associated with bacteria classified within the Lachnospiraceae, Ruminococcaceae, and unclassified Clostridiales families. In contrast, members of these taxa were inversely associated with primary bile acids. The longitudinal aspect of this study allowed us to characterize individualized patterns of recovery, revealing variability between and within patients following FMT.
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Affiliation(s)
- Anna M Seekatz
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Casey M Theriot
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Yu-Ming Chang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Alison E Freeman
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John Y Kao
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, United States.
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