Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications
Tóm tắt
Từ khóa
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
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, 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
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