Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

Cell Host & Microbe - Tập 12 Số 5 - Trang 611-622 - 2012
Fredrik Bäckhed1, Claire M. Fraser2, Yehuda Ringel3, Mary Ellen Sanders4, R. Balfour Sartor5, Philip M. Sherman6, James Versalovic7, Vincent B. Young8, B. Brett Finlay9
1The Wallenberg Laboratory, University of Gothenburg, Sahlgrenska University Hospital, Göteborg, Sweden 41345.
2Institute for Genome Sciences at the University of Maryland School of Medicine, Baltimore, MD 21201, USA
3Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
4Dairy & Food Culture Technologies, Centennial, CO 80122, USA
5Division of Gastroenterology and Hepatology, Microbiology, and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
6Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, University of Toronto, Toronto, Canada M5G 1X8
7Departments of Pathology and Immunology, Pediatrics, and Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
8Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
9Michael Smith Laboratories, Departments of Biochemistry and Molecular Biology, and Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z4

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Tài liệu tham khảo

Andrews, 1992, Chronic constipation reversed by restoration of bowel flora. A case and a hypothesis, Eur. J. Gastroenterol. Hepatol., 4, 245

Arumugam, 2011, Enterotypes of the human gut microbiome, Nature, 473, 174, 10.1038/nature09944

Bäckhed, 2005, Host-bacterial mutualism in the human intestine, Science, 307, 1915, 10.1126/science.1104816

Benson, 2010, Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors, Proc. Natl. Acad. Sci. USA, 107, 18933, 10.1073/pnas.1007028107

Biagi, 2010, Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians, PLoS ONE, 5, e10667, 10.1371/journal.pone.0010667

Bircher, 2005, Towards a dynamic definition of health and disease, Med. Health Care Philos., 8, 335, 10.1007/s11019-005-0538-y

Blaser, 2009, What are the consequences of the disappearing human microbiota?, Nat. Rev. Microbiol., 7, 887, 10.1038/nrmicro2245

Borody, 2003, Treatment of ulcerative colitis using fecal bacteriotherapy, J. Clin. Gastroenterol., 37, 42, 10.1097/00004836-200307000-00012

Brownawell, 2012, Prebiotics and the health benefits of fiber: current regulatory status, future research, and goals, J. Nutr., 142, 962, 10.3945/jn.112.158147

Cani, 2008, Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice, Diabetes, 57, 1470, 10.2337/db07-1403

Carroll, 2011, Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome, Am. J. Physiol. Gastrointest. Liver Physiol., 301, G799, 10.1152/ajpgi.00154.2011

Carroll, 2012, Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome, Neurogastroenterol. Motil., 24, 521, 10.1111/j.1365-2982.2012.01891.x

Chang, 2008, Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea, J. Infect. Dis., 197, 435, 10.1086/525047

Costello, 2009, Bacterial community variation in human body habitats across space and time, Science, 326, 1694, 10.1126/science.1177486

De Filippo, 2010, Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc. Natl. Acad. Sci. USA, 107, 14691, 10.1073/pnas.1005963107

Dethlefsen, 2011, Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation, Proc. Natl. Acad. Sci. USA, 108, 4554, 10.1073/pnas.1000087107

Dominguez-Bello, 2010, Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns, Proc. Natl. Acad. Sci. USA, 107, 11971, 10.1073/pnas.1002601107

Eiseman, 1958, Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis, Surgery, 44, 854

Ferreira, 2011, The intestinal microbiota plays a role in Salmonella-induced colitis independent of pathogen colonization, PLoS ONE, 6, e20338, 10.1371/journal.pone.0020338

Frank, 2010, The human nasal microbiota and Staphylococcus aureus carriage, PLoS ONE, 5, e10598, 10.1371/journal.pone.0010598

Franks, 1998, Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes, Appl. Environ. Microbiol., 64, 3336, 10.1128/AEM.64.9.3336-3345.1998

Garcia-Mazcorro, 2011, Effect of a multi-species synbiotic formulation on fecal bacterial microbiota of healthy cats and dogs as evaluated by pyrosequencing, FEMS Microbiol. Ecol., 78, 542, 10.1111/j.1574-6941.2011.01185.x

Gibson, 2010, Vol. 7

Gibson, 2004, Dietary modulation of the human colonic microbiota: updating the concept of prebiotics, Nutr. Res. Rev., 17, 259, 10.1079/NRR200479

Giongo, 2011, Toward defining the autoimmune microbiome for type 1 diabetes, ISME J., 5, 82, 10.1038/ismej.2010.92

Gough, 2011, Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection, Clin. Infect. Dis., 53, 994, 10.1093/cid/cir632

Grice, 2009, Topographical and temporal diversity of the human skin microbiome, Science, 324, 1190, 10.1126/science.1171700

Guarner, 2008

Hartman, 2009, Human gut microbiome adopts an alternative state following small bowel transplantation, Proc. Natl. Acad. Sci. USA, 106, 17187, 10.1073/pnas.0904847106

Hildebrandt, 2009, High-fat diet determines the composition of the murine gut microbiome independently of obesity, Gastroenterology, 137, 10.1053/j.gastro.2009.08.042

Holling, 1973, Resilience and stability of ecological systems, Annu. Rev. Ecol. Syst., 4, 1, 10.1146/annurev.es.04.110173.000245

Honda, 2012, The microbiome in infectious disease and inflammation, Annu. Rev. Immunol., 30, 759, 10.1146/annurev-immunol-020711-074937

2012, A framework for human microbiome research, Nature, 486, 215, 10.1038/nature11209

2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234

Hviid, 2011, Antibiotic use and inflammatory bowel diseases in childhood, Gut, 60, 49, 10.1136/gut.2010.219683

Jalanka-Tuovinen, 2011, Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms, PLoS ONE, 6, e23035, 10.1371/journal.pone.0023035

Jernberg, 2007, Long-term ecological impacts of antibiotic administration on the human intestinal microbiota, ISME J., 1, 56, 10.1038/ismej.2007.3

Karami, 2007, Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics, J. Antimicrob. Chemother., 60, 1142, 10.1093/jac/dkm327

Khan, 2011, Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis, Am. J. Gastroenterol., 106, 661, 10.1038/ajg.2011.72

Khoruts, 2010, Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea, J. Clin. Gastroenterol., 44, 354, 10.1097/MCG.0b013e3181c87e02

Konturek, 2011, Stress and the gut: pathophysiology, clinical consequences, diagnostic approach and treatment options, J. Physiol. Pharmacol., 62, 591

Kovacs, 2011, Genotype is a stronger determinant than sex of the mouse gut microbiota, Microb. Ecol., 61, 423, 10.1007/s00248-010-9787-2

Kuczynski, 2012, Experimental and analytical tools for studying the human microbiome, Nat. Rev. Genet., 13, 47, 10.1038/nrg3129

Ley, 2005, Obesity alters gut microbial ecology, Proc. Natl. Acad. Sci. USA, 102, 11070, 10.1073/pnas.0504978102

Li, 2012, Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition, PLoS ONE, 7, e26284, 10.1371/journal.pone.0026284

Lupp, 2007, Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae, Cell Host Microbe, 2, 119, 10.1016/j.chom.2007.06.010

Mai, 2011, Fecal microbiota in premature infants prior to necrotizing enterocolitis, PLoS ONE, 6, e20647, 10.1371/journal.pone.0020647

Manichanh, 2006, Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach, Gut, 55, 205, 10.1136/gut.2005.073817

McNulty, 2011, The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins, Sci. Transl. Med., 3, 106ra106, 10.1126/scitranslmed.3002701

Morowitz, 2011, Strain-resolved community genomic analysis of gut microbial colonization in a premature infant, Proc. Natl. Acad. Sci. USA, 108, 1128, 10.1073/pnas.1010992108

Nicholson, 2012, Host-gut microbiota metabolic interactions, Science, 336, 1262, 10.1126/science.1223813

O’Toole, 2008, Probiotic bacteria influence the composition and function of the intestinal microbiota, Interdiscip. Perspect. Infect. Dis., 2008, 175285

Palmer, 2007, Development of the human infant intestinal microbiota, PLoS Biol., 5, e177, 10.1371/journal.pbio.0050177

Pimentel, 2011, Rifaximin therapy for patients with irritable bowel syndrome without constipation, N. Engl. J. Med., 364, 22, 10.1056/NEJMoa1004409

Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821

Rajilić-Stojanović, 2011, Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome, Gastroenterology, 141, 1792, 10.1053/j.gastro.2011.07.043

Rauch, 2012, The potential for probiotic manipulation of the gastrointestinal microbiome, Curr. Opin. Biotechnol., 23, 192, 10.1016/j.copbio.2011.11.004

Reeves, 2011, The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection, Gut Microbes, 2, 145, 10.4161/gmic.2.3.16333

Ringel, 2009, Alterations in the intestinal microbiota and functional bowel symptoms, Gastrointest. Endosc. Clin. N. Am., 19, 141, 10.1016/j.giec.2008.12.004

Ringel, 2012, Probiotics and Gastrointestinal Disorders, Am. J. Gastroenterol., 34, 10.1038/ajgsup.2012.7

Sartor, 2010, Genetics and environmental interactions shape the intestinal microbiome to promote inflammatory bowel disease versus mucosal homeostasis, Gastroenterology, 139, 1816, 10.1053/j.gastro.2010.10.036

Sartor, 2008, Microbial influences in inflammatory bowel diseases, Gastroenterology, 134, 577, 10.1053/j.gastro.2007.11.059

Saulnier, 2011, Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome, Gastroenterology, 141, 1782, 10.1053/j.gastro.2011.06.072

Segata, 2011, Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies, PLoS ONE, 6, e24704, 10.1371/journal.pone.0024704

Sekirov, 2010, Gut microbiota in health and disease, Physiol. Rev., 90, 859, 10.1152/physrev.00045.2009

Sepehri, 2007, Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease, Inflamm. Bowel Dis., 13, 675, 10.1002/ibd.20101

Siegmund, 2009, Targeted therapies in inflammatory bowel disease, Dig. Dis., 27, 465, 10.1159/000233284

Sokol, 2008, Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients, Proc. Natl. Acad. Sci. USA, 105, 16731, 10.1073/pnas.0804812105

Sommer, 2009, Functional characterization of the antibiotic resistance reservoir in the human microflora, Science, 325, 1128, 10.1126/science.1176950

Sonnenburg, 2010, Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations, Cell, 141, 1241, 10.1016/j.cell.2010.05.005

Spor, 2011, Unravelling the effects of the environment and host genotype on the gut microbiome, Nat. Rev. Microbiol., 9, 279, 10.1038/nrmicro2540

Tiihonen, 2010, Human intestinal microbiota and healthy ageing, Ageing Res. Rev., 9, 107, 10.1016/j.arr.2009.10.004

Turnbaugh, 2008, Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome, Cell Host Microbe, 3, 213, 10.1016/j.chom.2008.02.015

Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540

Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414

Virgin, 2011, Metagenomics and personalized medicine, Cell, 147, 44, 10.1016/j.cell.2011.09.009

Walker, 2011, Dominant and diet-responsive groups of bacteria within the human colonic microbiota, ISME J., 5, 220, 10.1038/ismej.2010.118

Wallace, 2010, Alleviating cancer drug toxicity by inhibiting a bacterial enzyme, Science, 330, 831, 10.1126/science.1191175

Willing, 2011, Shifting the balance: antibiotic effects on host-microbiota mutualism, Nat. Rev. Microbiol., 9, 233, 10.1038/nrmicro2536

Willing, 2011, Altering host resistance to infections through microbial transplantation, PLoS ONE, 6, e26988, 10.1371/journal.pone.0026988

Wlodarska, 2011, Antibiotic treatment alters the colonic mucus layer and predisposes the host to exacerbated Citrobacter rodentium-induced colitis, Infect. Immun., 79, 1536, 10.1128/IAI.01104-10

Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science, 334, 105, 10.1126/science.1208344

Yap, 2008, Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse, J. Proteome Res., 7, 3718, 10.1021/pr700864x

Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature, 486, 222, 10.1038/nature11053

Young, 2011, Studying the enteric microbiome in inflammatory bowel diseases: getting through the growing pains and moving forward, Front Microbiol., 2, 144, 10.3389/fmicb.2011.00144

Zoetendal, 1998, Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria, Appl. Environ. Microbiol., 64, 3854, 10.1128/AEM.64.10.3854-3859.1998

Zupancic, 2012, Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome, PLoS ONE, 7, e43052, 10.1371/journal.pone.0043052