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Xie H, Guo R, Zhong H, Feng Q, Lan Z, Qin B, Ward KJ, Jackson MA, Xia Y, Chen X, Chen B, Xia H, Xu C, Li F, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Wang J, Steves CJ, Bell JT, Li J, Spector TD, Jia H. Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome. Cell Syst 2016; 3:572-584.e3. [PMID: 27818083 PMCID: PMC6309625 DOI: 10.1016/j.cels.2016.10.004] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 07/13/2016] [Accepted: 10/05/2016] [Indexed: 12/14/2022]
Abstract
The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those associated with diseases. Moreover, we identified 8 million SNPs in the gut microbiome and observe a high similarity in microbiome SNPs between twins that slowly decreases after decades of living apart. The results shed new light on the genetic and environmental influences on the composition and function of the gut microbiome that could relate to risk of complex diseases.
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Affiliation(s)
- Hailiang Xie
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Ruijin Guo
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Huanzi Zhong
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiang Feng
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhou Lan
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Kirsten J Ward
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Matthew A Jackson
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Yan Xia
- BGI-Shenzhen, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xu Chen
- BGI-Shenzhen, Shenzhen 518083, China; Qingdao University-BGI Joint Innovation College, Qingdao University, Qingdao 266071, China
| | - Bing Chen
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Huihua Xia
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Changlu Xu
- BGI-Shenzhen, Shenzhen 518083, China; Qingdao University-BGI Joint Innovation College, Qingdao University, Qingdao 266071, China
| | - Fei Li
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.
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352
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Yang L, Wang L, Wang X, Xian CJ, Lu H. A Possible Role of Intestinal Microbiota in the Pathogenesis of Ankylosing Spondylitis. Int J Mol Sci 2016; 17:ijms17122126. [PMID: 27999312 PMCID: PMC5187926 DOI: 10.3390/ijms17122126] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/09/2016] [Accepted: 12/14/2016] [Indexed: 12/12/2022] Open
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory disease primarily affecting the sacroiliac joints and the spine, for which the pathogenesis is thought to be a result of the combination of host genetic factors and environmental triggers. However, the precise factors that determine one’s susceptibility to AS remain to be unraveled. With 100 trillion bacteria residing in the mammalian gut having established a symbiotic relation with their host influencing many aspects of host metabolism, physiology, and immunity, a growing body of evidence suggests that intestinal microbiota may play an important role in AS. Several mechanisms have been suggested to explain the potential role of the microbiome in the etiology of AS, such as alterations of intestinal permeability, stimulation of immune responses, and molecular mimicry. In this review, the existing evidence for the involvement of the microbiome in AS pathogenesis was discussed and the potential of intestinal microbiome-targeting strategies in the prevention and treatment of AS was evaluated.
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Affiliation(s)
- Lianjun Yang
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
| | - Liping Wang
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
- Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide SA5001, Australia.
| | - Xin Wang
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane QLD4059, Australia.
| | - Cory J Xian
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
- Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide SA5001, Australia.
| | - Hai Lu
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
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353
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Koopen AM, Groen AK, Nieuwdorp M. Human microbiome as therapeutic intervention target to reduce cardiovascular disease risk. Curr Opin Lipidol 2016; 27:615-622. [PMID: 27676197 DOI: 10.1097/mol.0000000000000357] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW The absolute burden of cardiovascular risk remains high despite currently available preventive and therapeutic options. In search for novel therapeutic leads, mounting evidence has linked the gut microbiota as well as their metabolites to the development of cardiometabolic diseases. RECENT FINDINGS The intestinal microbiota influences the host via different metabolic pathways as inducer of endotoxemia, formation of trimethylamine-N-oxide, production of short chain fatty acids, and is a regulator in intestinal bile acid metabolism. Disruption of the gut microbiome may disturb the homeostasis of the microbial ecosystem to an alternative stable state associated with pathophysiological traits in microbiota and host. However, causality has not been shown yet. SUMMARY We are just beginning to understand how the gut microbiota influence our cardiometabolic health and various innovative therapeutic options are in the developing (preclinical) phase. This review focuses on the current evidence whether and to what extent the intestinal microbiota are involved in cardiovascular disease and whether this is based on merely association or causal relations.
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Affiliation(s)
- Annefleur M Koopen
- aDepartment of Vascular Medicine, Academic Medical Center, Amsterdam bLaboratory of Metabolic Diseases, Department of Pediatrics, UMCG, Groningen, The Netherlands cWallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden dDepartment of Internal Medicine eICAR, VU University Medical Center, Amsterdam, The Netherlands
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355
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Pigneur B, Sokol H. Fecal microbiota transplantation in inflammatory bowel disease: the quest for the holy grail. Mucosal Immunol 2016; 9:1360-1365. [PMID: 27461176 DOI: 10.1038/mi.2016.67] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/22/2016] [Indexed: 02/04/2023]
Abstract
Inflammatory bowel disease (IBD) is due to an aberrant immune response toward luminal antigens, probably commensal bacteria, in genetically susceptible subjects and is also influenced by environmental factors. An imbalanced intestinal microbiota known as "dysbiosis," characterized by an increased proportion of pro-inflammatory microorganisms and a decreased proportion of anti-inflammatory microorganisms, has been repeatedly observed in IBD and is now recognized as a key factor in the gut inflammatory process. Fecal microbiota transplantation (FMT) has gained interest as a novel treatment option in IBD. The goal of FMT in IBD is not only to correct the dysbiosis, but also to restore a normal dialog between the host immune system and the microbiota. Data are still scarce, but the results of the first studies suggest that FMT could be a promising therapy in IBD. More studies are needed to define the best indications, optimal timing, frequency, mode of delivery, and the optimal donor for each patient.
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Affiliation(s)
- B Pigneur
- Institut National de la Santé et de la Recherche Médicale INSERM UMR1163, Laboratory of Intestinal Immunity, Institut Imagine, Paris, France.,Department of Pediatric Gastroenterology, Hepatology and Nutrition, Necker Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris Descartes-Sorbonne Paris Cite, Paris, France.,French Group of Faecal Microbiota Transplantation (GFTF)
| | - H Sokol
- French Group of Faecal Microbiota Transplantation (GFTF).,Sorbonne University-UPMC Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, Paris, France.,INRA, UMR1319 Micalis and AgroParisTech, Jouy-en-Josas, France.,Department of Gastroenterology, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France
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356
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Moelling K, Broecker F. Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases. BACTERIOPHAGE 2016; 6:e1251380. [PMID: 28090385 DOI: 10.1080/21597081.2016.1251380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/13/2016] [Accepted: 10/18/2016] [Indexed: 12/16/2022]
Abstract
We have analyzed fecal bacterial and viral communities of a patient with recurrent C. difficile infection (rCDI) who was cured by fecal microbiota transplantation (FMT). The "Zürich Patient" experienced immediate cure and has remained free of symptoms for now over 5 y. Donor-similar bacterial compositions after 4.5 y post-FMT demonstrated sustainable engraftment of donor microbiota predominated by Bacteroidetes and Firmicutes bacteria. Appearance of beneficial species Faecalibacterium prausnitzii and Akkermansia municiphila was detected while disease-related Proteobacteria decreased. Stabilization of the microbiota took longer than expected from the rapidly improving clinical symptoms, suggesting the need for longer-lasting patient observation. The virome was mainly composed of Caudovirales bacteriophages but surprisingly also contained sequences related to a Chlorella giant virus that normally infects green algae not known to inhabitate the human intestine. FMT is highly effective against rCDI and is presently broadening its application to other conditions including inflammatory bowel disease (IBD). Here, we discuss the prospects and challenges of FMT against rCDI and other indications including a focus on bacteriophages.
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Affiliation(s)
- Karin Moelling
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical Microbiology, Unversity of Zürich, Zürich, Switzerland
| | - Felix Broecker
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical Microbiology, Unversity of Zürich, Zürich, Switzerland; Max Planck Institute of Colloids and Interfaces, Potsdam, Germany; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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357
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Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res 2016; 26:1612-1625. [PMID: 27803195 PMCID: PMC5088602 DOI: 10.1101/gr.201863.115] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 09/08/2016] [Indexed: 01/19/2023]
Abstract
We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution.
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Affiliation(s)
- Stephen Nayfach
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA
| | | | - Nandita Garud
- Gladstone Institutes, San Francisco, California 94158, USA
| | - Katherine S Pollard
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA.,Institute for Human Genetics, Institute for Computational Health Sciences, and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94158, USA
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358
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Jalanka J, Mattila E, Jouhten H, Hartman J, de Vos WM, Arkkila P, Satokari R. Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection. BMC Med 2016; 14:155. [PMID: 27724956 PMCID: PMC5057499 DOI: 10.1186/s12916-016-0698-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/16/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Faecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (rCDI). It restores the disrupted intestinal microbiota and subsequently suppresses C. difficile. The long-term stability of the intestinal microbiota and the recovery of mucosal microbiota, both of which have not been previously studied, are assessed herein. Further, the specific bacteria behind the treatment efficacy are also investigated. METHODS We performed a high-throughput microbiota profiling using a phylogenetic microarray analysis of 131 faecal and mucosal samples from 14 rCDI patients pre- and post-FMT during a 1-year follow-up and 23 samples from the three universal donors over the same period. RESULTS The FMT treatment was successful in all patients. FMT reverted the patients' bacterial community to become dominated by Clostridium clusters IV and XIVa, the major anaerobic bacterial groups of the healthy gut. In the mucosa, the amount of facultative anaerobes decreased, whereas Bacteroidetes increased. Post-FMT, the patients' microbiota profiles were more similar to their own donors than what is generally observed for unrelated subjects and this striking similarity was retained throughout the 1-year follow-up. Furthermore, the universal donor approach allowed us to identify bacteria commonly established in all CDI patients and revealed a commonly acquired core microbiota consisting of 24 bacterial taxa. CONCLUSIONS FMT induces profound microbiota changes, therefore explaining the high clinical efficacy for rCDI. The identification of commonly acquired bacteria could lead to effective bacteriotherapeutic formulations. FMT can affect microbiota in the long-term and offers a means to modify it relatively permanently for the treatment of microbiota-associated diseases.
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Affiliation(s)
- Jonna Jalanka
- Immunobiology Research Program and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eero Mattila
- Department of Infectious Disease, Helsinki University Central Hospital, Helsinki, Finland
| | - Hanne Jouhten
- Immunobiology Research Program and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jorn Hartman
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Immunobiology Research Program and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Perttu Arkkila
- Department of Gastroenterology, Helsinki University Central Hospital, Helsinki, Finland
| | - Reetta Satokari
- Immunobiology Research Program and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,, PO Box 21, Haartmaninkatu 3, 00290, Helsinki, Finland.
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359
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Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome. Cell Host Microbe 2016; 20:515-526. [DOI: 10.1016/j.chom.2016.09.001] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/25/2016] [Accepted: 09/08/2016] [Indexed: 12/18/2022]
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360
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Carlucci C, Petrof EO, Allen-Vercoe E. Fecal Microbiota-based Therapeutics for Recurrent Clostridium difficile Infection, Ulcerative Colitis and Obesity. EBioMedicine 2016; 13:37-45. [PMID: 27720396 PMCID: PMC5264253 DOI: 10.1016/j.ebiom.2016.09.029] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/21/2016] [Accepted: 09/29/2016] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiome is a complex ecosystem of fundamental importance to human health. Our increased understanding of gut microbial composition and functional interactions in health and disease states has spurred research efforts examining the gut microbiome as a valuable target for therapeutic intervention. This review provides updated insight into the state of the gut microbiome in recurrent Clostridium difficile infection (CDI), ulcerative colitis (UC), and obesity while addressing the rationale for the modulation of the gut microbiome using fecal microbiota transplant (FMT)-based therapies. Current microbiome-based therapeutics in pre-clinical or clinical development are discussed. We end by putting this within the context of the current regulatory framework surrounding FMT and related therapies. There is an increased understanding of gut microbial composition and functional interactions in health and disease states. FMT is effective for rCDI and has led to the development of fecal microbiota-based therapeutics for other indications. For stool-substitute therapies to enter mainstream medicine, further mechanistic studies, RCTs and regulations are needed.
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Affiliation(s)
- Christian Carlucci
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
| | - Elaine O Petrof
- Division of Infectious Diseases/GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen's University, 76 Stuart Street, Kingston, Ontario K7L 2V7, Canada.
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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361
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Ellegaard KM, Engel P. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota. Front Microbiol 2016; 7:1475. [PMID: 27708630 PMCID: PMC5030217 DOI: 10.3389/fmicb.2016.01475] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/05/2016] [Indexed: 12/31/2022] Open
Abstract
Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.
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Affiliation(s)
- Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
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362
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Affiliation(s)
- Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.
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363
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Abstract
The gut microbiome research is going from a descriptive into an intervention phase. To optimize beneficial microbe–host interaction, we need to understand how to steer the system by modulating the nutrient input with which the system is literally fed (e.g. diets, fibres, prebiotics, human milk oligosaccharides), and we must learn how to modulate the composition of the gut microbiota by adding beneficial microbes (e.g. probiotics, faecal transplants) and by eliminating disturbing microbial members using, for example, bacteriophages in this highly complex ecosystem. The current status of the field is reviewed together with an outlook what might be expected until 2020, highlighting obstacles to progress and possible solutions to these problems.
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Affiliation(s)
- Harald Brüssow
- Nestlé Research Center, Nutrition and Health Research, Host-Microbe Interaction, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
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364
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Ray K. Gut microbiota: FMT - enduring strains. Nat Rev Gastroenterol Hepatol 2016; 13:376. [PMID: 27188820 DOI: 10.1038/nrgastro.2016.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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365
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Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Front Microbiol 2016; 7:979. [PMID: 27446020 PMCID: PMC4923077 DOI: 10.3389/fmicb.2016.00979] [Citation(s) in RCA: 930] [Impact Index Per Article: 116.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/07/2016] [Indexed: 12/11/2022] Open
Abstract
With the increasing amount of evidence linking certain disorders of the human body to a disturbed gut microbiota, there is a growing interest for compounds that positively influence its composition and activity through diet. Besides the consumption of probiotics to stimulate favorable bacterial communities in the human gastrointestinal tract, prebiotics such as inulin-type fructans (ITF) and arabinoxylan-oligosaccharides (AXOS) can be consumed to increase the number of bifidobacteria in the colon. Several functions have been attributed to bifidobacteria, encompassing degradation of non-digestible carbohydrates, protection against pathogens, production of vitamin B, antioxidants, and conjugated linoleic acids, and stimulation of the immune system. During life, the numbers of bifidobacteria decrease from up to 90% of the total colon microbiota in vaginally delivered breast-fed infants to <5% in the colon of adults and they decrease even more in that of elderly as well as in patients with certain disorders such as antibiotic-associated diarrhea, inflammatory bowel disease, irritable bowel syndrome, obesity, allergies, and regressive autism. It has been suggested that the bifidogenic effects of ITF and AXOS are the result of strain-specific yet complementary carbohydrate degradation mechanisms within cooperating bifidobacterial consortia. Except for a bifidogenic effect, ITF and AXOS also have shown to cause a butyrogenic effect in the human colon, i.e., an enhancement of colon butyrate production. Butyrate is an essential metabolite in the human colon, as it is the preferred energy source for the colon epithelial cells, contributes to the maintenance of the gut barrier functions, and has immunomodulatory and anti-inflammatory properties. It has been shown that the butyrogenic effects of ITF and AXOS are the result of cross-feeding interactions between bifidobacteria and butyrate-producing colon bacteria, such as Faecalibacterium prausnitzii (clostridial cluster IV) and Anaerostipes, Eubacterium, and Roseburia species (clostridial cluster XIVa). These kinds of interactions possibly favor the co-existence of bifidobacterial strains with other bifidobacteria and with butyrate-producing colon bacteria in the human colon.
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Affiliation(s)
| | | | | | | | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit BrusselBrussels, Belgium
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Jouhten H, Mattila E, Arkkila P, Satokari R. Reduction of Antibiotic Resistance Genes in Intestinal Microbiota of Patients With Recurrent Clostridium difficile Infection After Fecal Microbiota Transplantation. Clin Infect Dis 2016; 63:710-1. [PMID: 27317794 DOI: 10.1093/cid/ciw390] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Hanne Jouhten
- Immunobiology Research Program, Faculty of Medicine, University of Helsinki
| | | | - Perttu Arkkila
- Department of Gastroenterology, Helsinki University Central Hospital, Finland
| | - Reetta Satokari
- Immunobiology Research Program, Faculty of Medicine, University of Helsinki
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Research Highlights. Nat Biotechnol 2016. [DOI: 10.1038/nbt.3595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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