The human gut microbiome: current knowledge, challenges, and future directions.

[1]  W. Moore,et al.  Human fecal flora: the normal flora of 20 Japanese-Hawaiians. , 1974, Applied microbiology.

[2]  D. Savage Microbial ecology of the gastrointestinal tract. , 1977, Annual review of microbiology.

[3]  C. Woese,et al.  Phylogenetic structure of the prokaryotic domain: The primary kingdoms , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[4]  W. Whitman,et al.  Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[5]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

[6]  P. Brigidi,et al.  Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial. , 2000, Gastroenterology.

[7]  H. Harmsen,et al.  Analysis of the Fecal Microflora of Human Subjects Consuming a Probiotic Product Containing Lactobacillus rhamnosusDR20 , 2000, Applied and Environmental Microbiology.

[8]  J. Handelsman,et al.  Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms , 2000, Applied and Environmental Microbiology.

[9]  E. Delong,et al.  Environmental diversity of bacteria and archaea. , 2001, Systematic biology.

[10]  J. Lederberg,et al.  `Ome Sweet `Omics--A Genealogical Treasury of Words , 2001 .

[11]  J. Doré,et al.  Comparative Study of Bacterial Groups within the Human Cecal and Fecal Microbiota , 2001, Applied and Environmental Microbiology.

[12]  Willem M. de Vos,et al.  The Host Genotype Affects the Bacterial Community in the Human Gastrointestinal Tract , 2001 .

[13]  H. Hayashi,et al.  Phylogenetic Analysis of the Human Gut Microbiota Using 16S rDNA Clone Libraries and Strictly Anaerobic Culture‐Based Methods , 2002, Microbiology and immunology.

[14]  Martin J Blaser,et al.  Bacterial biota in the human distal esophagus , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  M. Stolte,et al.  Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine , 2004, Gut.

[16]  J. Handelsman Metagenomics: Application of Genomics to Uncultured Microorganisms , 2004, Microbiology and Molecular Biology Reviews.

[17]  Vincent B. Young,et al.  Antibiotic-Associated Diarrhea Accompanied by Large-Scale Alterations in the Composition of the Fecal Microbiota , 2004, Journal of Clinical Microbiology.

[18]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[19]  Mitsuo Sakamoto,et al.  Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. , 2005, Journal of medical microbiology.

[20]  F. Bäckhed,et al.  Host-Bacterial Mutualism in the Human Intestine , 2005, Science.

[21]  J. Doré,et al.  Biodiversity of the Mucosa‐Associated Microbiota Is Stable Along the Distal Digestive Tract in Healthy Individuals and Patients With Ibd , 2005, Inflammatory bowel diseases.

[22]  Michiel Kleerebezem,et al.  Isolation of DNA from bacterial samples of the human gastrointestinal tract , 2006, Nature Protocols.

[23]  J. Doré,et al.  Differences in Fecal Microbiota in Different European Study Populations in Relation to Age, Gender, and Country: a Cross-Sectional Study , 2006, Applied and Environmental Microbiology.

[24]  F. Shanahan,et al.  Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn's Disease , 2006, Journal of Clinical Microbiology.

[25]  R. Ley,et al.  Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine , 2006, Cell.

[26]  P. Whorwell,et al.  Efficacy of an Encapsulated Probiotic Bifidobacterium infantis 35624 in Women with Irritable Bowel Syndrome , 2006, The American Journal of Gastroenterology.

[27]  V. Mai,et al.  Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition , 2006, Gut.

[28]  A. Nocker,et al.  Genotypic Microbial Community Profiling: A Critical Technical Review , 2007, Microbial Ecology.

[29]  Elisabeth M Bik,et al.  Molecular analysis of the bacterial microbiota in the human stomach. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[30]  J. Jansson,et al.  Long-term ecological impacts of antibiotic administration on the human intestinal microbiota , 2013, The ISME Journal.

[31]  James R. Cole,et al.  The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data , 2006, Nucleic Acids Res..

[32]  Daniel B. DiGiulio,et al.  Development of the Human Infant Intestinal Microbiota , 2007, PLoS biology.

[33]  D. Relman,et al.  An ecological and evolutionary perspective on human–microbe mutualism and disease , 2007, Nature.

[34]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[35]  N. Pace,et al.  Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. , 2008, Cell host & microbe.

[36]  M. Wagner,et al.  Microbial diversity and the genetic nature of microbial species , 2008, Nature Reviews Microbiology.

[37]  Alan W Walker,et al.  The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities. , 2008, Environmental microbiology.

[38]  R. Knight,et al.  Evolution of Mammals and Their Gut Microbes , 2008, Science.

[39]  Les Dethlefsen,et al.  The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing , 2008, PLoS biology.

[40]  P. Moayyedi,et al.  The efficacy of probiotics in the treatment of irritable bowel syndrome: a systematic review , 2008, Gut.

[41]  S. Dublin,et al.  Meta-analysis of probiotics for the treatment of irritable bowel syndrome. , 2008, World journal of gastroenterology.

[42]  Hilary G. Morrison,et al.  Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation , 2009, Infection and Immunity.

[43]  G. Casella,et al.  Influence of Fecal Sample Storage on Bacterial Community Diversity , 2009, The open microbiology journal.

[44]  W. Chey,et al.  The Utility of Probiotics in the Treatment of Irritable Bowel Syndrome: A Systematic Review , 2007, The American Journal of Gastroenterology.

[45]  A. Neish,et al.  REVIEWS IN BASIC AND CLINICAL GASTROENTEROLOGY Microbes in Gastrointestinal Health and Disease , 2009 .

[46]  R. Knight,et al.  Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. , 2009, Genome research.

[47]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[48]  A. Sood,et al.  The probiotic preparation, VSL#3 induces remission in patients with mild-to-moderately active ulcerative colitis. , 2009, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

[49]  Rafael Perera,et al.  A systematic review and meta-analysis: probiotics in the treatment of irritable bowel syndrome , 2009, BMC gastroenterology.

[50]  C. Quince,et al.  Accurate determination of microbial diversity from 454 pyrosequencing data , 2009, Nature Methods.

[51]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.

[52]  Anne Salonen,et al.  Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. , 2010, Microbiology.

[53]  A. Keshavarzian,et al.  Quantitative Assessment of the Human Gut Microbiome Using Multitag Pyrosequencing , 2010, Chemistry & biodiversity.

[54]  Marcus J. Claesson,et al.  Composition, variability, and temporal stability of the intestinal microbiota of the elderly , 2010, Proceedings of the National Academy of Sciences.

[55]  L. T. Angenent,et al.  Succession of microbial consortia in the developing infant gut microbiome , 2010, Proceedings of the National Academy of Sciences.

[56]  John C. Wooley,et al.  Metagenomics: Facts and Artifacts, and Computational Challenges , 2010, Journal of Computer Science and Technology.

[57]  Jean M. Macklaim,et al.  Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products , 2010, PLoS ONE.

[58]  R. Knight,et al.  Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns , 2010, Proceedings of the National Academy of Sciences.

[59]  F. Bushman,et al.  Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags , 2010, BMC Microbiology.

[60]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[61]  B. Haas,et al.  A Catalog of Reference Genomes from the Human Microbiome , 2010, Science.

[62]  D. Relman,et al.  Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation , 2010, Proceedings of the National Academy of Sciences.

[63]  Forest Rohwer,et al.  Viruses in the fecal microbiota of monozygotic twins and their mothers , 2010, Nature.

[64]  Rob Knight,et al.  Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. , 2010, FEMS microbiology letters.

[65]  Akbar K Waljee,et al.  Machine Learning in Medicine: A Primer for Physicians , 2010, The American Journal of Gastroenterology.

[66]  A. Gasbarrini,et al.  Treatment of Relapsing Mild-to-Moderate Ulcerative Colitis With the Probiotic VSL#3 as Adjunctive to a Standard Pharmaceutical Treatment: A Double-Blind, Randomized, Placebo-Controlled Study , 2010, The American Journal of Gastroenterology.

[67]  P. Brigidi,et al.  Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians , 2010, PloS one.

[68]  K. Rioux,et al.  Influences of intestinal bacteria in human inflammatory bowel disease. , 2010, Infectious disease clinics of North America.

[69]  Patrick D. Schloss,et al.  Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis , 2011, Applied and Environmental Microbiology.

[70]  J. Clemente,et al.  Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans , 2011, Science.

[71]  L. Dieleman,et al.  Probiotics in the Treatment of Human Inflammatory Bowel Diseases: Update 2011 , 2011, Journal of clinical gastroenterology.

[72]  R. Hayes,et al.  Oral Microbiome Profiles: 16S rRNA Pyrosequencing and Microarray Assay Comparison , 2011, PloS one.

[73]  R. Knight,et al.  Moving pictures of the human microbiome , 2011, Genome Biology.

[74]  M. Dave,et al.  A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum , 2011, Gut.

[75]  Rafael P. Mellado,et al.  Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows , 2011, BMC Bioinformatics.

[76]  Konstantinos Krampis,et al.  Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community , 2012, BMC Bioinformatics.

[77]  F. Bushman,et al.  Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes , 2011, Science.

[78]  P. Bork,et al.  Enterotypes of the human gut microbiome , 2011, Nature.

[79]  R. Knight,et al.  Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. , 2011, Gastroenterology.

[80]  H. Ochman,et al.  Illumina-based analysis of microbial community diversity , 2011, The ISME Journal.