2801
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Abstract
The gut microbiota affects numerous biological functions throughout the body and its characterisation has become a major research area in biomedicine. Recent studies have suggested that gut bacteria play a fundamental role in diseases such as obesity, diabetes and cardiovascular disease. Data are accumulating in animal models and humans suggesting that obesity and type 2 diabetes (T2D) are associated with a profound dysbiosis. First human metagenome-wide association studies demonstrated highly significant correlations of specific intestinal bacteria, certain bacterial genes and respective metabolic pathways with T2D. Importantly, especially butyrate-producing bacteria such as Roseburia intestinalis and Faecalibacterium prausnitzii concentrations were lower in T2D subjects. This supports the increasing evidence, that butyrate and other short-chain fatty acids are able to exert profound immunometabolic effects. Endotoxaemia, most likely gut-derived has also been observed in patients with metabolic syndrome and T2D and might play a key role in metabolic inflammation. A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism. Interestingly, certain antidiabetic drugs such as metformin also interfere with the intestinal microbiota. Specific members of the microbiota such as Akkermansia muciniphila might be decreased in diabetes and when administered to murines exerted antidiabetic effects. Therefore, as a 'gut signature' becomes more evident in T2D, a better understanding of the role of the microbiota in diabetes might provide new aspects regarding its pathophysiological relevance and pave the way for new therapeutic principles.
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Affiliation(s)
- Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Endocrinology & Metabolism, Medical University Innsbruck, Innsbruck, Austria
| | - Alexander R Moschen
- Department of Internal Medicine I, Gastroenterology, Endocrinology & Metabolism, Medical University Innsbruck, Innsbruck, Austria
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2802
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O’Connor A, Quizon PM, Albright JE, Lin FT, Bennett BJ. Responsiveness of cardiometabolic-related microbiota to diet is influenced by host genetics. Mamm Genome 2014; 25:583-99. [PMID: 25159725 PMCID: PMC4239785 DOI: 10.1007/s00335-014-9540-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/04/2014] [Indexed: 01/04/2023]
Abstract
Intestinal microbial community structure is driven by host genetics in addition to environmental factors such as diet. In comparison with environmental influences, the effect of host genetics on intestinal microbiota, and how host-driven differences alter host metabolism is unclear. Additionally, the interaction between host genetics and diet, and the impact on the intestinal microbiome and possible down-stream effect on host metabolism is not fully understood, but represents another aspects of inter-individual variation in disease risk. The objectives of this study were to investigate how diet and genetic background shape microbial communities, and how these diet- and genetic-driven microbial differences relate to cardiometabolic phenotypes. To determine these effects, we used the 8 progenitor strains of the collaborative cross/diversity outbred mapping panels (C57BL/6J, A/J, NOD/ShiLtJ, NZO/HILtJ, WSB/EiJ, CAST/EiJ, PWK/PhJ, and 129S1/SvImJ). 16s rRNA profiling of enteric microbial communities in addition to the assessment of phenotypes central to cardiometabolic health was conducted under baseline nutritional conditions and in response to diets varying in atherogenic nutrient (fat, cholesterol, cholic acid) composition. These studies revealed strain-driven differences in enteric microbial communities which were retained with dietary intervention. Diet–strain interactions were seen for a core group of cardiometabolic-related microbial taxa. In conclusion, these studies highlight diet and genetically regulated cardiometabolic-related microbial taxa. Furthermore, we demonstrate the progenitor model is useful for nutrigenomic-based studies and screens seeking to investigate the interaction between genetic background and the phenotypic and microbial response to diet.
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Affiliation(s)
- Annalouise O’Connor
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Pamela M. Quizon
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Jody E. Albright
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Fred T. Lin
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Brian J. Bennett
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Nutrition, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
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2803
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Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics. Sci Rep 2014; 4:6185. [PMID: 25155166 PMCID: PMC5385803 DOI: 10.1038/srep06185] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/04/2014] [Indexed: 02/08/2023] Open
Abstract
We analyzed bacterial communities of six distinct gut sites (the food bolus and mucus layer of the proximal small intestine, cecum and distal large intestine), using wild folivorous flying squirrels. We found significant spatial heterogeneity in composition, diversity, and species abundance distributions (SADs) of gut microbiota, corresponding to physicochemical conditions. High diversity was detected in the mucus layer of small intestine and the food bolus of cecum, followed by the food bolus of large intestine and the mucus layer of cecum, and relatively low diversity in the food bolus of small intestine and the mucus layer of large intestine, likely due to disturbance and resource partitioning. The SADs showed succession-like patterns in the food bolus communities from the proximal to distal gut. Notably, each mucus layer community had a unique pattern different from the food bolus community of the same compartment, with distinct relative abundances of dominant species. In combination with data from other mammalian fecal samples, we concluded that gut microbiota were apparently dynamic in community structure, from low species richness with unequal abundances to high species richness with equal abundances; these findings were interpreted as strong habitat effects on bacterial communities.
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2804
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Exploring the influence of the gut microbiota and probiotics on health: a symposium report. Br J Nutr 2014; 112 Suppl 1:S1-18. [PMID: 24953670 PMCID: PMC4077244 DOI: 10.1017/s0007114514001275] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present report describes the presentations delivered at the 7th International Yakult Symposium, ‘The Intestinal Microbiota and Probiotics: Exploiting Their Influence on Health’, in London on 22–23 April 2013. The following two themes associated with health risks were covered: (1) the impact of age and diet on the gut microbiota and (2) the gut microbiota's interaction with the host. The strong influence of the maternal gut microbiota on neonatal colonisation was reported, as well as rapid changes in the gut microbiome of older people who move from community living to residential care. The effects of dietary changes on gut metabolism were described and the potential influence of inter-individual microbiota differences was noted, in particular the presence/absence of keystone species involved in butyrate metabolism. Several speakers highlighted the association between certain metabolic disorders and imbalanced or less diverse microbiota. Data from metagenomic analyses and novel techniques (including an ex vivo human mucosa model) provided new insights into the microbiota's influence on coeliac, obesity-related and inflammatory diseases, as well as the potential of probiotics. Akkermansia muciniphila and Faecalibacterium prausnitzii were suggested as targets for intervention. Host–microbiota interactions were explored in the context of gut barrier function, pathogenic bacteria recognition, and the ability of the immune system to induce either tolerogenic or inflammatory responses. There was speculation that the gut microbiota should be considered a separate organ, and whether analysis of an individual's microbiota could be useful in identifying their disease risk and/or therapy; however, more research is needed into specific diseases, different population groups and microbial interventions including probiotics.
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2805
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Systems vaccinology: probing humanity's diverse immune systems with vaccines. Proc Natl Acad Sci U S A 2014; 111:12300-6. [PMID: 25136102 DOI: 10.1073/pnas.1400476111] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Homo sapiens are genetically diverse, but dramatic demographic and socioeconomic changes during the past century have created further diversification with respect to age, nutritional status, and the incidence of associated chronic inflammatory disorders and chronic infections. These shifting demographics pose new challenges for vaccination, as emerging evidence suggests that age, the metabolic state, and chronic infections can exert major influences on the immune system. Thus, a key public health challenge is learning how to reprogram suboptimal immune systems to induce effective vaccine immunity. Recent advances have applied systems biological analysis to define molecular signatures induced early after vaccination that correlate with and predict the later adaptive immune responses in humans. Such "systems vaccinology" approaches offer an integrated picture of the molecular networks driving vaccine immunity, and are beginning to yield novel insights about the immune system. Here we discuss the promise of systems vaccinology in probing humanity's diverse immune systems, and in delineating the impact of genes, the environment, and the microbiome on protective immunity induced by vaccination. Such insights will be critical in reengineering suboptimal immune systems in immunocompromised populations.
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2806
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Udayappan SD, Hartstra AV, Dallinga-Thie GM, Nieuwdorp M. Intestinal microbiota and faecal transplantation as treatment modality for insulin resistance and type 2 diabetes mellitus. Clin Exp Immunol 2014; 177:24-9. [PMID: 24528224 DOI: 10.1111/cei.12293] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2014] [Indexed: 12/17/2022] Open
Abstract
The prevalence of obesity and diabetes mellitus type 2 is increasing rapidly around the globe. Recent insights have generated an entirely new perspective that the intestinal microbiota may play a significant role in the development of these metabolic disorders. Alterations in the intestinal microbiota composition promote systemic inflammation that is a hallmark of obesity and subsequent insulin resistance. Thus, it is important to understand the reciprocal relationship between intestinal microbiota composition and metabolic health in order to eventually prevent disease progression. In this respect, faecal transplantation studies have implicated that butyrate-producing intestinal bacteria are crucial in this process and be considered as key players in regulating diverse signalling cascades associated with human glucose and lipid metabolism.
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Affiliation(s)
- S D Udayappan
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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2807
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Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice. Sci Rep 2014; 4:5922. [PMID: 25082483 PMCID: PMC4118149 DOI: 10.1038/srep05922] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/15/2014] [Indexed: 02/07/2023] Open
Abstract
Transferring gut microbiota from one individual to another may enable researchers to “humanize” the gut of animal models and transfer phenotypes between species. To date, most studies of gut microbiota transfer are performed in germ-free mice. In the studies presented, it was tested whether an antibiotic treatment approach could be used instead. C57BL/6 mice were treated with ampicillin prior to inoculation at weaning or eight weeks of age with gut microbiota from lean or obese donors. The gut microbiota and clinical parameters of the recipients was characterized one and six weeks after inoculation. The results demonstrate, that the donor gut microbiota was introduced, established, and changed the gut microbiota of the recipients. Six weeks after inoculation, the differences persisted, however alteration of the gut microbiota occurred with time within the groups. The clinical parameters of the donor phenotype were partly transmissible from obese to lean mice, in particularly β cell hyperactivity in the obese recipients. Thus, a successful inoculation of gut microbiota was not age dependent in order for the microbes to colonize, and transferring different microbial compositions to conventional antibiotic-treated mice was possible at least for a time period during which the microbiota may permanently modulate important host functions.
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2808
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Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014; 11:506-14. [PMID: 24912386 DOI: 10.1038/nrgastro.2014.66] [Citation(s) in RCA: 4517] [Impact Index Per Article: 451.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An expert panel was convened in October 2013 by the International Scientific Association for Probiotics and Prebiotics (ISAPP) to discuss the field of probiotics. It is now 13 years since the definition of probiotics and 12 years after guidelines were published for regulators, scientists and industry by the Food and Agriculture Organization of the United Nations and the WHO (FAO/WHO). The FAO/WHO definition of a probiotic--"live microorganisms which when administered in adequate amounts confer a health benefit on the host"--was reinforced as relevant and sufficiently accommodating for current and anticipated applications. However, inconsistencies between the FAO/WHO Expert Consultation Report and the FAO/WHO Guidelines were clarified to take into account advances in science and applications. A more precise use of the term 'probiotic' will be useful to guide clinicians and consumers in differentiating the diverse products on the market. This document represents the conclusions of the ISAPP consensus meeting on the appropriate use and scope of the term probiotic.
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Affiliation(s)
- Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | | | - Gregor Reid
- Lawson Health Research Institute and Departments of Microbiology &Immunology, and Surgery, University of Western Ontario, 268 Grosvenor Street, London, ON N6A 4V2, Canada
| | - Glenn R Gibson
- Department of Food and Nutritional Sciences, The University of Reading, Whiteknights, PO Box 226, Reading RG6 6AP, UK
| | - Daniel J Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Building D 240, 4000 Reservoir Road NW, Washington, DC 20007, USA
| | - Bruno Pot
- Center for Infection and Immunity, Institut Pasteur de Lille, 1 Rue Prof Calmette, Lille 59019, France
| | - Lorenzo Morelli
- Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, Piacenza 29122, Italy
| | - Roberto Berni Canani
- Department of Translational Medical Science and European Laboratory for the Investigation of Food Induced Diseases, University of Naples Federico II, Naples 80131, Italy
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku 20014, Finland
| | - Philip C Calder
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, 7119 S. Glencoe Court, Centennial, CO 80122, USA
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2809
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Viaud S, Daillère R, Boneca IG, Lepage P, Pittet MJ, Ghiringhelli F, Trinchieri G, Goldszmid R, Zitvogel L. Harnessing the intestinal microbiome for optimal therapeutic immunomodulation. Cancer Res 2014; 74:4217-21. [PMID: 25074615 DOI: 10.1158/0008-5472.can-14-0987] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Distinct cytotoxic agents currently used in the oncological armamentarium mediate their clinical benefit by influencing, directly or indirectly, the immune system in such a way that innate and adaptive immunity contributes to the tumoricidal activity. Now, we bring up evidence that both arms of anticancer immunity can be triggered through the intervention of the intestinal microbiota. Alkylating agents, such as cyclophosphamide, set up the stage for enhanced permeability of the small intestine, facilitating the translocation of selected arrays of Gram-positive bacteria against which the host mounts effector pTh17 cells and memory Th1 responses. In addition, gut commensals, through lipopolysaccharide and other bacterial components, switch the tumor microenvironment, in particular the redox equilibrium and the TNF production of intratumoral myeloid cells during therapies with platinum salts or intratumoral TLR9 agonists combined with systemic anti-IL10R Ab respectively. Consequently, antibiotics can compromise the efficacy of certain chemotherapeutic or immunomodulatory regimens.
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Affiliation(s)
- S Viaud
- Institut National de la Santé et de la Recherche Médicale, U1015, Gustave Roussy, Villejuif, France. Université Paris-Sud, Kremlin Bicêtre, France
| | - R Daillère
- Institut National de la Santé et de la Recherche Médicale, U1015, Gustave Roussy, Villejuif, France. Université Paris-Sud, Kremlin Bicêtre, France
| | - I G Boneca
- Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France. Institut National de la Santé et de la Recherche Médicale, Group Avenir, Paris, France
| | - P Lepage
- Institut National de la Recherche Agronomique, Micalis UMR1319, Jouy-en-Josas, France. AgroParisTech, Micalis UMR1319, Jouy-en-Josas, France
| | - M J Pittet
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - F Ghiringhelli
- Institut National de la Santé et de la Recherche Médicale, U866, Centre Georges François Leclerc, Dijon, France. Institut National de la Santé et de la Recherche Médicale, Group Avenir, Dijon, France. Faculté de Médecine, Université de Bourgogne, Dijon, France
| | - G Trinchieri
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland
| | - R Goldszmid
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland
| | - L Zitvogel
- Institut National de la Santé et de la Recherche Médicale, U1015, Gustave Roussy, Villejuif, France. Université Paris-Sud, Kremlin Bicêtre, France. Centre d'Investigation Clinique Biothérapie CICBT 507, Gustave Roussy, Villejuif, France.
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2810
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Kormas KA, Meziti A, Mente E, Frentzos A. Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata). Microbiologyopen 2014; 3:718-28. [PMID: 25066034 PMCID: PMC4234263 DOI: 10.1002/mbo3.202] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/29/2014] [Accepted: 07/03/2014] [Indexed: 02/06/2023] Open
Abstract
We compared the gut prokaryotic communities in wild, organically-, and conventionally reared sea bream (Sparus aurata) individuals. Gut microbial communities were identified using tag pyrosequencing of the 16S rRNA genes. There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. Most of the Bacteria belonged to the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The number of bacterial operational taxonomic units (OTUs) was reduced from the wild to the conventionally reared fish, implying a response of the gut microorganisms to the supplied food and possibly alterations in food assimilation. The dominant bacterial OTU in all examined fish was closely related to the genus Diaphorobacter. This is the first time that a member of the β-Proteobacteria, which dominate in freshwaters, are so important in a marine fish gut. In total the majority of the few Archaea OTUs found, were related to methane metabolism. The inferred physiological roles of the dominant prokaryotes are related to the metabolism of carbohydrates and nitrogenous compounds. This study showed the responsive feature of the sea bream gut prokaryotic communities to their diets and also the differences of the conventional in comparison to the organic and wild sea bream gut microbiota.
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Affiliation(s)
- Konstantinos A Kormas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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2811
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Liu CM, Osborne BJW, Hungate BA, Shahabi K, Huibner S, Lester R, Dwan MG, Kovacs C, Contente-Cuomo TL, Benko E, Aziz M, Price LB, Kaul R. The semen microbiome and its relationship with local immunology and viral load in HIV infection. PLoS Pathog 2014; 10:e1004262. [PMID: 25058515 PMCID: PMC4110035 DOI: 10.1371/journal.ppat.1004262] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/06/2014] [Indexed: 12/02/2022] Open
Abstract
Semen is a major vector for HIV transmission, but the semen HIV RNA viral load (VL) only correlates moderately with the blood VL. Viral shedding can be enhanced by genital infections and associated inflammation, but it can also occur in the absence of classical pathogens. Thus, we hypothesized that a dysregulated semen microbiome correlates with local HIV shedding. We analyzed semen samples from 49 men who have sex with men (MSM), including 22 HIV-uninfected and 27 HIV-infected men, at baseline and after starting antiretroviral therapy (ART) using 16S rRNA gene-based pyrosequencing and quantitative PCR. We studied the relationship of semen bacteria with HIV infection, semen cytokine levels, and semen VL by linear regression, non-metric multidimensional scaling, and goodness-of-fit test. Streptococcus, Corynebacterium, and Staphylococcus were common semen bacteria, irrespective of HIV status. While Ureaplasma was the more abundant Mollicutes in HIV-uninfected men, Mycoplasma dominated after HIV infection. HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART. In HIV-infected men, semen bacterial load correlated with seven pro-inflammatory semen cytokines, including IL-6 (p = 0.024), TNF-α (p = 0.009), and IL-1b (p = 0.002). IL-1b in particular was associated with semen VL (r2 = 0.18, p = 0.02). Semen bacterial load was also directly linked to the semen HIV VL (r2 = 0.15, p = 0.02). HIV infection reshapes the relationship between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, which supports a role of the semen microbiome in HIV sexual transmission. The classical paradigm of HIV infectivity centers on the blood HIV RNA viral load. However, while other fluid compartments such as semen and cerebrospinal fluid can have distinct viral loads from blood, the causes of localized HIV shedding are not fully understood. Since the semen viral load is an independent predictor of HIV transmission risk, it is critical to understand the local factors that trigger increased semen viral shedding in order to develop novel preventative strategies. Here, we evaluated the semen microbiome, bacterial load, and cytokine levels in 22 HIV-uninfected men who have sex with men (MSM) and in 27 HIV-infected MSM before and after initiation of antiretroviral therapy (ART). We found that HIV infection reduces semen microbiome biodiversity, which is restored with ART and immune reconstitution. We also found that semen bacterial load in untreated, HIV-infected men is associated with the levels of seven semen cytokines, relationships not seen in the uninfected controls. In particular, the cytokine IL-1b was uniquely correlated with both semen bacterial and viral load. Our findings support the interaction between semen microbiome and local immunology, and suggest that IL-1b could be a mechanism for semen microbiome to trigger semen viral shedding.
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Affiliation(s)
- Cindy M. Liu
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | | | - Bruce A. Hungate
- Department of Biology, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Sanja Huibner
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Richard Lester
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Michael G. Dwan
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Colin Kovacs
- Department of Medicine, University of Toronto, Toronto, Canada
- Maple Leaf Medical Centre, Toronto, Canada
| | - Tania L. Contente-Cuomo
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | | | - Maliha Aziz
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Department of Environmental and Occupational Health, George Washington University School of Public Health, Washington, D.C., United States of America
| | - Lance B. Price
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Department of Environmental and Occupational Health, George Washington University School of Public Health, Washington, D.C., United States of America
- * E-mail: (LBP); (RK)
| | - Rupert Kaul
- Department of Medicine, University of Toronto, Toronto, Canada
- Department of Medicine, University Health Network, Toronto, Canada
- * E-mail: (LBP); (RK)
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2812
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Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, Guo J, Le Chatelier E, Yao J, Wu L, Zhou J, Ni S, Liu L, Pons N, Batto JM, Kennedy SP, Leonard P, Yuan C, Ding W, Chen Y, Hu X, Zheng B, Qian G, Xu W, Ehrlich SD, Zheng S, Li L. Alterations of the human gut microbiome in liver cirrhosis. Nature 2014; 513:59-64. [PMID: 25079328 DOI: 10.1038/nature13568] [Citation(s) in RCA: 1330] [Impact Index Per Article: 133.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/09/2014] [Indexed: 02/07/2023]
Abstract
Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.
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Affiliation(s)
- Nan Qin
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]
| | - Fengling Yang
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]
| | - Ang Li
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]
| | - Edi Prifti
- 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2]
| | - Yanfei Chen
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]
| | - Li Shao
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]
| | - Jing Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | | | - Jian Yao
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Lingjiao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Jiawei Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Shujun Ni
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Lin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Jean Michel Batto
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Sean P Kennedy
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Pierre Leonard
- Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
| | - Chunhui Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Wenchao Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Yuanting Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Xinjun Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Beiwen Zheng
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
| | - Guirong Qian
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - Wei Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China
| | - S Dusko Ehrlich
- 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | - Shusen Zheng
- 1] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [2] Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University, 310003 Hangzhou, China
| | - Lanjuan Li
- 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China
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2813
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Maier L, Vyas R, Cordova CD, Lindsay H, Schmidt TSB, Brugiroux S, Periaswamy B, Bauer R, Sturm A, Schreiber F, von Mering C, Robinson MD, Stecher B, Hardt WD. Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem. Cell Host Microbe 2014; 14:641-51. [PMID: 24331462 DOI: 10.1016/j.chom.2013.11.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/01/2013] [Accepted: 11/11/2013] [Indexed: 01/09/2023]
Abstract
The intestinal microbiota features intricate metabolic interactions involving the breakdown and reuse of host- and diet-derived nutrients. The competition for these resources can limit pathogen growth. Nevertheless, some enteropathogenic bacteria can invade this niche through mechanisms that remain largely unclear. Using a mouse model for Salmonella diarrhea and a transposon mutant screen, we discovered that initial growth of Salmonella Typhimurium (S. Tm) in the unperturbed gut is powered by S. Tm hyb hydrogenase, which facilitates consumption of hydrogen (H2), a central intermediate of microbiota metabolism. In competitive infection experiments, a hyb mutant exhibited reduced growth early in infection compared to wild-type S. Tm, but these differences were lost upon antibiotic-mediated disruption of the host microbiota. Additionally, introducing H2-consuming bacteria into the microbiota interfered with hyb-dependent S. Tm growth. Thus, H2 is an Achilles' heel of microbiota metabolism that can be subverted by pathogens and might offer opportunities to prevent infection.
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Affiliation(s)
- Lisa Maier
- Institute of Microbiology, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Rounak Vyas
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Helen Lindsay
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Sandrine Brugiroux
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität Munich, 80336 Munich, Germany
| | | | - Rebekka Bauer
- Institute of Microbiology, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Alexander Sturm
- Institute of Microbiology, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Frank Schreiber
- Department of Environmental Microbiology, Eawag and Department of Environmental Systems Sciences, ETH Zurich, CH-8600 Dübendorf, Switzerland
| | - Christian von Mering
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität Munich, 80336 Munich, Germany
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2814
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Afshar S, Kelly SB, Seymour K, Lara J, Woodcock S, Mathers JC. The Effects of Bariatric Surgery on Colorectal Cancer Risk: Systematic Review and Meta-analysis. Obes Surg 2014; 24:1793-9. [DOI: 10.1007/s11695-014-1359-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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2815
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Abeles SR, Pride DT. Molecular bases and role of viruses in the human microbiome. J Mol Biol 2014; 426:3892-906. [PMID: 25020228 PMCID: PMC7172398 DOI: 10.1016/j.jmb.2014.07.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/30/2014] [Accepted: 07/04/2014] [Indexed: 12/24/2022]
Abstract
Viruses are dependent biological entities that interact with the genetic material of most cells on the planet, including the trillions within the human microbiome. Their tremendous diversity renders analysis of human viral communities ("viromes") to be highly complex. Because many of the viruses in humans are bacteriophage, their dynamic interactions with their cellular hosts add greatly to the complexities observed in examining human microbial ecosystems. We are only beginning to be able to study human viral communities on a large scale, mostly as a result of recent and continued advancements in sequencing and bioinformatic technologies. Bacteriophage community diversity in humans not only is inexorably linked to the diversity of their cellular hosts but also is due to their rapid evolution, horizontal gene transfers, and intimate interactions with host nucleic acids. There are vast numbers of observed viral genotypes on many body surfaces studied, including the oral, gastrointestinal, and respiratory tracts, and even in the human bloodstream, which previously was considered a purely sterile environment. The presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed these communities are substantially altered when mucosal defenses are weakened. Perhaps the most interesting aspect of human viral communities is the extent to which they can carry gene functions involved in the pathogenesis of their hosts, particularly antibiotic resistance. Persons in close contact with each other have been shown to share a fraction of oral virobiota, which could potentially have important implications for the spread of antibiotic resistance to healthy individuals. Because viruses can have a large impact on ecosystem dynamics through mechanisms such as the transfers of beneficial gene functions or the lysis of certain populations of cellular hosts, they may have both beneficial and detrimental roles that affect human health, including improvements in microbial resilience to disturbances, immune evasion, maintenance of physiologic processes, and altering the microbial community in ways that promote or prevent pathogen colonization.
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Affiliation(s)
- Shira R Abeles
- Department of Medicine, University of California, San Diego, CA 92093, USA
| | - David T Pride
- Department of Medicine, University of California, San Diego, CA 92093, USA; Department of Pathology, University of California, San Diego, CA 92093, USA.
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2816
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Karlsson FH, Nookaew I, Nielsen J. Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue. PLoS Comput Biol 2014; 10:e1003706. [PMID: 25010449 PMCID: PMC4091689 DOI: 10.1371/journal.pcbi.1003706] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/19/2014] [Indexed: 12/29/2022] Open
Abstract
Metagenomic sequencing has contributed important new knowledge about the microbes that live in a symbiotic relationship with humans. With modern sequencing technology it is possible to generate large numbers of sequencing reads from a metagenome but analysis of the data is challenging. Here we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. Using MEDUSA we mapped 782 gut metagenomes to the global gene catalogue and a catalogue of sequenced microbial species. Hereby we find that all studies share about half a million genes and that on average 300,000 genes are shared by half the studied subjects. The gene richness is higher in the European studies compared to Chinese and American and this is also reflected in the species richness. Even though it is possible to identify common species and a core set of genes, we find that there are large variations in abundance of species and genes.
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Affiliation(s)
- Fredrik H. Karlsson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Intawat Nookaew
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail:
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2817
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Lahti L, Salojärvi J, Salonen A, Scheffer M, de Vos WM. Tipping elements in the human intestinal ecosystem. Nat Commun 2014; 5:4344. [PMID: 25003530 PMCID: PMC4102116 DOI: 10.1038/ncomms5344] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/09/2014] [Indexed: 01/19/2023] Open
Abstract
The microbial communities living in the human intestine can have profound impact on our well-being and health. However, we have limited understanding of the mechanisms that control this complex ecosystem. Here, based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults, we identify groups of bacteria that exhibit robust bistable abundance distributions. These bacteria are either abundant or nearly absent in most individuals, and exhibit decreased temporal stability at the intermediate abundance range. The abundances of these bimodally distributed bacteria vary independently, and their abundance distributions are not affected by short-term dietary interventions. However, their contrasting alternative states are associated with host factors such as ageing and overweight. We propose that the bistable groups reflect tipping elements of the intestinal microbiota, whose critical transitions may have profound health implications and diagnostic potential. Intestinal microbes can have important effects on our health. Here, the authors analyse the gut microbiota composition in 1,000 western adults and find that certain bacteria are either abundant or nearly absent, and that these alternative states are associated with ageing and overweight.
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Affiliation(s)
- Leo Lahti
- 1] Department of Veterinary Biosciences, University of Helsinki, PO Box 66, FI-00014 Helsinki, Finland [2] Laboratory of Microbiology, Wageningen University, PO Box 8033, 6700 EJ Wageningen, The Netherlands
| | - Jarkko Salojärvi
- 1] Department of Veterinary Biosciences, University of Helsinki, PO Box 66, FI-00014 Helsinki, Finland [2]
| | - Anne Salonen
- 1] Department of Bacteriology and Immunology, Immunobiology Research Program, Haartman Institute, University of Helsinki, PO Box 21, FI-00014 Helsinki, Finland [2]
| | - Marten Scheffer
- Aquatic Ecology, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands
| | - Willem M de Vos
- 1] Department of Veterinary Biosciences, University of Helsinki, PO Box 66, FI-00014 Helsinki, Finland [2] Laboratory of Microbiology, Wageningen University, PO Box 8033, 6700 EJ Wageningen, The Netherlands [3] Department of Bacteriology and Immunology, Immunobiology Research Program, Haartman Institute, University of Helsinki, PO Box 21, FI-00014 Helsinki, Finland
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2818
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An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 2014; 32:834-41. [DOI: 10.1038/nbt.2942] [Citation(s) in RCA: 1217] [Impact Index Per Article: 121.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/03/2014] [Indexed: 02/08/2023]
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2819
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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 2014; 32:822-8. [PMID: 24997787 DOI: 10.1038/nbt.2939] [Citation(s) in RCA: 655] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/22/2014] [Indexed: 12/13/2022]
Abstract
Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.
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2820
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Kawamoto S, Maruya M, Kato L, Suda W, Atarashi K, Doi Y, Tsutsui Y, Qin H, Honda K, Okada T, Hattori M, Fagarasan S. Foxp3+ T Cells Regulate Immunoglobulin A Selection and Facilitate Diversification of Bacterial Species Responsible for Immune Homeostasis. Immunity 2014; 41:152-65. [DOI: 10.1016/j.immuni.2014.05.016] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/09/2014] [Indexed: 02/06/2023]
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2821
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Caricilli AM, Saad MJA. Gut microbiota composition and its effects on obesity and insulin resistance. Curr Opin Clin Nutr Metab Care 2014; 17:312-8. [PMID: 24848531 DOI: 10.1097/mco.0000000000000067] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Rising evidence suggest that variation in the gut microbiome at gene and species levels defines subsets of individuals who have increased risk of obesity-related metabolic disorders, including insulin resistance and type 2 diabetes, which is influenced by diet and genetic profile of the host. Our goal in this review is gathering the newest findings concerning gut microbiota composition and effects on host's metabolism. RECENT FINDINGS Dietary changes have been shown as the most prominent shaper of gut microbiota composition, reflecting major phenotypes, which can also be transmitted to other individuals, in spite of genetic variances. Gut microbiota composition has also been presented as diversity, which may have important implications in metabolite production and consequent interference with inflammatory activation, insulin resistance, and obesity. SUMMARY Specific approaches made it possible to comprehend some of the interactions between certain bacterial strains and their host, and how their metabolites may interfere with host's cell signaling, changing its metabolic profile. Herein, we discuss some of the mechanisms by which alterations in the gut microbiota composition may contribute to the pathophysiology of obesity and its related comorbidities.
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Affiliation(s)
- Andrea M Caricilli
- Department of Internal Medicine, State University of Campinas, Campinas, Sau Paulo, Brazil
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2822
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Abstract
The human gastrointestinal tract hosts a large number of microbial cells which exceed their mammalian counterparts by approximately 3-fold. The genes expressed by these microorganisms constitute the gut microbiome and may participate in diverse functions that are essential to the host, including digestion, regulation of energy metabolism, and modulation of inflammation and immunity. The gut microbiome can be modulated by dietary changes, antibiotic use, or disease. Different ailments have distinct associated microbiomes in which certain species or genes are present in different relative quantities. Thus, identifying specific disease-associated signatures in the microbiome as well as the factors that alter microbial populations and gene expression will lead to the development of new products such as prebiotics, probiotics, antimicrobials, live biotherapeutic products, or more traditional drugs to treat these disorders. Gained knowledge on the microbiome may result in molecular lab tests that may serve as personalized tools to guide the use of the aforementioned products and monitor interventional progress.
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Affiliation(s)
| | | | | | | | - Satya Prakash
- Micropharma Limited; Montreal, QC Canada; Biomedical Technology and Cell Therapy Research Laboratory; Department of Biomedical Engineering; Faculty of Medicine; McGill University; Montreal, QC Canada
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2823
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Munukka E, Pekkala S, Wiklund P, Rasool O, Borra R, Kong L, Ojanen X, Cheng SM, Roos C, Tuomela S, Alen M, Lahesmaa R, Cheng S. Gut-adipose tissue axis in hepatic fat accumulation in humans. J Hepatol 2014; 61:132-8. [PMID: 24613361 DOI: 10.1016/j.jhep.2014.02.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/27/2014] [Accepted: 02/25/2014] [Indexed: 01/08/2023]
Abstract
BACKGROUND & AIMS Recent evidence suggests that in animals gut microbiota composition (GMC) affects the onset and progression of hepatic fat accumulation. The aim of this study was to investigate in humans whether subjects with high hepatic fat content (HHFC) differ in their GMC from those with low hepatic fat content (LHFC), and whether these differences are associated with body composition, biomarkers and abdominal adipose tissue inflammation. METHODS Hepatic fat content (HFC) was measured using proton magnetic resonance spectroscopy ((1)H MRS). Fecal GMC was profiled by 16S rRNA fluorescence in situ hybridization and flow cytometry. Adipose tissue gene expression was analyzed using Affymetrix microarrays and quantitative PCR. RESULTS The HHFC group had unfavorable GMC described by lower amount of Faecalibacterium prausnitzii (FPrau) (p<0.05) and relatively higher Enterobacteria than the LHFC group. Metabolically dysbiotic GMC associated with HOMA-IR and triglycerides (p<0.05 for both). Several inflammation-related adipose tissue genes were differentially expressed and correlated with HFC (p<0.05). In addition, the expression of certain genes correlated with GMC dysbiosis, i.e., low FPrau-to-Bacteroides ratio. CONCLUSIONS HHFC subjects differ unfavorably in their GMC from LHFC subjects. Adipose tissue inflammation may be an important link between GMC, metabolic disturbances, and hepatic fat accumulation.
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Affiliation(s)
- Eveliina Munukka
- Department of Health Sciences, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland; Department of Medical Microbiology and Immunology, University of Turku, Finland
| | - Satu Pekkala
- Department of Health Sciences, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Petri Wiklund
- Department of Health Sciences, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Omid Rasool
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ronald Borra
- Department of Diagnostic Radiology, Turku University Hospital, Turku, Finland
| | - Lingjia Kong
- Tampere University of Technology, Tampere, Finland
| | - Xiaowei Ojanen
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
| | - Shu Mei Cheng
- Department of Health Sciences, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | | | - Soile Tuomela
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Markku Alen
- Department of Medical Rehabilitation, Oulu University Hospital, Oulu, Finland; Institute of Health Sciences, University of Oulu, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sulin Cheng
- Department of Health Sciences, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland; Department of Physical Education, Shanghai Jiao Tong University, Shanghai, China.
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2824
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Kanai T, Matsuoka K, Naganuma M, Hayashi A, Hisamatsu T. Diet, microbiota, and inflammatory bowel disease: lessons from Japanese foods. Korean J Intern Med 2014; 29:409-15. [PMID: 25045286 PMCID: PMC4101585 DOI: 10.3904/kjim.2014.29.4.409] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/22/2014] [Indexed: 02/07/2023] Open
Abstract
The incidence and prevalence of inflammatory bowel diseases (IBDs) including ulcerative colitis and Crohn disease are rapidly increasing in Western countries and in developed Asian countries. Although biologic agents targeting the immune system have been effective in patients with IBD, cessation of treatment leads to relapse in the majority of patients, suggesting that intrinsic immune dysregulation is an effect, not a cause, of IBD. Dramatic changes in the environment, resulting in the dysregulated composition of intestinal microbiota or dysbiosis, may be associated with the fundamental causes of IBD. Japan now has upgraded water supply and sewerage systems, as well as dietary habits and antibiotic overuse that are similar to such features found in developed Western countries. The purpose of this review article was to describe the association of diet, particularly Japanese food and microbiota, with IBD.
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Affiliation(s)
- Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Katsuyoshi Matsuoka
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Makoto Naganuma
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Atsushi Hayashi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tadakazu Hisamatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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2825
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Clavel T, Desmarchelier C, Haller D, Gérard P, Rohn S, Lepage P, Daniel H. Intestinal microbiota in metabolic diseases: from bacterial community structure and functions to species of pathophysiological relevance. Gut Microbes 2014; 5:544-51. [PMID: 25003516 DOI: 10.4161/gmic.29331] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The trillions of bacterial cells that colonize the mammalian digestive tract influence both host physiology and the fate of dietary compounds. Gnotobionts and fecal transplantation have been instrumental in revealing the causal role of intestinal bacteria in energy homeostasis and metabolic dysfunctions such as type-2 diabetes. However, the exact contribution of gut bacterial metabolism to host energy balance is still unclear and knowledge about underlying molecular mechanisms is scant. We have previously characterized cecal bacterial community functions and host responses in diet-induced obese mice using omics approaches. Based on these studies, we here discuss issues on the relevance of mouse models, give evidence that the metabolism of cholesterol-derived compounds by gut bacteria is of particular importance in the context of metabolic disorders and that dominant species of the family Coriobacteriaceae are good models to study these functions.
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Affiliation(s)
- Thomas Clavel
- Junior Research Group Intestinal Microbiome; ZIEL-Research Center for Nutrition and Food Sciences; Technische Universität München; Freising-Weihenstephan, Germany
| | - Charles Desmarchelier
- Molecular Nutrition Unit; ZIEL-Research Center for Nutrition and Food Sciences; Technische Universität München; Freising-Weihenstephan, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology; Biofunctionality Unit; ZIEL-Research Center for Nutrition and Food Sciences; Technische Universität München; Freising-Weihenstephan, Germany
| | - Philippe Gérard
- INRA / AgroParisTech; Micalis UMR1319; Jouy-en-Josas, France
| | - Sascha Rohn
- Institute of Food Chemistry; Hamburg School of Food Science; University of Hamburg; Hamburg, Germany
| | - Patricia Lepage
- INRA / AgroParisTech; Micalis UMR1319; Jouy-en-Josas, France
| | - Hannelore Daniel
- Molecular Nutrition Unit; ZIEL-Research Center for Nutrition and Food Sciences; Technische Universität München; Freising-Weihenstephan, Germany
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2826
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Abstract
MOTIVATION Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale. RESULTS In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regular nearest neighbor graph. This framework allows refinement of the database over time by continual application of random hash functions, with the effect of each hash function encoded in the nearest neighbor graph. This eliminates the need to explicitly maintain the hash functions in order for query efficiency to benefit from the accumulated randomness. Results on real and simulated data show that Amordad can support logarithmic query time for identifying similar metagenomes even as the database size reaches into the millions. AVAILABILITY AND IMPLEMENTATION Source code, licensed under the GNU general public license (version 3) is freely available for download from http://smithlabresearch.org/amordad CONTACT andrewds@usc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ehsan Behnam
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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2827
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Barbut F, Collignon A, Butel MJ, Bourlioux P. [Fecal microbiota transplantation: review]. ANNALES PHARMACEUTIQUES FRANÇAISES 2014; 73:13-21. [PMID: 25577013 DOI: 10.1016/j.pharma.2014.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/20/2014] [Accepted: 05/20/2014] [Indexed: 12/17/2022]
Abstract
Fecal microbiota transplantation (FMT) has gained an increasing medical interest, since the recognition of the role of disturbed microbiota in the development of various diseases. To date, FMT is an established treatment modality for multiple recurrent Clostridium difficile infection (RCDI), despite lack of standardization of the procedure. Persisting normalization of the disturbed colonic microbiota associated with RCDI seems to be responsible for the therapeutic effect of FMT. For other diseases, FMT should be considered strictly experimental, only offered to patients in an investigational clinical setting. Although the concept of FMT is appealing, current expectations should be damped until future evidence arises.
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Affiliation(s)
- F Barbut
- Laboratoire Clostridium difficile associé au CNR des anaérobies et du botulisme, unité du lutte contre les infections nosocomiales (UHLIN), hôpital Saint-Antoine, 184, rue du Faubourg-Saint-Antoine, 75012 Paris, France; Groupe de recherche clinique n(o) 2 EPIDIFF, université Pierre-et-Marie-Curie, 75012 Paris, France.
| | - A Collignon
- EA4043, faculté de pharmacie, université Paris Sud, 92290 Châtenay-Malabry, France; Service de microbiologie, hôpital Jean-Verdier, AP-HP, 93140 Bondy, France
| | - M-J Butel
- Écosystème intestinal, probiotiques, antibiotiques (EA4065), université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - P Bourlioux
- EA4043, faculté de pharmacie, université Paris Sud, 92290 Châtenay-Malabry, France; Académie nationale de pharmacie, 4, avenue de l'Observatoire, 75270 Paris cedex 06, France
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2828
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Dickson RP, Erb-Downward JR, Huffnagle GB. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. THE LANCET RESPIRATORY MEDICINE 2014; 2:238-46. [PMID: 24621685 DOI: 10.1016/s2213-2600(14)70028-1] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pneumonia is a major cause of morbidity and mortality for which no new methods of treatment have entered clinical practice since the discovery of antibiotics. Innovations in the techniques of culture-independent microbial identification have shown that the lungs, previously deemed sterile in the absence of infection, contain diverse and dynamic communities of microbes. In this Personal View, we argue that these observations have shown the inadequacy of traditional conceptual models of lung microbiology and the pathogenesis of pneumonia, hampering progress in research and practice. We propose three new conceptual models to replace the traditional models of lung microbiology: an adapted island model of lung biogeography, the effect of environmental gradients on lung microbiota, and pneumonia as an emergent phenomenon propelled by unexplored positive feedback loops. We argue that the ecosystem of lung microbiota has all of the features of a complex adaptive system: diverse entities interacting with each other within a common space, showing interdependent actions and possessing the capacity to adapt to changes in conditions. Complex adaptive systems are fundamentally different in behaviour from the simple, linear systems typified by the traditional model of pneumonia pathogenesis, and need distinct analytical approaches.
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Affiliation(s)
- Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - John R Erb-Downward
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan MI, USA
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2829
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Wesolowska-Andersen A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, Licht TR. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. MICROBIOME 2014; 2:19. [PMID: 24949196 PMCID: PMC4063427 DOI: 10.1186/2049-2618-2-19] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/25/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND In recent years, studies on the human intestinal microbiota have attracted tremendous attention. Application of next generation sequencing for mapping of bacterial phylogeny and function has opened new doors to this field of research. However, little attention has been given to the effects of choice of methodology on the output resulting from such studies. RESULTS IN THIS STUDY WE CONDUCTED A SYSTEMATIC COMPARISON OF THE DNA EXTRACTION METHODS USED BY THE TWO MAJOR COLLABORATIVE EFFORTS: The European MetaHIT and the American Human Microbiome Project (HMP). Additionally, effects of homogenizing the samples before extraction were addressed. We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol. CONCLUSIONS Whereas it is comforting that the inter-individual variation clearly exceeded the variation resulting from choice of extraction method, our data highlight the challenge of comparing data across studies applying different methodologies.
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Affiliation(s)
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark
| | - Vera Carvalho
- National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence analysis, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Ramneek Gupta
- Center for Biological Sequence analysis, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark
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2830
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Affiliation(s)
- Patrick Hanaway
- Institute for Functional Medicine, Federal Way, Washington, United States
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2831
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Rapidly expanding knowledge on the role of the gut microbiome in health and disease. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1981-1992. [PMID: 24882755 DOI: 10.1016/j.bbadis.2014.05.023] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 05/03/2014] [Accepted: 05/24/2014] [Indexed: 12/19/2022]
Abstract
The human gut is colonized by a wide diversity of micro-organisms, which are now known to play a key role in the human host by regulating metabolic functions and immune homeostasis. Many studies have indicated that the genomes of our gut microbiota, known as the gut microbiome or our "other genome" could play an important role in immune-related, complex diseases, and growing evidence supports a causal role for gut microbiota in regulating predisposition to diseases. A comprehensive analysis of the human gut microbiome is thus important to unravel the exact mechanisms by which the gut microbiota are involved in health and disease. Recent advances in next-generation sequencing technology, along with the development of metagenomics and bioinformatics tools, have provided opportunities to characterize the microbial communities. Furthermore, studies using germ-free animals have shed light on how the gut microbiota are involved in autoimmunity. In this review we describe the different approaches used to characterize the human microbiome, review current knowledge about the gut microbiome, and discuss the role of gut microbiota in immune homeostasis and autoimmunity. Finally, we indicate how this knowledge could be used to improve human health by manipulating the gut microbiota. This article is part of a Special Issue entitled: From Genome to Function.
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2832
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Cammarota G, Ianiro G, Bibbò S, Gasbarrini A. Gut microbiota modulation: probiotics, antibiotics or fecal microbiota transplantation? Intern Emerg Med 2014; 9:365-73. [PMID: 24664520 DOI: 10.1007/s11739-014-1069-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/10/2014] [Indexed: 12/11/2022]
Abstract
Gut microbiota is known to have a relevant role in our health, and is also related to both gastrointestinal and extradigestive diseases. Therefore, restoring the alteration of gut microbiota represents an outstanding clinical target for the treatment of gut microbiota-related diseases. The modulation of gut microbiota is perhaps an ancestral, innate concept for human beings. At this time, the restoration of gut microbiota impairment is a well-established concept in mainstream medicine, and several therapeutic approaches have been developed in this regard. Antibiotics, prebiotics and probiotics are the best known and commercially available options to overcome gastrointestinal dysbiosis. Fecal microbiota transplantation is an old procedure that has recently become popular again. It has shown a clear effectiveness in the treatment of C. difficile infection, and now represents a cutting-edge option for the restoration of gut microbiota. Nevertheless, such weapons should be used with caution. Antibiotics can indeed harm and alter gut microbiota composition. Probiotics, instead, are not at all the same thing, and thinking in terms of different strains is probably the only way to improve clinical outcomes. Moreover, fecal microbiota transplantation has shown promising results, but stronger proofs are needed. Considerable efforts are needed to increase our knowledge in the field of gut microbiota, especially with regard to the future use in its modulation for therapeutic purposes.
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2833
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2834
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High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model. Nat Commun 2014; 5:3889. [PMID: 24846660 PMCID: PMC4078997 DOI: 10.1038/ncomms4889] [Citation(s) in RCA: 300] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 04/14/2014] [Indexed: 02/07/2023] Open
Abstract
The intestinal microbiome is a unique ecosystem and an essential mediator of metabolism and obesity in mammals. However, studies investigating the impact of the diet on the establishment of the gut microbiome early in life are generally lacking, and most notably so in primate models. Here we report that a high-fat maternal or postnatal diet, but not obesity per se, structures the offspring’s intestinal microbiome in Macaca fuscata (Japanese macaque). The resultant microbial dysbiosis is only partially corrected by a low-fat, control diet after weaning. Unexpectedly, early exposure to a high-fat diet diminished the abundance of non-pathogenic Campylobacter in the juvenile gut, suggesting a potential role for dietary fat in shaping commensal microbial communities in primates. Our data challenge the concept of an obesity-causing gut microbiome, and rather provide evidence for a contribution of the maternal diet in establishing the microbiota, which in turn affects intestinal maintenance of metabolic health.
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2835
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Are stool samples suitable for studying the link between gut microbiota and obesity? Eur J Epidemiol 2014; 29:307-9. [PMID: 24838696 DOI: 10.1007/s10654-014-9905-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/18/2014] [Indexed: 01/24/2023]
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2836
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Gut microbiota in older subjects: variation, health consequences and dietary intervention prospects. Proc Nutr Soc 2014; 73:441-51. [PMID: 24824449 DOI: 10.1017/s0029665114000597] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alterations in intestinal microbiota composition and function have been linked to conditions including functional gastrointestinal disorders, obesity and diabetes. The gut microbiome encodes metabolic capability in excess of that encoded by the human genome, and bacterially produced enzymes are important for releasing nutrients from complex dietary ingredients. Previous culture-based studies had indicated that the gut microbiota of older people was different from that of younger adults, but the detailed findings were contradictory. Small-scale studies had also shown that the microbiota composition could be altered by dietary intervention or supplementation. We showed that the core microbiota and aggregate composition in 161 seniors was distinct from that of younger persons. To further investigate the reasons for this variation, we analysed the microbiota composition of 178 elderly subjects for whom the dietary intake data were available. The data revealed distinct microbiota composition groups, which overlapped with distinct dietary patterns that were governed by where people lived: at home, in rehabilitation or in long-term residential care. These diet-microbiota separations correlated with cluster analysis of NMR-derived faecal metabolites and shotgun metagenomic data. Major separations in the microbiota correlated with selected clinical measurements. It should thus be possible to programme the microbiota to enrich bacterial species and activities that promote healthier ageing. A number of other studies have investigated the effect of certain dietary components and their ability to modulate the microbiota composition to promote health. This review will discuss dietary interventions conducted thus far, especially those in elderly populations and highlight their impact on the intestinal microbiota.
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2837
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Papillo VA, Vitaglione P, Graziani G, Gokmen V, Fogliano V. Release of antioxidant capacity from five plant foods during a multistep enzymatic digestion protocol. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:4119-4126. [PMID: 24716796 DOI: 10.1021/jf500695a] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This study aimed at elucidating the influence of food matrix on the release of antioxidant activity from five plant foods (apple, spinach, walnut, red bean, and whole wheat). To this purpose a protocol based on sequential enzymatic digestion was adopted. The total antioxidant capacity (TAC) of both solubilized and insoluble materials was measured at each step. Results showed that the overall TAC obtained by enzyme treatments was usually higher than that obtained by chemical extraction-based methods. In apple most of the TAC was released upon water washing and after pepsin treatment, whereas in spinach, beans, and whole wheat the TAC released by treatments with bacterial enzymes was prominent. Walnut had the highest TAC value, which was mainly released after pancreatin treatment. Therefore, the enzyme treatment is fundamental to estimate the overall potential TAC of foods having a high amount of polyphenols bound to dietary fiber or entrapped in the food matrix.
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2838
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Abstract
Bioactive compounds in foods have been gaining interest, and processes to consider them for public health recommendations are being discussed. However, the evidence base is difficult to assemble. It is difficult to demonstrate causality, and there often is not a single compound-single effect relation. Furthermore, health benefits may be due to metabolites produced by the host or gut microbiome rather than the food constituent per se. Properties that can be measured in a food may not translate to in vivo health effects. Compounds that are being pursued may increase gut microbial diversity, improve endothelial function, improve cognitive function, reduce bone loss, and so forth. A new type of bioactive component is emerging from epigenetic modifications by our diet, including microRNA transfer from our diet, which can regulate expression of human genes. Policy processes are needed to establish the level of evidence needed to determine dietary advice and policy recommendations and to set research agendas.
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2839
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Selkrig J, Wong P, Zhang X, Pettersson S. Metabolic tinkering by the gut microbiome: Implications for brain development and function. Gut Microbes 2014; 5:369-80. [PMID: 24685620 PMCID: PMC4153776 DOI: 10.4161/gmic.28681] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Brain development is an energy demanding process that relies heavily upon diet derived nutrients. Gut microbiota enhance the host's ability to extract otherwise inaccessible energy from the diet via fermentation of complex oligosaccharides in the colon. This nutrient yield is estimated to contribute up to 10% of the host's daily caloric requirement in humans and fluctuates in response to environmental variations. Research over the past decade has demonstrated a surprising role for the gut microbiome in normal brain development and function. In this review we postulate that perturbations in the gut microbial-derived nutrient supply, driven by environmental variation, profoundly impacts upon normal brain development and function.
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Affiliation(s)
- Joel Selkrig
- School of Biological Sciences; Nanyang Technological University; Singapore, Singapore,Lee Kong Chain School of Medicine; Nanyang Technological University; Singapore, Singapore
| | - Peiyan Wong
- Program in Neuroscience and Behavioral Disorders; Duke-NUS Graduate Medical School Singapore; Singapore, Singapore,Behavioural Phenotyping Core Facility; Duke-NUS; Duke University Medical Center; Durham, NC USA
| | - Xiaodong Zhang
- Program in Neuroscience and Behavioral Disorders; Duke-NUS Graduate Medical School Singapore; Singapore, Singapore,Department of Physiology; National University of Singapore; Singapore, Singapore,Departments of Psychiatry and Behavioral Sciences; Duke University Medical Center; Durham, NC USA
| | - Sven Pettersson
- Lee Kong Chain School of Medicine; Nanyang Technological University; Singapore, Singapore,Department of Microbiology, Tumor, and Cell Biology (MTC); Karolinska Institute; Stockholm, Sweden,Correspondence to: Sven Pettersson,
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2840
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Wang Y, Kasper LH. The role of microbiome in central nervous system disorders. Brain Behav Immun 2014; 38:1-12. [PMID: 24370461 PMCID: PMC4062078 DOI: 10.1016/j.bbi.2013.12.015] [Citation(s) in RCA: 488] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/19/2013] [Accepted: 12/19/2013] [Indexed: 12/12/2022] Open
Abstract
Mammals live in a co-evolutionary association with the plethora of microorganisms that reside at a variety of tissue microenvironments. The microbiome represents the collective genomes of these co-existing microorganisms, which is shaped by host factors such as genetics and nutrients but in turn is able to influence host biology in health and disease. Niche-specific microbiome, prominently the gut microbiome, has the capacity to effect both local and distal sites within the host. The gut microbiome has played a crucial role in the bidirectional gut-brain axis that integrates the gut and central nervous system (CNS) activities, and thus the concept of microbiome-gut-brain axis is emerging. Studies are revealing how diverse forms of neuro-immune and neuro-psychiatric disorders are correlated with or modulated by variations of microbiome, microbiota-derived products and exogenous antibiotics and probiotics. The microbiome poises the peripheral immune homeostasis and predisposes host susceptibility to CNS autoimmune diseases such as multiple sclerosis. Neural, endocrine and metabolic mechanisms are also critical mediators of the microbiome-CNS signaling, which are more involved in neuro-psychiatric disorders such as autism, depression, anxiety, stress. Research on the role of microbiome in CNS disorders deepens our academic knowledge about host-microbiome commensalism in central regulation and in practicality, holds conceivable promise for developing novel prognostic and therapeutic avenues for CNS disorders.
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Affiliation(s)
- Yan Wang
- Departments of Microbiology/Immunology and Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Lloyd H. Kasper
- Departments of Microbiology/Immunology and Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
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2841
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Abstract
A multitude of metagenomic studies has brought to light an enormous richness of human gut microbiota compositions. In this space of possible configurations, clinical specialists are trying to mine the markers of healthy microbiota via case-control and longitudinal studies. We have discovered potentially beneficial communities while examining the microbial diversity in rural Russians in comparison with the urban dwellers. In this addendum, we further examine the data by elaborating on some of the less common types and suggesting the possible co-metabolism of their drivers. In the light of the first validated clinically effective bacterial transplantation, we discuss the concept of a reference healthy microbiota, outline the problems encountered on the way to its restoration in the developed world, and speculate if rural communities can serve as a source for its prototype.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Correspondence to: Alexander V Tyakht,
| | - Dmitry G Alexeev
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Moscow Institute of Physics and Technology; Dolgoprudny, Russia
| | - Anna S Popenko
- Research Institute of Physico-Chemical Medicine; Moscow, Russia
| | - Elena S Kostryukova
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Kazan' (Volga Region) Federal University; Kazan', Russia
| | - Vadim M Govorun
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Moscow Institute of Physics and Technology; Dolgoprudny, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences; Moscow, Russia
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2842
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Albenberg LG, Wu GD. Diet and the intestinal microbiome: associations, functions, and implications for health and disease. Gastroenterology 2014; 146:1564-72. [PMID: 24503132 PMCID: PMC4216184 DOI: 10.1053/j.gastro.2014.01.058] [Citation(s) in RCA: 403] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/24/2014] [Accepted: 01/31/2014] [Indexed: 12/13/2022]
Abstract
The mutual relationship between the intestinal microbiota and its mammalian host is influenced by diet. Consumption of various nutrients affects the structure of the microbial community and provides substrates for microbial metabolism. The microbiota can produce small molecules that are absorbed by the host and affect many important physiological processes. Age-dependent and societal differences in the intestinal microbiota could result from differences in diet. Examples include differences in the intestinal microbiota of breastfed vs formula-fed infants or differences in microbial richness in people who consume an agrarian plant-based vs a Western diet, which is high in meat and fat. We review how diet affects the structure and metabolome of the human intestinal microbiome and may contribute to health or the pathogenesis of disorders such as coronary vascular disease and inflammatory bowel disease.
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Affiliation(s)
| | - Gary D. Wu
- Corresponding Author: Gary D. Wu, M.D. Division of Gastroenterology Perelman School of Medicine University of Pennsylvania 915 BRB II/III 421 Curie Blvd Philadelphia, PA 19104 Phone: 215-898-0158 Fax: 215-573-2024
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2843
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Nieuwdorp M, Gilijamse PW, Pai N, Kaplan LM. Role of the microbiome in energy regulation and metabolism. Gastroenterology 2014; 146:1525-33. [PMID: 24560870 DOI: 10.1053/j.gastro.2014.02.008] [Citation(s) in RCA: 263] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/25/2014] [Accepted: 02/16/2014] [Indexed: 02/06/2023]
Abstract
Intestinal microbes regulate metabolic function and energy balance; an altered microbial ecology is believed to contribute to the development of several metabolic diseases. Relative species abundance and metabolic characteristics of the intestinal microbiota change substantially in those who are obese or have other metabolic disorders and in response to ingested nutrients or therapeutic agents. The mechanisms through which the intestinal microbiota and its metabolites affect host homeostasis are just beginning to be understood. We review the relationships between the intestinal microbiota and host metabolism, including energy intake, use, and expenditure, in relation to glucose and lipid metabolism. These associations, along with interactions among the intestinal microbiota, mucus layer, bile acids, and mucosal immune responses, reveal potential mechanisms by which the microbiota affect metabolism. We discuss how controlled studies involving direct perturbations of microbial communities in human and animal models are required to identify effective therapeutic targets in the microbiota.
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Affiliation(s)
- Max Nieuwdorp
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Wallenberg Laboratory, Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Göteborg, Göteborg, Sweden.
| | - Pim W Gilijamse
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Endocrinology and Metabolism, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Nikhil Pai
- Department of Pediatric Gastroenterology & Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Obesity, Metabolism and Nutrition Institute and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lee M Kaplan
- Obesity, Metabolism and Nutrition Institute and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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2844
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Hollister EB, Gao C, Versalovic J. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology 2014; 146:1449-58. [PMID: 24486050 PMCID: PMC4181834 DOI: 10.1053/j.gastro.2014.01.052] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/13/2014] [Accepted: 01/24/2014] [Indexed: 12/13/2022]
Abstract
The human gastrointestinal tract contains distinct microbial communities that differ in composition and function based on their location, as well as age, sex, race/ethnicity, and diet of their host. We describe the bacterial taxa present in different locations of the GI tract, and their specific metabolic features. The distinct features of these specific microbial communities might affect human health and disease. Several bacterial taxa and metabolic modules (biochemical functions) have been associated with human health and the absence of disease. Core features of the healthy microbiome might be defined and targeted to prevent disease and optimize human health.
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Affiliation(s)
- Emily B. Hollister
- Department of Pathology & Immunology, Baylor College of Medicine,Department of Pathology, Texas Children’s Hospital
| | - Chunxu Gao
- Department of Pathology & Immunology, Baylor College of Medicine,Department of Molecular Virology & Microbiology, Baylor College of Medicine,Department of Pathology, Texas Children’s Hospital
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas.
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2845
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Goldsmith JR, Sartor B. The role of diet on intestinal microbiota metabolism: downstream impacts on host immune function and health, and therapeutic implications. J Gastroenterol 2014; 49:785-98. [PMID: 24652102 PMCID: PMC4035358 DOI: 10.1007/s00535-014-0953-z] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 03/10/2014] [Indexed: 02/07/2023]
Abstract
Dietary impacts on health may be one of the oldest concepts in medicine; however, only in recent years have technical advances in mass spectroscopy, gnotobiology, and bacterial sequencing enabled our understanding of human physiology to progress to the point where we can begin to understand how individual dietary components can affect specific illnesses. This review explores the current understanding of the complex interplay between dietary factors and the host microbiome, concentrating on the downstream implications on host immune function and the pathogenesis of disease. We discuss the influence of the gut microbiome on body habitus and explore the primary and secondary effects of diet on enteric microbial community structure. We address the impact of consumption of non-digestible polysaccharides (prebiotics and fiber), choline, carnitine, iron, and fats on host health as mediated by the enteric microbiome. Disease processes emphasized include non-alcoholic fatty liver disease/non-alcoholic steatohepatitis, IBD, and cardiovascular disease/atherosclerosis. The concepts presented in this review have important clinical implications, although more work needs to be done to develop fully and validate potential therapeutic approaches. Specific dietary interventions offer exciting potential for nontoxic, physiologic ways to alter enteric microbial structure and metabolism to benefit the natural history of many intestinal and systemic disorders.
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Affiliation(s)
| | - Balfour Sartor
- Departments of Medicine, Microbiology and Immunology University of North Carolina at Chapel Hill
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2846
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Mayer EA, Savidge T, Shulman RJ. Brain-gut microbiome interactions and functional bowel disorders. Gastroenterology 2014; 146:1500-12. [PMID: 24583088 PMCID: PMC4114504 DOI: 10.1053/j.gastro.2014.02.037] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/02/2014] [Accepted: 02/25/2014] [Indexed: 12/02/2022]
Abstract
Alterations in the bidirectional interactions between the intestine and the nervous system have important roles in the pathogenesis of irritable bowel syndrome (IBS). A body of largely preclinical evidence suggests that the gut microbiota can modulate these interactions. A small and poorly defined role for dysbiosis in the development of IBS symptoms has been established through characterization of altered intestinal microbiota in IBS patients and reported improvement of subjective symptoms after its manipulation with prebiotics, probiotics, or antibiotics. It remains to be determined whether IBS symptoms are caused by alterations in brain signaling from the intestine to the microbiota or primary disruption of the microbiota, and whether they are involved in altered interactions between the brain and intestine during development. We review the potential mechanisms involved in the pathogenesis of IBS in different groups of patients. Studies are needed to better characterize alterations to the intestinal microbiome in large cohorts of well-phenotyped patients, and to correlate intestinal metabolites with specific abnormalities in gut-brain interactions.
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Affiliation(s)
- Emeran A Mayer
- Oppenheimer Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California.
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Department of Pathology, Houston, Texas; Texas Children's Hospital, Houston, Texas
| | - Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Children's Nutrition Research Center, Houston, Texas; Texas Children's Hospital, Houston, Texas
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2847
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Marette A, Picard-Deland E. Yogurt consumption and impact on health: focus on children and cardiometabolic risk. Am J Clin Nutr 2014; 99:1243S-7S. [PMID: 24646821 DOI: 10.3945/ajcn.113.073379] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An accumulating body of epidemiologic data, clinical trials, and mechanistic studies suggests that yogurt consumption as part of a healthy diet may be beneficial to cardiometabolic health. This brief review focuses on children and adolescents, introducing new concepts underlying the effect of yogurt consumption on body weight maintenance and the prevention of cardiovascular diseases. Specific properties of yogurt are discussed, which highlight that yogurt is an easy-to-digest, nutrient-dense, and satiating food that contains high-quality protein and specific amino acids. Moreover, the role of yogurt as a modulator of the gut microbiota in infancy is explored. We also propose the idea that the specific matrix of yogurt has bioavailability and metabolic properties that can be exploited to increase the functionality of this dairy product.
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Affiliation(s)
- André Marette
- Department of Medicine, Faculty of Medicine, Cardiology Axis of the Institut Universitaire de Cardiologie et de Pneumologie de Québec (Hôpital Laval), Quebec City, Canada, and The Institute of Nutrition and Functional Foods, Laval University, Quebec City, Canada (AM and EP-D)
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2848
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Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh PJ, Knight R. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology 2014; 146:1470-6. [PMID: 24631493 PMCID: PMC4102302 DOI: 10.1053/j.gastro.2014.03.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent advances that allow us to collect more data on DNA sequences and metabolites have increased our understanding of connections between the intestinal microbiota and metabolites at a whole-systems level. We can also now better study the effects of specific microbes on specific metabolites. Here, we review how the microbiota determines levels of specific metabolites, how the metabolite profile develops in infants, and prospects for assessing a person's physiological state based on their microbes and/or metabolites. Although data acquisition technologies have improved, the computational challenges in integrating data from multiple levels remain formidable; developments in this area will significantly improve our ability to interpret current and future data sets.
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Affiliation(s)
- Luke K. Ursell
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Henry J. Haiser
- Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Will Van Treuren
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Neha Garg
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Lavanya Reddivari
- Department of Plant Science, Pennsylvania State University, University Park, PA
| | - Jairam Vanamala
- Department of Food Science, Pennsylvania State University, University Park, PA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Peter J. Turnbaugh
- Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado; BioFrontiers Institute, University of Colorado at Boulder, Boulder, Colorado; Howard Hughes Medical Institute, Boulder, Colorado.
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2849
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Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 2014; 146:1489-99. [PMID: 24560869 PMCID: PMC4034132 DOI: 10.1053/j.gastro.2014.02.009] [Citation(s) in RCA: 1131] [Impact Index Per Article: 113.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 02/12/2014] [Accepted: 02/17/2014] [Indexed: 12/14/2022]
Abstract
Studies of the roles of microbial communities in the development of inflammatory bowel disease (IBD) have reached an important milestone. A decade of genome-wide association studies and other genetic analyses have linked IBD with loci that implicate an aberrant immune response to the intestinal microbiota. More recently, profiling studies of the intestinal microbiome have associated the pathogenesis of IBD with characteristic shifts in the composition of the intestinal microbiota, reinforcing the view that IBD results from altered interactions between intestinal microbes and the mucosal immune system. Enhanced technologies can increase our understanding of the interactions between the host and its resident microbiota and their respective roles in IBD from both a large-scale pathway view and at the metabolic level. We review important microbiome studies of patients with IBD and describe what we have learned about the mechanisms of intestinal microbiota dysfunction. We describe the recent progress in microbiome research from exploratory 16S-based studies, reporting associations of specific organisms with a disease, to more recent studies that have taken a more nuanced view, addressing the function of the microbiota by metagenomic and metabolomic methods. Finally, we propose study designs and methodologies for future investigations of the microbiome in patients with inflammatory gut and autoimmune diseases in general.
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Affiliation(s)
- Aleksandar D. Kostic
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Ramnik J. Xavier
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts,Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dirk Gevers
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
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2850
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Lactobacillus plantarum IFPL935 impacts colonic metabolism in a simulator of the human gut microbiota during feeding with red wine polyphenols. Appl Microbiol Biotechnol 2014; 98:6805-15. [PMID: 24764016 DOI: 10.1007/s00253-014-5744-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 03/28/2014] [Accepted: 03/30/2014] [Indexed: 01/15/2023]
Abstract
The colonic microbiota plays an important role in the bioavailibility of dietary polyphenols. This work has evaluated the impact on the gut microbiota of long-term feeding with both a red wine polyphenolic extract and the flavan-3-ol metabolizer strain Lactobacillus plantarum IFPL935. The study was conducted in the dynamic Simulator of the Human Intestinal Microbial Ecosystem (SHIME). The feeding of the gut microbiota model with red wine polyphenols caused an initial decrease in the counts of total bacteria in the ascending colon (AC), with Bacteroides, Clostridium coccoides/Eubacterium rectale and Bifidobacterium being the most affected bacterial groups. The bacterial counts recovered to initial numbers faster than the overall microbial fermentation and proteolysis, which seemed to be longer affected by polyphenols. Addition of L. plantarum IFPL935 helped to promptly recover total counts, Lactobacillus and Enterobacteriaceae and led to an increase in lactic acid formation in the AC vessel at the start of the polyphenol treatment as well as butyric acid in the transverse (TC) and descending (DC) vessels after 5 days. Moreover, L. plantarum IFPL935 favoured the conversion in the DC vessel of monomeric flavan-3-ols and their intermediate metabolites into phenylpropionic acids and in particular 3-(3'-hydroxyphenyl)propionic acid. The results open the possibilities of using L. plantarum IFPL935 as a food ingredient for helping individuals showing a low polyphenol-fermenting metabotype to increase their colonic microbial capacities of metabolizing dietary polyphenols.
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