401
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Abstract
The gut microbiota and its metabolic products interact with the host in many different ways, influencing gut homoeostasis and health outcomes. The species composition of the gut microbiota has been shown to respond to dietary change, determined by competition for substrates and by tolerance of gut conditions. Meanwhile, the metabolic outputs of the microbiota, such as SCFA, are influenced both by the supply of dietary components and via diet-mediated changes in microbiota composition. There has been significant progress in identifying the phylogenetic distribution of pathways responsible for formation of particular metabolites among human colonic bacteria, based on combining cultural microbiology and sequence-based approaches. Formation of butyrate and propionate from hexose sugars, for example, can be ascribed to different bacterial groups, although propionate can be formed via alternative pathways from deoxy-sugars and from lactate by a few species. Lactate, which is produced by many gut bacteria in pure culture, can also be utilised by certain Firmicutes to form butyrate, and its consumption may be important for maintaining a stable community. Predicting the impact of diet upon such a complex and interactive system as the human gut microbiota not only requires more information on the component groups involved but, increasingly, the integration of such information through modelling approaches.
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402
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403
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Faith JJ, Ahern PP, Ridaura VK, Cheng J, Gordon JI. Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci Transl Med 2014; 6:220ra11. [PMID: 24452263 DOI: 10.1126/scitranslmed.3008051] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Identifying a scalable, unbiased method for discovering which members of the human gut microbiota influence specific physiologic, metabolic, and immunologic phenotypes remains a challenge. We describe a method in which a clonally arrayed collection of cultured, sequenced bacteria was generated from one of several human fecal microbiota samples found to transmit a particular phenotype to recipient germ-free mice. Ninety-four bacterial consortia of diverse size, randomly drawn from the culture collection, were introduced into germ-free animals. We identified an unanticipated range of bacterial strains that promoted accumulation of colonic regulatory T cells (T(regs)) and expansion of Nrp1(lo/-) peripheral T(regs), as well as strains that modulated mouse adiposity and cecal metabolite concentrations, using feature selection algorithms and follow-up monocolonizations. This combinatorial approach enables a systems-level understanding of microbial contributions to human biology.
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Affiliation(s)
- Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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404
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Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity 2014; 40:843-54. [PMID: 24950204 DOI: 10.1016/j.immuni.2014.05.013] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Indexed: 02/06/2023]
Abstract
The inflammatory bowel diseases (IBDs) are among the most closely studied chronic inflammatory disorders that involve environmental, host genetic, and commensal microbial factors. This combination of features has made IBD both an appropriate and a high-priority platform for translatable research in host-microbiome interactions. Decades of epidemiology have identified environmental risk factors, although most mechanisms of action remain unexplained. The genetic architecture of IBD has been carefully dissected in multiple large populations, identifying several responsible host epithelial and immune pathways but without yet a complete systems-level explanation. Most recently, the commensal gut microbiota have been found to be both ecologically and functionally perturbed during the disease, but with as-yet-unexplained heterogeneity among IBD subtypes and individual patients. IBD thus represents perhaps the most comprehensive current model for understanding the human microbiome's role in complex inflammatory disease. Here, we review the influences of the microbiota on IBD and its potential for translational medicine.
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Affiliation(s)
- Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Aleksandar D Kostic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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405
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Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014; 38:996-1047. [PMID: 24861948 PMCID: PMC4262072 DOI: 10.1111/1574-6976.12075] [Citation(s) in RCA: 722] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/29/2014] [Accepted: 05/09/2014] [Indexed: 02/06/2023] Open
Abstract
The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
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Affiliation(s)
- Mirjana Rajilić-Stojanović
- Department for Biotechnology and Biochemical Engineering, Faculty of Technology and Metallurgy, University of BelgradeBelgrade, Serbia
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
- Departments of Bacteriology and Immunology, and Veterinary Biosciences, University of HelsinkiHelsinki, Finland
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406
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Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria. Nat Commun 2014; 5:4714. [PMID: 25163406 DOI: 10.1038/ncomms5714] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/15/2014] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiota is linked to a variety of human health issues and implicated in antibiotic resistance gene dissemination. Most of these associations rely on culture-independent methods, since it is commonly believed that gut microbiota cannot be easily or sufficiently cultured. Here, we show that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling. We use this approach to determine the phylogenetic distribution of antibiotic tolerance phenotypes for 16 antibiotics in the human gut microbiota. Based on the phenotypic mapping, we tailor antibiotic combinations to specifically select for previously uncultivated bacteria. Utilizing this method we cultivate and sequence the genomes of four isolates, one of which apparently belongs to the genus Oscillibacter; uncultivated Oscillibacter strains have been previously found to be anti-correlated with Crohn's disease.
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407
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Ahmed T, Auble D, Berkley JA, Black R, Ahern PP, Hossain M, Hsieh A, Ireen S, Arabi M, Gordon JI. An evolving perspective about the origins of childhood undernutrition and nutritional interventions that includes the gut microbiome. Ann N Y Acad Sci 2014; 1332:22-38. [PMID: 25118072 PMCID: PMC4514967 DOI: 10.1111/nyas.12487] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Sackler Institute for Nutrition Science and the World Health Organization (WHO) have worked together to formulate a research agenda for nutrition science. Undernutrition of children has profound effects on health, development, and achievement of full human capacity. Undernutrition is not simply caused by a lack of food, but results from a complex interplay of intra- and intergenerational factors. Representative preclinical models and comprehensive well-controlled longitudinal clinical studies are needed to further understand the contributions and the interrelationships among these factors and to develop interventions that are effective and durable. This paper summarizes work on mechanisms underlying the varied manifestations of childhood undernutrition and discusses current gaps in knowledge and challenges to our understanding of undernutrition and infection/immunity throughout the human life cycle, focusing on early childhood growth. It proposes a series of basic and clinical studies to address this global health challenge.
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Affiliation(s)
- Tahmeed Ahmed
- Centre for Nutrition and Food Security, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
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408
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Kumar R, Eipers P, Little RB, Crowley M, Crossman DK, Lefkowitz EJ, Morrow CD. Getting started with microbiome analysis: sample acquisition to bioinformatics. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 82:18.8.1-18.8.29. [PMID: 25042718 PMCID: PMC4383038 DOI: 10.1002/0471142905.hg1808s82] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Historically, in order to study microbes, it was necessary to grow them in the laboratory. It was clear though that many microbe communities were refractory to study because none of the members could be grown outside of their native habitat. The development of culture-independent methods to study microbiota using high-throughput sequencing of the 16S ribosomal RNA gene variable regions present in all prokaryotic organisms has provided new opportunities to investigate complex microbial communities. In this unit, the process for a microbiome analysis is described. Many of the components required for this process may already exist. A pipeline is described for acquisition of samples from different sites on the human body, isolation of microbial DNA, and DNA sequencing using the Illumina MiSeq sequencing platform. Finally, a new analytical workflow for basic bioinformatics data analysis, QWRAP, is described, which can be used by clinical and basic science investigators.
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Affiliation(s)
- Ranjit Kumar
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham Alabama 35294
| | - Peter Eipers
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham Alabama 35294
| | - Rebecca B. Little
- Department of Nutrition Sciencesm, University of Alabama at Birmingham, Birmingham Alabama 35233
| | - Michael Crowley
- Department of Genetics and Heflin Center for Genomic Sciencel, University of Alabama at Birmingham, Birmingham Alabama 35294
| | - David K. Crossman
- Department of Genetics and Heflin Center for Genomic Sciencel, University of Alabama at Birmingham, Birmingham Alabama 35294
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham Alabama 35294
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham Alabama 35294
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409
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Martens EC, Kelly AG, Tauzin AS, Brumer H. The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes. J Mol Biol 2014; 426:3851-65. [PMID: 25026064 DOI: 10.1016/j.jmb.2014.06.022] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/13/2014] [Accepted: 06/29/2014] [Indexed: 12/16/2022]
Abstract
The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide-degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health.
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Affiliation(s)
- Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Amelia G Kelly
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexandra S Tauzin
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
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410
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Smith MI, Turpin W, Tyler AD, Silverberg MS, Croitoru K. Microbiome analysis - from technical advances to biological relevance. F1000PRIME REPORTS 2014; 6:51. [PMID: 25184041 PMCID: PMC4108955 DOI: 10.12703/p6-51] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The development of culture-independent techniques and next-generation sequencing has led to a staggering rise in the number of microbiome studies over the last decade. Although it remains important to identify the taxa of microbes present in a variety of environmental samples, including the gut microbiomes of healthy and diseased individuals, the next stage of microbiome research will need to focus on uncovering the role of the microbiome rather than its mere composition. Here, we introduce techniques that go beyond identifying the taxa present within a sample and examine the biological function of the microbiome or the host-microbiome interaction.
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Affiliation(s)
- Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
| | - Andrea D Tyler
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
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411
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Ahern PP, Faith JJ, Gordon JI. Mining the human gut microbiota for effector strains that shape the immune system. Immunity 2014; 40:815-23. [PMID: 24950201 PMCID: PMC4118768 DOI: 10.1016/j.immuni.2014.05.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/24/2014] [Indexed: 02/07/2023]
Abstract
The gut microbiota codevelops with the immune system beginning at birth. Mining the microbiota for bacterial strains responsible for shaping the structure and dynamic operations of the innate and adaptive arms of the immune system represents a formidable combinatorial problem but one that needs to be overcome to advance mechanistic understanding of microbial community and immune system coregulation and to develop new diagnostic and therapeutic approaches that promote health. Here, we discuss a scalable, less biased approach for identifying effector strains in complex microbial communities that impact immune function. The approach begins by identifying uncultured human fecal microbiota samples that transmit immune phenotypes to germ-free mice. Clonally arrayed sequenced collections of bacterial strains are constructed from representative donor microbiota. If the collection transmits phenotypes, effector strains are identified by testing randomly generated subsets with overlapping membership in individually housed germ-free animals. Detailed mechanistic studies of effector strain-host interactions can then be performed.
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Affiliation(s)
- Philip P Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA; Immunology Institute and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
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412
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Moraes ACFD, Silva ITD, Almeida-Pititto BD, Ferreira SRG. Microbiota intestinal e risco cardiometabólico: mecanismos e modulação dietética. ACTA ACUST UNITED AC 2014; 58:317-27. [DOI: 10.1590/0004-2730000002940] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/24/2014] [Indexed: 12/26/2022]
Abstract
A microbiota intestinal, adquirida no período pós-natal, é composta por grande diversidade de bactérias que desempenham diferentes funções no hospedeiro humano, entre elas a absorção de nutrientes, proteção contra patógenos e modulação do sistema imune. O conteúdo bacteriano intestinal ainda não é totalmente conhecido, mas sabe-se que é influenciado por fatores internos e principalmente externos que modulam sua composição e função. Estudos indicam que a microbiota intestinal difere em indivíduos magros e obesos e ainda naqueles que mantêm hábitos alimentares diferentes. Há evidências de que as relações entre dieta, inflamação, resistência à insulina e risco cardiometabólico são em parte mediadas pela composição de bactérias intestinais. Conhecimentos sobre a microbiota poderão reverter em diferentes estratégias para manipular as populações bacterianas e promover saúde. Esta revisão aborda a relevância do conhecimento sobre o papel de fatores ou padrões alimentares na composição da microbiota, assim como mecanismos fisiopatológicos de doenças metabólicas crônicas e as potencialidades de prebióticos e probióticos sobre o perfil de risco cardiometabólico.
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413
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Mantzaris GJ. When can we cure Crohn's? Best Pract Res Clin Gastroenterol 2014; 28:519-29. [PMID: 24913390 DOI: 10.1016/j.bpg.2014.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/15/2014] [Accepted: 04/13/2014] [Indexed: 01/31/2023]
Abstract
Crohn's disease is a life-long idiopathic inflammatory disease which affects the entire gastrointestinal tract and occasionally extra-intestinal organs. CD is thought to result from complex interactions between environmental factors, the gut microbes, and the genetic background and the immune system of the host. In the last decades research on these pathogenetic components, and especially on mucosal immunity, has led to the development of biologic agents and therapeutic strategies that have improved dramatically the treatment of CD but we are still far away from curing the disease. If there is a treatment for CD that will probably evolve through methodical steps towards integrating research on all the components involved in the pathogenesis of CD. This holistic and global approach may aid at unravelling the mysteries of CD and developing novel agents and therapeutic strategies which by targeting multiple pathogenetic pathways and at different stages of disease may lead hopefully to cure.
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Affiliation(s)
- Gerassimos J Mantzaris
- Department of Gastroenterology, Evangelismos Hospital, 45-47 Ypsilantou Street, 10676 Athens, Greece.
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414
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Barzegari A, Saeedi N, Saei AA. Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks. Future Microbiol 2014; 9:639-56. [DOI: 10.2217/fmb.14.22] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT: The Human Microbiome Project (HMP) revealed the significance of the gut microbiome in promoting health. Disruptions in microbiome composition are associated with the pathogenesis of numerous diseases. The indigenous microflora has co-evolved with humans for millions of years and humans have preserved the inherited microbiomes through consumption of fermented foods and interactions with environmental microbes. Through modernization, traditional foods were abandoned, native food starters were substituted with industrial products, vaccines and antibiotics were used, extreme hygiene measures were taken, the rate of cesarean section increased, and breast feeding changed into formula. These factors have reduced human exposure to microbial symbionts and led to shrinkage of the core microbiome. Reduction in microbiome biodiversity can compromise the human immune system and predispose individuals to several modern diseases. This article suggests launching microbiome biobanks for archiving native microbiomes, supervising antibiotic use, probiotic design and native starter production, as well as advertising a revisit to native lifestyles.
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Affiliation(s)
- Abolfazl Barzegari
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazli Saeedi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Ata Saei
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
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415
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Abstract
The impact of the gut microbiota on immune homeostasis within the gut and, importantly, also at systemic sites has gained tremendous research interest over the last few years. The intestinal microbiota is an integral component of a fascinating ecosystem that interacts with and benefits its host on several complex levels to achieve a mutualistic relationship. Host-microbial homeostasis involves appropriate immune regulation within the gut mucosa to maintain a healthy gut while preventing uncontrolled immune responses against the beneficial commensal microbiota potentially leading to chronic inflammatory bowel diseases (IBD). Furthermore, recent studies suggest that the microbiota composition might impact on the susceptibility to immune-mediated disorders such as autoimmunity and allergy. Understanding how the microbiota modulates susceptibility to these diseases is an important step toward better prevention or treatment options for such diseases.
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416
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Abstract
Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings. The increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of resistance are complex, and a better understanding of the impacts of antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of antibiotic resistance genes, which may affect distribution of antibiotic resistance genes in human pathogens. Previous studies have focused on antibiotic resistance genes in manures of animals subjected to intensive antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse antibiotic resistance genes in the cow microbiome, demonstrating that it is a significant reservoir of antibiotic resistance genes. The genomic resource presented here lays the groundwork for understanding the dispersal of antibiotic resistance from the agroecosystem to other settings.
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417
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Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F, Manichanh C. Short-term effect of antibiotics on human gut microbiota. PLoS One 2014; 9:e95476. [PMID: 24748167 PMCID: PMC3991704 DOI: 10.1371/journal.pone.0095476] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/27/2014] [Indexed: 12/13/2022] Open
Abstract
From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002). At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016). Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04). The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.
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Affiliation(s)
- Suchita Panda
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Ismail El khader
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Francesc Casellas
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josefa López Vivancos
- Internal Medicine Department, Capio Hospital General de Catalunya, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Montserrat García Cors
- Internal Medicine Department, Capio Hospital General de Catalunya, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Alba Santiago
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Silvia Cuenca
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Francisco Guarner
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Chaysavanh Manichanh
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- * E-mail:
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418
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419
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Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol 2014; 22:267-74. [PMID: 24698744 DOI: 10.1016/j.tim.2014.03.001] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/03/2014] [Accepted: 03/03/2014] [Indexed: 01/02/2023]
Abstract
The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.
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420
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Dantas G, Sommer MOA, Degnan PH, Goodman AL. Experimental approaches for defining functional roles of microbes in the human gut. Annu Rev Microbiol 2014; 67:459-75. [PMID: 24024637 DOI: 10.1146/annurev-micro-092412-155642] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The complex and intimate relationship between humans and their gut microbial communities is becoming less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-independent surveys of the composition and gene content of these communities. These studies build upon, and are complemented by, experimental efforts to define underlying mechanisms of host-microbe interactions in simplified model systems. This review highlights the intersection of these approaches. Experimental studies now leverage the advances in high-throughput DNA sequencing that have driven the explosion of microbial genome and community profiling projects, and the loss-of-function and gain-of-function strategies long employed in model organisms are now being extended to microbial genes, species, and communities from the human gut. These developments promise to deepen our understanding of human gut host-microbiota relationships and are readily applicable to other host-associated and free-living microbial communities.
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Affiliation(s)
- Gautam Dantas
- Center for Genome Sciences & Systems Biology and Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri 63108;
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421
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Chen J, He X, Huang J. Diet effects in gut microbiome and obesity. J Food Sci 2014; 79:R442-51. [PMID: 24621052 DOI: 10.1111/1750-3841.12397] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/15/2014] [Indexed: 12/21/2022]
Abstract
The 100 trillion microbes in human gut coevolve with the host and exert significant influences on human health. The gut microbial composition presents dynamic changes correlated with various factors including host genotypes, age, and external environment. Effective manipulation of the gut microbiota through diets (both long-term and short-term diet patterns), probiotics and/or prebiotics, and antibiotics has been proved being potential to prevent from metabolic disorders such as obesity in many studies. The dietary regulation exerts influences on microbial metabolism and host immune functions through several pathways, of which may include selectively bacterial fermentation of nutrients, lower intestinal barrier function, overexpression of genes associated with disorders, and disruptions to both innate and adaptive immunity. Discoveries in the interrelationship between diet, intestinal microbiome, and body immune system provide us novel perceptions to the specific action mechanisms and will promote the development of therapeutic approaches for obesity.
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Affiliation(s)
- Jia Chen
- School of Chemical Engineering & Technology, Tianjin Univ, Tianjin, 300072, China
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422
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Hintze KJ, Cox JE, Rompato G, Benninghoff AD, Ward RE, Broadbent J, Lefevre M. Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer. Gut Microbes 2014; 5:183-91. [PMID: 24637796 PMCID: PMC4063843 DOI: 10.4161/gmic.28403] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Traditionally, mouse humanization studies have used human fecal transfer to germ-free animals. This practice requires gnotobiotic facilities and is restricted to gnotobiotic mouse lines, which limits humanized mouse research. We have developed a generalizable method to humanize non germ-free mice using antibiotic treatment and human fecal transfer. The method involves depleting resident intestinal microbiota with broad-spectrum antibiotics, introducing human microbiota from frozen fecal samples by weekly gavage, and maintaining mice in HEPA-filtered microisolator cages. Pyrosequencing cecal microbiota 16S rRNA genes showed that recipient mice adopt a humanized microbiota profile analogous to their human donors, and distinct from mice treated with only antibiotics (no fecal transfer) or untreated control mice. In the humanized mice, 75% of the sequence mass was observed in their respective human donor and conversely, 68% of the donor sequence mass was recovered in the recipient mice. Principal component analyses of GC- and HPLC-separated cecal metabolites were performed to determine effects of transplanted microbiota on the metabolome. Cecal metabolite profiles of mice treated with only antibiotics (no fecal transfer) and control mice were dissimilar from each other and from humanized mice. Metabolite profiles for mice humanized from different donor samples clustered near each other, yet were sufficiently distinct that separate clusters were apparent for each donor. Also, cecal concentrations of 57 metabolites were significantly different between humanization treatments. These data demonstrate that our protocol can be used to humanize non germ-free mice and is sufficiently robust to generate metabolomic differences between mice humanized from different human donors.
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Affiliation(s)
- Korry J Hintze
- Dept. of Nutrition, Dietetics, and Food Sciences; Utah State University; Logan, UT USA,Applied Nutrition Research; Utah Science Technology and Research Initiative (USTAR); Logan, UT USA,Correspondence to: Korry J Hintze,
| | - James E Cox
- Department of Biochemistry; University of Utah; Salt Lake City, UT USA
| | - Giovanni Rompato
- Center of Integrated BioSystems; Utah State University; Logan, UT USA
| | - Abby D Benninghoff
- Applied Nutrition Research; Utah Science Technology and Research Initiative (USTAR); Logan, UT USA,Dept. of Animal, Dairy, and Veterinary Sciences; Utah State University; Logan, UT USA
| | - Robert E Ward
- Dept. of Nutrition, Dietetics, and Food Sciences; Utah State University; Logan, UT USA,Applied Nutrition Research; Utah Science Technology and Research Initiative (USTAR); Logan, UT USA
| | - Jeff Broadbent
- Dept. of Nutrition, Dietetics, and Food Sciences; Utah State University; Logan, UT USA,Applied Nutrition Research; Utah Science Technology and Research Initiative (USTAR); Logan, UT USA
| | - Michael Lefevre
- Dept. of Nutrition, Dietetics, and Food Sciences; Utah State University; Logan, UT USA,Applied Nutrition Research; Utah Science Technology and Research Initiative (USTAR); Logan, UT USA
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423
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Probiotics and prebiotics in neonatal necrotizing enterocolitis: New opportunities for translational research. ACTA ACUST UNITED AC 2014; 21:35-46. [PMID: 24594006 DOI: 10.1016/j.pathophys.2013.11.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neonatal necrotizing enterocolitis (NEC) in premature infants has been recognized as a defined disease entity for at least four decades. Although survival has increased due to the advent of more sophisticated intensive care, incidence and long term health impacts due to NEC remain unchanged and no preventive therapy is currently available. Different probiotic strains of bacteria have been examined in their ability to prevent NEC with varied but encouraging results. Undigestable prebiotic sugars known to promote the growth of probiotic bacteria in the colon have been used in neonates with no clear benefit. The literature on NEC and probiotics is now cluttered with more reviews and meta-analyses than number of clinical trials. On the other hand, significant new information is available on microbiota and their impact on gut immunity. This review attempts to reiterate the risk factors of NEC and the pathogenesis of NEC with special reference to gut permeability. The reader is then introduced to gut microbiota, uniqueness and differences among probiotic strains, and how multiple resident flora talk to each other in the community setting in the human gut. After presenting a concise review of available clinical research results, the reader is challenged to question as to why no precise answer is available at present. Some modalities to examine the complex microflora and changes in the neonatal gut are then proposed including non-invasive methods and mathematical modeling. The review concludes by attracting the reader's attention to known immunomodulators of inflammation and injury. Justice to this review will be done only if the readers, clinical, and basic science investigators from multiple fields gather courage for a paradigm shift and embark on understanding the pathophysiology of the disease and attempt to discern the difference from equally preterm, equally vulnerable neonates that do not develop NEC. Learning about the developing microbiota in neonatal gut and its immunological impacts on the host in the face of many variables will provide a leap in our pursuit to select better, if not the best candidate probiotics, and put them to work against this stubborn disease that continues to take a toll on our precious neonates and the society.
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424
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Liu Y, Li Y, Liu K, Shen J. Exposing to cadmium stress cause profound toxic effect on microbiota of the mice intestinal tract. PLoS One 2014; 9:e85323. [PMID: 24498261 PMCID: PMC3911910 DOI: 10.1371/journal.pone.0085323] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/26/2013] [Indexed: 12/27/2022] Open
Abstract
Cadmium (Cd), one of the heavy metals, is an important environmental pollutant and a potent toxicant to organism. It poses a severe threat to the growth of the organism, and also has been recognized as a human carcinogen. However, the toxicity of cadmium and its influences on microbiota in mammal's intestine are still unclear. In our experiment, the changes of intestinal microbiota in two groups of mice were investigated, which were supplied with 20 and 100 mg kg(-1) cadmium chloride respectively for 3 weeks. The control group was treated with water free from cadmium chloride only. This study demonstrated that Cd accumulated in some tissues of mice after Cd administration and the gut barrier was impaired. Cd exposure also significantly elevated the colonic level of TNF-α. On the other hand, Cd-treatment could slow down the growth of gut microbiota and reduced the abundance of total intestinal bacteria of the mice. Among them, the growth of Bacteroidetes was significantly suppressed while Firmicutes growth was not. The probiotics including Lactobacillus and Bifidobacterium were notably inhibited. We also observed that the copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids (SCFAs) were lower in Cd-treated groups than control. As a result, the levels of short-chain fatty acids in colonic decreased significantly. In summary, this study provides valuable insight into the effects of Cd intake on mice gut microbiota.
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Affiliation(s)
- Yehao Liu
- School of Public Health, Anhui Medical University, Hefei, Anhui Province, People′s Republic of China
| | - Yuhui Li
- Department of Biological and Environmental Engineering, Hefei Univeristy, Hefei, Anhui Province, People′s Republic of China
| | - Kaiyong Liu
- School of Public Health, Anhui Medical University, Hefei, Anhui Province, People′s Republic of China
| | - Jie Shen
- School of Public Health, Anhui Medical University, Hefei, Anhui Province, People′s Republic of China
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425
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Ahmer BMM. In this issue of Gut Microbes. Gut Microbes 2014; 5:83-5. [PMID: 24468723 PMCID: PMC4049943 DOI: 10.4161/gmic.28007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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426
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Satoor SN, Patil DP, Kristensen HD, Joglekar MV, Shouche Y, Hardikar AA. Manipulation and assessment of gut microbiome for metabolic studies. Methods Mol Biol 2014; 1194:449-69. [PMID: 25064120 DOI: 10.1007/978-1-4939-1215-5_26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mammalian gut is inhabited by a complex and highly diverse population of bacteria. About 100 trillion microbes are present in the human gut, a number ten times more than the total number of cells in an adult human body. These microorganisms play an important role in several fundamental and crucial processes such as immunity, digestion, synthesis of vitamins, and metabolizing bile acids, sterols, and xenobiotics in the host, thereby influencing human health. Identification and manipulation of these metabolic interfaces is therefore critical. Here, we present a set of methods for manipulation and targeting the 16S rRNA based identification of rodent gut microbiota using Sanger's and next-generation sequencing platforms. Novel methods for manipulation of gut microbiota are also presented. In principle, these methods can be easily adapted to most rodent models for successful screening and manipulation of gut microbiome, to generate a better understanding of their role in metabolic disease.
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Affiliation(s)
- Sarang N Satoor
- NHMRC Clinical Trials Centre, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW, 2050, Australia
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427
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Fodor A. Utilizing “Omics” Tools to Study the Complex Gut Ecosystem. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 817:25-38. [DOI: 10.1007/978-1-4939-0897-4_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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428
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Siddharth J, Holway N, Parkinson SJ. A Western diet ecological module identified from the 'humanized' mouse microbiota predicts diet in adults and formula feeding in children. PLoS One 2013; 8:e83689. [PMID: 24391809 PMCID: PMC3877084 DOI: 10.1371/journal.pone.0083689] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/06/2013] [Indexed: 12/15/2022] Open
Abstract
The interplay between diet and the microbiota has been implicated in the growing frequency of chronic diseases associated with the Western lifestyle. However, the complexity and variability of microbial ecology in humans and preclinical models has hampered identification of the molecular mechanisms underlying the association of the microbiota in this context. We sought to address two key questions. Can the microbial ecology of preclinical models predict human populations? And can we identify underlying principles that surpass the plasticity of microbial ecology in humans? To do this, we focused our study on diet; perhaps the most influential factor determining the composition of the gut microbiota. Beginning with a study in ‘humanized’ mice we identified an interactive module of 9 genera allied with Western diet intake. This module was applied to a controlled dietary study in humans. The abundance of the Western ecological module correctly predicted the dietary intake of 19/21 top and 21/21 of the bottom quartile samples inclusive of all 5 Western and ‘low-fat’ diet subjects, respectively. In 98 volunteers the abundance of the Western module correlated appropriately with dietary intake of saturated fatty acids, fat-soluble vitamins and fiber. Furthermore, it correlated with the geographical location and dietary habits of healthy adults from the Western, developing and third world. The module was also coupled to dietary intake in children (and piglets) correlating with formula (vs breast) feeding and associated with a precipitous development of the ecological module in young children. Our study provides a conceptual platform to translate microbial ecology from preclinical models to humans and identifies an ecological network module underlying the association of the gut microbiota with Western dietary habits.
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Affiliation(s)
- Jay Siddharth
- Host Commensal Hub, Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nicholas Holway
- Scientific Computing, NIBR IT, Novartis Institutes Biomedical Research, Basel, Switzerland
| | - Scott J Parkinson
- Host Commensal Hub, Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Basel, Switzerland
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429
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Pham TAN, Lawley TD. Emerging insights on intestinal dysbiosis during bacterial infections. Curr Opin Microbiol 2013; 17:67-74. [PMID: 24581695 PMCID: PMC3969284 DOI: 10.1016/j.mib.2013.12.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 12/18/2022]
Abstract
Diverse enteric pathogens often induce significant perturbations to the microbiota or thrive during dysbiosis. Infection-associated dysbiosis is commonly characterized by decreased diversity and metabolic function. The dysbiotic microbiota may act as a pathogenic community to perpetuate host pathology. Pathogens can exploit dysbiosis for host colonization, genome evolution, and transmission. Bacteriotherapy represents a potential viable strategy to restore intestinal homeostasis.
Infection of the gastrointestinal tract is commonly linked to pathological imbalances of the resident microbiota, termed dysbiosis. In recent years, advanced high-throughput genomic approaches have allowed us to examine the microbiota in an unprecedented manner, revealing novel biological insights about infection-associated dysbiosis at the community and individual species levels. A dysbiotic microbiota is typically reduced in taxonomic diversity and metabolic function, and can harbour pathobionts that exacerbate intestinal inflammation or manifest systemic disease. Dysbiosis can also promote pathogen genome evolution, while allowing the pathogens to persist at high density and transmit to new hosts. A deeper understanding of bacterial pathogenicity in the context of the intestinal microbiota should unveil new approaches for developing diagnostics and therapies for enteropathogens.
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Affiliation(s)
- Tu Anh N Pham
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Trevor D Lawley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom.
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430
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Wu J, Liu W, He L, Huang F, Chen J, Cui P, Shen Y, Zhao J, Wang W, Zhang Y, Zhu M, Zhang W, Zhang Y. Sputum microbiota associated with new, recurrent and treatment failure tuberculosis. PLoS One 2013; 8:e83445. [PMID: 24349510 PMCID: PMC3862690 DOI: 10.1371/journal.pone.0083445] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 11/04/2013] [Indexed: 01/18/2023] Open
Abstract
Microbiota have recently been shown to be associated with many disease conditions. However, the microbiota associated with tuberculosis (TB) infection, recurrence and treatment outcome have not been systematically characterized. Here, we used high throughput 16S RNA sequencing to analyze the sputum microbiota associated with Mycobacterium tuberculosis infection and also to identify the microorganisms associated with different outcomes of TB treatment. We recruited 25 new TB patients, 30 recurrent TB patients and 20 TB patients with treatment failure, as well as 20 healthy controls. Streptococcus, Gramulicatella and Pseudomonas were more abundant in TB patients while Prevotella, Leptotrichia, Treponema, Catonella and Coprococcus were less abundant in TB patients than in the healthy controls. We found reduced frequency and abundance of some genera such as Bulleidia and Atopobium in recurrent TB patients compared with those in new TB patients. In addition, the ratio of Pseudomonas / Mycobacterium in recurrent TB was higher than that in new TB while the ratio of Treponema / Mycobacterium in recurrent TB was lower than that in new TB, indicating that disruption of these bacteria may be a risk factor of TB recurrence. Furthermore, Pseudomonas was more abundant and more frequently present in treatment failure patients than in cured new patients, and the ratio of Pseudomonas / Mycobacterium in treatment failure was higher than that in new TB. Our data suggest that the presence of certain bacteria and the disorder of lung microbiota may be associated with not only onset of TB but also its recurrence and treatment failure. These findings indicate that lung microbiota may play a role in pathogenesis and treatment outcome of TB and may need to be taken into consideration for improved treatment and control of TB in the future.
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Affiliation(s)
- Jing Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei Liu
- Hangzhou Center for Disease Control and Prevention, Zhejiang, China
| | - Lei He
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Fuli Huang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaojie Shen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Zhao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenjie Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yan Zhang
- Department of Tuberculosis Branch, Hangzhou Red Cross Hospital, Zhejiang, China
| | - Min Zhu
- Department of Tuberculosis Branch, Hangzhou Red Cross Hospital, Zhejiang, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
- MOH and MOE Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai, China
- * (WHZ); (YZ)
| | - Ying Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
- MOH and MOE Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * (WHZ); (YZ)
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431
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS One 2013; 8:e82985. [PMID: 24349412 PMCID: PMC3861447 DOI: 10.1371/journal.pone.0082985] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/29/2013] [Indexed: 12/27/2022] Open
Abstract
Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for “salt tolerance locus A”) with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Roy D. Sleator
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Department of Hepatology and Gastroenterology, Imperial College London, London, United Kingdom
- * E-mail: (RS); (JM); (CH)
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
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432
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Feria-Gervasio D, Tottey W, Gaci N, Alric M, Cardot JM, Peyret P, Martin JF, Pujos E, Sébédio JL, Brugère JF. Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota. J Microbiol Methods 2013; 96:111-8. [PMID: 24333608 DOI: 10.1016/j.mimet.2013.11.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/25/2013] [Accepted: 11/30/2013] [Indexed: 02/07/2023]
Abstract
The technical and ethical difficulties in studying the gut microbiota in vivo warrant the development and improvement of in vitro systems able to simulate and control the physicochemical factors of the gut biology. Moreover, the functional regionalization of this organ implies a model simulating these differences. Here we propose an improved and alternative three-stage continuous bioreactor called 3S-ECSIM (three-stage Environmental Control System for Intestinal Microbiota) to study the human large intestine. Its main feature compared with other in vitro systems is the anaerobic atmosphere originating directly from the microbiota metabolism, leading to different gas ratios of CO2 and H2 in each compartment. Analyses of the metabolic and microbiological profiles (LC-MS and a phylogenetic microarray) show different profiles together with a maintenance of this differentiation between the three compartments, simulating respectively a proximal, a transversal and a distal colon. Moreover, the last reactor presents a high similarity with the initial fecal sample, at the microbiological diversity level. Based on our results, this in-vitro process improvement is a valuable alternative tool to dynamically study the structure and metabolism of gut microbiota, and its response to nutrients, prebiotics, probiotics, drugs or xenobiotics.
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Affiliation(s)
- David Feria-Gervasio
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - William Tottey
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Nadia Gaci
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Monique Alric
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Jean-Michel Cardot
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Pierre Peyret
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France
| | - Jean-François Martin
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, F-63122 Saint Genès Champanelle, France
| | - Estelle Pujos
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, F-63122 Saint Genès Champanelle, France
| | - Jean-Louis Sébédio
- INRA, UMR 1019, Plateforme d'Exploration du Métabolisme, Nutrition Humaine, F-63122 Saint Genès Champanelle, France
| | - Jean-François Brugère
- EA 4678 CIDAM, Clermont-Université, Université d'Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.
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433
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Interspecies interactions determine the impact of the gut microbiota on nutrient allocation in Drosophila melanogaster. Appl Environ Microbiol 2013; 80:788-96. [PMID: 24242251 DOI: 10.1128/aem.02742-13] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The animal gut is perpetually exposed to microorganisms, and this microbiota affects development, nutrient allocation, and immune homeostasis. A major challenge is to understand the contribution of individual microbial species and interactions among species in shaping these microbe-dependent traits. Using the Drosophila melanogaster gut microbiota, we tested whether microbe-dependent performance and nutritional traits of Drosophila are functionally modular, i.e., whether the impact of each microbial taxon on host traits is independent of the presence of other microbial taxa. Gnotobiotic flies were constructed with one or a set of five of the Acetobacter and Lactobacillus species which dominate the gut microbiota of conventional flies (Drosophila with untreated microbiota). Axenic (microbiota-free) flies exhibited prolonged development time and elevated glucose and triglyceride contents. The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. In contrast, the development rates and triglyceride levels in monocolonized flies varied depending on the taxon present: Acetobacter species supported the largest reductions, while most Lactobacillus species had no effect. Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. This could be attributed to two processes: Lactobacillus-mediated promotion of Acetobacter abundance in the fly and a significant negative correlation between fly triglyceride content and Acetobacter abundance. We conclude that the microbial basis of host traits varies in both specificity and modularity; microbe-mediated reduction in glucose is relatively nonspecific and modular, while triglyceride content is influenced by interactions among microbes.
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434
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Angelakis E, Merhej V, Raoult D. Related actions of probiotics and antibiotics on gut microbiota and weight modification. THE LANCET. INFECTIOUS DISEASES 2013; 13:889-99. [PMID: 24070562 DOI: 10.1016/s1473-3099(13)70179-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibiotics and probiotics are widely used as growth promoters in agriculture. Most antibiotics prescribed in clinical practice are natural products that originate from Streptomyces spp, which were first used as agricultural probiotics. Antibiotics and probiotics both modify the gut microbiota. The effect of a probiotic species on the digestive flora depends on the strain and is largely determined by bacteriocin production. In human beings, as in animals, specific probiotics are associated with weight gain or loss. Improved understanding of the ability of specific probiotics to harvest energy from the host diet might lead to development of new treatments for obesity and malnutrition. In this Review, we present the effects of probiotics and antibiotics on the gut microbiota of human beings and animals and discuss their potential therapeutic use as interventions for weight gain and loss in human beings.
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Affiliation(s)
- Emmanouil Angelakis
- Unité des Rickettsies, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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435
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Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, Qin X, Tarr PI, Dantas G. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One 2013; 8:e78822. [PMID: 24236055 PMCID: PMC3827270 DOI: 10.1371/journal.pone.0078822] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/10/2013] [Indexed: 12/13/2022] Open
Abstract
Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway). This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. The observed transferability of gut-associated resistance genes to a gram-negative (E. coli) host also suggests that the potential for gut-associated resistomes to threaten human health by mediating antibiotic resistance in pathogens warrants further investigation.
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Affiliation(s)
- Aimée M. Moore
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanket Patel
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin J. Forsberg
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bin Wang
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gayle Bentley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yasmin Razia
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Gastroenterology, Department of Pediatrics, Children’s Hospital and Regional Medical Center, Seattle, Washington, United States of America
| | - Xuan Qin
- Department of Microbiology, Seattle Children’s Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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436
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Abstract
The gastrointestinal tract is heavily colonized with commensal microbes with the concentration of bacteria increasing longitudinally down the length of the intestine. Bacteria are also spatially distributed transversely from the epithelial surface to the intestinal lumen with the inner mucus layer normally void of bacteria. Maintenance of this equilibrium is extremely important for human health and, as the dominant immunoglobulin at mucosal sites, IgA influences mutualism between the host and its normal microbiota. In this review we focus on the links between immune and microbial geography of the mammalian intestinal tract.
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437
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Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013; 341:1241214. [PMID: 24009397 DOI: 10.1126/science.1241214] [Citation(s) in RCA: 2537] [Impact Index Per Article: 230.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The role of specific gut microbes in shaping body composition remains unclear. We transplanted fecal microbiota from adult female twin pairs discordant for obesity into germ-free mice fed low-fat mouse chow, as well as diets representing different levels of saturated fat and fruit and vegetable consumption typical of the U.S. diet. Increased total body and fat mass, as well as obesity-associated metabolic phenotypes, were transmissible with uncultured fecal communities and with their corresponding fecal bacterial culture collections. Cohousing mice harboring an obese twin's microbiota (Ob) with mice containing the lean co-twin's microbiota (Ln) prevented the development of increased body mass and obesity-associated metabolic phenotypes in Ob cage mates. Rescue correlated with invasion of specific members of Bacteroidetes from the Ln microbiota into Ob microbiota and was diet-dependent. These findings reveal transmissible, rapid, and modifiable effects of diet-by-microbiota interactions.
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Affiliation(s)
- Vanessa K Ridaura
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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438
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Moeller AH, Peeters M, Ndjango JB, Li Y, Hahn BH, Ochman H. Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res 2013; 23:1715-20. [PMID: 23804402 PMCID: PMC3787267 DOI: 10.1101/gr.154773.113] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/19/2013] [Indexed: 12/18/2022]
Abstract
The gut microbial communities within great apes have been shown to reflect the phylogenetic history of their hosts, indicating codiversification between great apes and their gut microbiota over evolutionary timescales. But because the great apes examined to date represent geographically isolated populations whose diets derive from different sources, it is unclear whether this pattern of codiversification has resulted from a long history of coadaptation between microbes and hosts (heritable factors) or from the ecological and geographic separation among host species (environmental factors). To evaluate the relative influences of heritable and environmental factors on the evolution of the great ape gut microbiota, we assayed the gut communities of sympatric and allopatric populations of chimpanzees, bonobos, and gorillas residing throughout equatorial Africa. Comparisons of these populations revealed that the gut communities of different host species can always be distinguished from one another but that the gut communities of sympatric chimpanzees and gorillas have converged in terms of community composition, sharing on average 53% more bacterial phylotypes than the gut communities of allopatric hosts. Host environment, independent of host genetics and evolutionary history, shaped the distribution of bacterial phylotypes across the Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria, the four most common phyla of gut bacteria. Moreover, the specific patterns of phylotype sharing among hosts suggest that chimpanzees living in sympatry with gorillas have acquired bacteria from gorillas. These results indicate that geographic isolation between host species has promoted the evolutionary differentiation of great ape gut bacterial communities.
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Affiliation(s)
- Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Martine Peeters
- Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, 34394 Montpellier Cedex 5, France
| | - Jean-Basco Ndjango
- Faculties of Sciences, University of Kisangani, Kisangani, BP 2012, Democratic Republic of the Congo
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Howard Ochman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
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439
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Abstract
Recent findings have demonstrated that the gut microbiome complements our human genome with at least 100-fold more genes. In contrast to our Homo sapiens-derived genes, the microbiome is much more plastic, and its composition changes with age and diet, among other factors. An altered gut microbiota has been associated with several diseases, including obesity and diabetes, but the mechanisms involved remain elusive. Here we discuss factors that affect the gut microbiome, how the gut microbiome may contribute to metabolic diseases, and how to study the gut microbiome. Next-generation sequencing and development of software packages have led to the development of large-scale sequencing efforts to catalog the human microbiome. Furthermore, the use of genetically engineered gnotobiotic mouse models may increase our understanding of mechanisms by which the gut microbiome modulates host metabolism. A combination of classical microbiology, sequencing, and animal experiments may provide further insights into how the gut microbiota affect host metabolism and physiology.
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MESH Headings
- Animals
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/microbiology
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/microbiology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/microbiology
- Diet
- Disease Models, Animal
- Female
- Gastrointestinal Tract/metabolism
- Gastrointestinal Tract/microbiology
- Genetic Variation
- Germ-Free Life
- Humans
- Male
- Mice
- Microbiota/genetics
- Microbiota/physiology
- Obesity/genetics
- Obesity/metabolism
- Obesity/microbiology
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, RNA/methods
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Affiliation(s)
- Fredrik Karlsson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Valentina Tremaroli
- The Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Bäckhed
- The Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Corresponding author: Fredrik Bäckhed,
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440
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Kirkup BC. Culture-independence for surveillance and epidemiology. Pathogens 2013; 2:556-70. [PMID: 25437208 PMCID: PMC4235693 DOI: 10.3390/pathogens2030556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/03/2013] [Accepted: 09/05/2013] [Indexed: 12/27/2022] Open
Abstract
Culture-independent methods in microbiology (quantitative PCR (qPCR), sequencing, microarrays, direct from sample matrix assisted laser desorption/ionization time of flight mass spectroscopy (MALDI-TOF MS), etc.) are disruptive technology. Rather than providing the same results as culture-based methods more quickly, more cheaply or with improved accuracy, they reveal an unexpected diversity of microbes and illuminate dark corners of undiagnosed disease. At times, they overturn existing definitions of presumably well-understood infections, generating new requirements for clinical diagnosis, surveillance and epidemiology. However, current diagnostic microbiology, infection control and epidemiology rest principally on culture methods elegantly optimized by clinical laboratorians. The clinical significance is interwoven; the new methods are out of context, difficult to interpret and impossible to act upon. Culture-independent diagnostics and surveillance methods will not be deployed unless the reported results can be used to select specific therapeutics or infection control measures. To cut the knots surrounding the adoption of culture-independent methods in medical microbiology, culture-dependent methods should be supported by consistent culture-independent methods providing the microbial context. This will temper existing biases and motivate appropriate scrutiny of the older methods and results.
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Affiliation(s)
- Benjamin C Kirkup
- Department of Wound Infections, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
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441
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Abstract
PURPOSE OF REVIEW The objective of this review is to outline the contribution of the gut microbiota to nutritional status and to highlight the mechanisms by which this can occur. RECENT FINDINGS Historically, research linking intestinal bacteria with nutritional status focused on the degradation of indigestible food components by bacterial enzymes and metabolites. Of late, emerging evidence suggests an independent role of the gut microbiota in the regulation of glucose and energy homeostasis via complex interactions between microbially derived metabolites and specific target tissue cells. In addition, novel findings highlight specific microbial species involved in the production of a number of micronutrient components, which could potentially improve nutritional status in certain population groups, if available to the host at sufficiently abundant levels. SUMMARY New insights into the role of the gut microbiota and its holistic effects on the host are now emerging. High-throughput technologies allow for a greater insight into the role of the intestinal microbiota and the mechanisms by which it can contribute to overall nutritional status. Further, exploration of this evolving field of research will advance our understanding of how this complex ecosystem could advance the area of personalized nutrition in the future.
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442
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McNulty NP, Wu M, Erickson AR, Pan C, Erickson BK, Martens EC, Pudlo NA, Muegge BD, Henrissat B, Hettich RL, Gordon JI. Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol 2013; 11:e1001637. [PMID: 23976882 PMCID: PMC3747994 DOI: 10.1371/journal.pbio.1001637] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/12/2013] [Indexed: 02/07/2023] Open
Abstract
Artificial human gut microbial communities implanted into germ-free mice provide insights into how species-level responses to changes in diet give rise to community-level structural and functional reconfiguration and how types of bacteria prioritize use of available nutrients in vivo. The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities. Our intestines are populated by an almost unimaginably large number of microbial cells, most of which are bacteria. This species assemblage operates as a microbial metabolic organ, performing myriad tasks that contribute to our well-being, including processing components of our diet. The way this incredible machine assembles itself and operates remains mysterious. One approach to understanding its properties is to create artificial communities composed of a limited number of sequenced human gut bacterial species and to install them in the guts of germ-free mice that are then fed different diets. In this report, we adopt this approach. We describe the genome sequence of a new gut bacterial isolate, Bacteroides cellulosilyticus WH2, which is equipped with an unprecedented number of carbohydrate active enzymes. Deploying four different “omics” technologies, we characterize the response to diet, the relative stability, and the temporal dynamics of a 12-species artificial bacterial assemblage (including B. cellulosilyticus WH2) implanted in germ-free mouse guts. We also combine high-throughput substrate utilization screens and RNA-Seq to generate reference data analogous to a “Rosetta stone” in order to decipher what types of carbohydrates B. cellulosilyticus encounters and uses within the gut, and how it interacts with other organisms that have similar and/or distinct “professions.” This work sets the stage for future ecological and metabolic studies of more complex assemblages that more fully emulate the properties of our native gut communities.
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Affiliation(s)
- Nathan P. McNulty
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Meng Wu
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Alison R. Erickson
- Graduate School of Genome Science and Technology, University of Tennessee–Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Brian K. Erickson
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brian D. Muegge
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille University, Marseille, France
| | - Robert L. Hettich
- Graduate School of Genome Science and Technology, University of Tennessee–Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jeffrey I. Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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443
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Molecular studies neglect apparently gram-negative populations in the human gut microbiota. J Clin Microbiol 2013; 51:3286-93. [PMID: 23885002 DOI: 10.1128/jcm.00473-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Studying the relationships between gut microbiota, human health, and diseases is a major challenge that generates contradictory results. Most studies draw conclusions about the gut repertoire using a single biased metagenomics approach. We analyzed 16 different stool samples collected from healthy subjects who were from different areas, had metabolic disorders, were immunocompromised, or were treated with antibiotics at the time of the stool collection. The analyses performed included Gram staining, flow cytometry, transmission electron microscopy (TEM), quantitative real-time PCR (qPCR) of the Bacteroidetes and Firmicutes phyla, and pyrosequencing of the 16S rRNA gene amplicons targeting the V6 region. We quantified 10(10) prokaryotes per gram of feces, which is less than was previously described. The Mann-Whitney test revealed that Gram-negative proportions of the prokaryotes obtained by Gram staining, TEM, and pyrosequencing differed according to the analysis used, with Gram-negative prokaryotes yielding median percentages of 70.6%, 31.0%, and 16.4%, respectively. A comparison of TEM and pyrosequencing analyses highlighted a difference of 14.6% in the identification of Gram-negative prokaryotes, and a Spearman test showed a tendency toward correlation, albeit not significant, in the Gram-negative/Gram-positive prokaryote ratio (ρ = 0.3282, P = 0.2146). In contrast, when comparing the qPCR and pyrosequencing results, a significant correlation was found for the Bacteroidetes/Firmicutes ratio (ρ = 0.6057, P = 0.0130). Our study showed that the entire diversity of the human gut microbiota remains unknown because different techniques generate extremely different results. We found that to assess the overall composition of bacterial communities, multiple techniques must be combined. The biases that exist for each technique may be useful in exploring the major discrepancies in molecular studies.
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444
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Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI. The long-term stability of the human gut microbiota. Science 2013; 341:1237439. [PMID: 23828941 DOI: 10.1126/science.1237439] [Citation(s) in RCA: 1341] [Impact Index Per Article: 121.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A low-error 16S ribosomal RNA amplicon sequencing method, in combination with whole-genome sequencing of >500 cultured isolates, was used to characterize bacterial strain composition in the fecal microbiota of 37 U.S. adults sampled for up to 5 years. Microbiota stability followed a power-law function, which when extrapolated suggests that most strains in an individual are residents for decades. Shared strains were recovered from family members but not from unrelated individuals. Sampling of individuals who consumed a monotonous liquid diet for up to 32 weeks indicated that changes in strain composition were better predicted by changes in weight than by differences in sampling interval. This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target.
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Affiliation(s)
- Jeremiah J Faith
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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445
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Adamu BO, Lawley TD. Bacteriotherapy for the treatment of intestinal dysbiosis caused by Clostridium difficile infection. Curr Opin Microbiol 2013; 16:596-601. [PMID: 23866975 PMCID: PMC3840269 DOI: 10.1016/j.mib.2013.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/25/2013] [Indexed: 12/21/2022]
Abstract
Antibiotics damage the intestinal microbiota and disrupt colonization resistance predisposing us to recurrent C. difficile infection (CDI). Faecal microbiota transplantation (FMT) is a promising treatment for recurrent C. difficile infection. Mixtures of beneficial bacteria known as bacteriotherapy should be developed for treatment of CDI and other diseases linked to dysbiosis in the intestinal microbiota.
Faecal microbiota transplantation (FMT) has been used for more than five decades to treat a variety of intestinal diseases associated with pathological imbalances within the resident microbiota, termed dysbiosis. FMT has been particularly effective for treating patients with recurrent Clostridium difficile infection who are left with few clinical options other than continued antibiotic therapy. Our increasing knowledge of the structure and function of the human intestinal microbiota and C. difficile pathogenesis has led to the understanding that FMT promotes intestinal ecological restoration and highlights the microbiota as a viable therapeutic target. However, the use of undefined faecal samples creates a barrier for widespread clinical use because of safety and aesthetic issues. An emerging concept of bacteriotherapy, the therapeutic use of a defined mixture of harmless, health-associated bacteria, holds promise for the treatment of patients with severe C. difficile infection, and possibly represents a paradigm shift for the treatment of diseases linked to intestinal dysbiosis.
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446
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Ursell LK, Van Treuren W, Metcalf JL, Pirrung M, Gewirtz A, Knight R. Replenishing our defensive microbes. Bioessays 2013; 35:810-7. [PMID: 23836415 DOI: 10.1002/bies.201300018] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Large-scale characterization of the human microbiota has largely focused on Western adults, yet these populations may be uncharacteristic because of their diets and lifestyles. In particular, the rise of "Western diseases" may in part stem from reduced exposure to, or even loss of, microbes with which humans have coevolved. Here, we review beneficial microbes associated with pathogen resistance, highlighting the emerging role of complex microbial communities in protecting against disease. We discuss ways in which modern lifestyles and practices may deplete physiologically important microbiota, and explore prospects for reintroducing or encouraging the growth of beneficial microbes to promote the restoration of healthy microbial ecosystems.
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Affiliation(s)
- Luke K Ursell
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
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447
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448
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de Vos WM. Fame and future of faecal transplantations--developing next-generation therapies with synthetic microbiomes. Microb Biotechnol 2013; 6:316-25. [PMID: 23574632 PMCID: PMC3917466 DOI: 10.1111/1751-7915.12047] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 02/20/2013] [Indexed: 12/13/2022] Open
Abstract
While practised for over thousand years, there is presently a renaissance in the interest of using of faecal transplantations to modify the intestinal microbiota of patients. This clinical practice consists of delivering large amounts of bowel microbes in various forms into the intestinal tract of the recipient that usually has been cleared previously. The major reason for the popularity of faecal transplantations is their effectiveness in treating a variety of diseases. Hence, there is a need to develop this procedure to the next level. While there are various developments to select, standardize and store the donor microbiota, it is more challenging to understand the intestinal microbial communities and develop ways to deliver these via robust biotechnological processes. The various approaches that have been followed to do so are discussed in this contribution that is also addressing the concept of the minimal microbiome as well as the production of the synthetic communities that can be instrumental in new therapeutic avenues to modify the intestinal microbiota.
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Affiliation(s)
- Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
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449
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Clavel T, Charrier C, Wenning M, Haller D. Parvibacter caecicola gen. nov., sp. nov., a bacterium of the family
Coriobacteriaceae
isolated from the caecum of a mouse. Int J Syst Evol Microbiol 2013; 63:2642-2648. [DOI: 10.1099/ijs.0.045344-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A single strain, NR06T, was isolated from the intestine of a TNFdeltaARE mouse. Based on phylogenetic analysis of partial 16S rRNA gene sequences, strain NR06T belongs in the family
Coriobacteriaceae
within the
Actinobacteria
. The most closely related species with validly published names are members of the genera
Adlercreutzia
,
Asaccharobacter
and
Enterorhabdus
(<96 % sequence similarity). Strain NR06T was characterized by a high prevalence of monomethylmenaquinone-6 (MMK-6; 76 %) and the presence of meso-diaminopimelic acid in the cell wall. One of the major cellular fatty acids of strain NR06T was C15 : 0 ISO. Glucose was detected as a whole cell sugar. Strain NR06T was resistant to the antibiotic colistin and was positive for arginine and leucine arylamidase activity. Based on these characteristics, strain NR06T differed from related described bacteria. Therefore, the name Parvibacter caecicola gen. nov., sp. nov. is proposed to accommodate the novel bacterium. The type strain of the type species is NR06T ( = DSM 22242T = CCUG 57646T).
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Affiliation(s)
- Thomas Clavel
- Biofunctionality Unit, ZIEL - Research Center for Nutrition and Food Sciences, TU München, Freising-Weihenstephan, Germany
| | | | - Mareike Wenning
- Microbiology Unit, ZIEL - Research Center for Nutrition and Food Sciences, TU München, Freising-Weihenstephan, Germany
| | - Dirk Haller
- Biofunctionality Unit, ZIEL - Research Center for Nutrition and Food Sciences, TU München, Freising-Weihenstephan, Germany
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450
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Guinane CM, Cotter PD. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therap Adv Gastroenterol 2013; 6:295-308. [PMID: 23814609 PMCID: PMC3667473 DOI: 10.1177/1756283x13482996] [Citation(s) in RCA: 477] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The human gut microbiota has become the subject of extensive research in recent years and our knowledge of the resident species and their potential functional capacity is rapidly growing. Our gut harbours a complex community of over 100 trillion microbial cells which influence human physiology, metabolism, nutrition and immune function while disruption to the gut microbiota has been linked with gastrointestinal conditions such as inflammatory bowel disease and obesity. Here, we review the many significant recent studies that have centred on further enhancing our understanding of the complexity of intestinal communities as well as their genetic and metabolic potential. These have provided important information with respect to what constitutes a 'healthy gut microbiota' while furthering our understanding of the role of gut microbes in intestinal diseases. We also highlight recently developed genomic and other tools that are used to study the gut microbiome and, finally, we consider the manipulation of the gut microbiota as a potential therapeutic option to treat chronic gastrointestinal disease.
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Affiliation(s)
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland The Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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