The human microbiome: at the interface of health and disease

Interest in the role of the microbiome in human health has burgeoned over the past decade with the advent of new technologies for interrogating complex microbial communities. The large-scale dynamics of the microbiome can be described by many of the tools and observations used in the study of population ecology. Deciphering the metagenome and its aggregate genetic information can also be used to understand the functional properties of the microbial community. Both the microbiome and metagenome probably have important functions in health and disease; their exploration is a frontier in human genetics.

[1]  T. Dobzhansky.  Further Data on the Variation of the Y Chromosome in Drosophila Pseudoobscura. , 1937, Genetics.

[2]  E. Mayr.  Systematics and the Origin of Species from the Viewpoint of a Zoologist , 1943 .

[3]  C. Nordling.  A New Theory on the Cancer-inducing Mechanism , 1953, British Journal of Cancer.

[4]  Nordling Co.  A New Theory on the Cancer-inducing Mechanism , 1953 .

[5]  A. B. Hill.  The Environment and Disease: Association or Causation? , 1965, Proceedings of the Royal Society of Medicine.

[6]  R. Paine.  Food Web Complexity and Species Diversity , 1966, The American Naturalist.

[7]  W. Hamilton.  The moulding of senescence by natural selection. , 1966, Journal of theoretical biology.

[8]  René Dubos,et al.  THE GASTROINTESTINAL EPITHELIUM AND ITS AUTOCHTHONOUS BACTERIAL FLORA , 1968, The Journal of experimental medicine.

[9]  The relationshp between the host and its intestinal microflora. , 1973, The Proceedings of the Nutrition Society.

[10]  John Maynard Smith.  Models in ecology , 1974 .

[11]  A. Evans.  Causation and Disease: The Henle-Koch Postulates Revisited 1 , 1976, The Yale journal of biology and medicine.

[12]  N. Osborne,et al.  Genital bacteriology: a comparative study of premenopausal women with postmenopausal women. , 1979, American journal of obstetrics and gynecology.

[13]  Antibiotics in feeds. , 1979, Science.

[14]  A M Kligman,et al.  The microbiology of the human axilla and its relationship to axillary odor. , 1981, The Journal of investigative dermatology.

[15]  N. Moran,et al.  A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts , 1993, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[16]  E Hentschel,et al.  Effect of ranitidine and amoxicillin plus metronidazole on the eradication of Helicobacter pylori and the recurrence of duodenal ulcer. , 1993, The New England journal of medicine.

[17]  A. Magurran,et al.  Biological diversity : the coexistence of species on changing landscapes , 1994 .

[18]  D. M. Newbery,et al.  M. A. Huston, Biological Diversity: the coexistence of species on changing landscapes . Cambridge University Press. ISBN 0-521-36930-4 (pbk). 681 + xix. pages. £24.95. , 1995, Journal of Tropical Ecology.

[19]  B. Grant,et al.  CULTURAL INHERITANCE OF SONG AND ITS ROLE IN THE EVOLUTION OF DARWIN'S FINCHES , 1996, Evolution; international journal of organic evolution.

[20]  A. Sonnenberg,et al.  Opposing time trends of peptic ulcer and reflux disease , 1998, Gut.

[21]  P. Kero,et al.  Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. , 1999, Journal of pediatric gastroenterology and nutrition.

[22]  MATERNAL AND PATERNAL EFFECTS ON OFFSPRING PHENOTYPE IN THE DUNG BEETLE ONTHOPHAGUS TAURUS , 2000, Evolution; international journal of organic evolution.

[23]  S. Krisanaprakornkit,et al.  Inducible Expression of Human β-Defensin 2 byFusobacterium nucleatum in Oral Epithelial Cells: Multiple Signaling Pathways and Role of Commensal Bacteria in Innate Immunity and the Epithelial Barrier , 2000, Infection and Immunity.

[24]  Ricard V. Solé,et al.  Complexity and fragility in ecological networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[25]  Mourad Sahbatou,et al.  Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease , 2001, Nature.

[26]  S. Strogatz.  Exploring complex networks , 2001, Nature.

[27]  Judy H. Cho,et al.  [Letters to Nature] , 1975, Nature.

[28]  David Tilman,et al.  Biodiversity as a barrier to ecological invasion , 2002, Nature.

[29]  T. Iannicelli,et al.  Prevalence of Bacterial Vaginosis and Vaginal Flora Changes in Peri- and Postmenopausal Women , 2002, Journal of Clinical Microbiology.

[30]  M. Blaser,et al.  Helicobacter pylori and gastrointestinal tract adenocarcinomas , 2002, Nature Reviews Cancer.

[31]  M. Blaser,et al.  Long-Term Persistence of Resistant Enterococcus Species after Antibiotics To Eradicate Helicobacter pylori , 2003, Annals of Internal Medicine.

[32]  Ting Wang,et al.  The gut microbiota as an environmental factor that regulates fat storage. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Sartorelli,et al.  Linear relationship between Wnt activity levels and apoptosis in colorectal carcinoma cells exposed to butyrate , 2004, International journal of cancer.

[34]  E. Kidd,et al.  The Microflora of the Erupting First Permanent Molar , 2004, Caries Research.

[35]  A. Labigne,et al.  Genetic and Transmission Analysis of Helicobacter pylori Strains within a Family , 2004, Emerging infectious diseases.

[36]  Giovanna Morelli,et al.  Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: lessons from Ladakh. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[37]  K. Van Steen,et al.  Deficient host-bacteria interactions in inflammatory bowel disease? The toll-like receptor (TLR)-4 Asp299gly polymorphism is associated with Crohn’s disease and ulcerative colitis , 2004, Gut.

[38]  N. Moran,et al.  Non-cultivable microorganisms from symbiotic associations of insects and other hosts , 1997, Antonie van Leeuwenhoek.

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

[40]  F. Bäckhed,et al.  Obesity alters gut microbial ecology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[41]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[42]  P. Caufield,et al.  Mode of Delivery and Other Maternal Factors Influence the Acquisition of Streptococcus mutans in Infants , 2005, Journal of dental research.

[43]  J. Slate,et al.  Heterozygote Advantage for Fecundity , 2006, PloS one.

[44]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[45]  C. Manichanh,et al.  Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach , 2005, Gut.

[46]  P. Turnbaugh,et al.  Microbial ecology: Human gut microbes associated with obesity , 2006, Nature.

[47]  Bo Ebenman,et al.  Early onset of secondary extinctions in ecological communities following the loss of top predators. , 2006, Ecology letters.

[48]  K. Madsen,et al.  The role of antibiotic and probiotic therapies in current and future management of inflammatory Bowel disease , 2006, Current gastroenterology reports.

[49]  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.

[50]  Natalia N. Ivanova,et al.  Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite , 2007, Nature.

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

[52]  Amid I. Ismail,et al.  Similarity of Bacterial Populations in Saliva from African-American Mother-Child Dyads , 2007, Journal of Clinical Microbiology.

[53]  Jeffrey I. Gordon,et al.  Mechanisms underlying the resistance to diet-induced obesity in germ-free mice , 2007, Proceedings of the National Academy of Sciences.

[54]  M. Blaser,et al.  The equilibria that allow bacterial persistence in human hosts , 2007, Nature.

[55]  Daniel Falush,et al.  An African origin for the intimate association between humans and Helicobacter pylori , 2007, Nature.

[56]  Yu Chen,et al.  Inverse associations of Helicobacter pylori with asthma and allergy. , 2007, Archives of internal medicine.

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

[58]  Owen L. Petchey,et al.  Trophically Unique Species Are Vulnerable to Cascading Extinction , 2008, The American Naturalist.

[59]  Martin J. Blaser,et al.  Substantial Alterations of the Cutaneous Bacterial Biota in Psoriatic Lesions , 2008, PloS one.

[60]  Anders F. Andersson,et al.  Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing , 2008, PloS one.

[61]  R. Knight,et al.  The influence of sex, handedness, and washing on the diversity of hand surface bacteria , 2008, Proceedings of the National Academy of Sciences.

[62]  Susan M. Huse,et al.  Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing , 2008, PLoS genetics.

[63]  S. Morris,et al.  The Earliest Annelids: Lower Cambrian Polychaetes from the Sirius Passet Lagerstätte, Peary Land, North Greenland , 2008 .

[64]  R. Knight,et al.  Worlds within worlds: evolution of the vertebrate gut microbiota , 2008, Nature Reviews Microbiology.

[65]  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.

[66]  Yu Chen,et al.  Does Helicobacter pylori protect against asthma and allergy? , 2008, Gut.

[67]  J. Gordon,et al.  Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells , 2008, Proceedings of the National Academy of Sciences.

[68]  F. Islami,et al.  Helicobacter pylori and Esophageal Cancer Risk: A Meta-analysis , 2008, Cancer Prevention Research.

[69]  R Balfour Sartor,et al.  Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. , 2008, Cell host & microbe.

[70]  Haifeng Lu,et al.  Symbiotic gut microbes modulate human metabolic phenotypes , 2008, Proceedings of the National Academy of Sciences.

[71]  Yihong Li,et al.  Association of mutans streptococci between caregivers and their children. , 2008, Pediatric dentistry.

[72]  S R Tannenbaum,et al.  Gut microbes define liver cancer risk in mice exposed to chemical and viral transgenic hepatocarcinogens , 2009, Gut.

[73]  A. Keshavarzian,et al.  Intestinal dysbiosis: a possible mechanism of alcohol-induced endotoxemia and alcoholic steatohepatitis in rats. , 2009, Alcoholism, clinical and experimental research.

[74]  W. R. Wikoff,et al.  Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites , 2009, Proceedings of the National Academy of Sciences.

[75]  M. Blaser,et al.  Coadaptation of Helicobacter pylori and humans: ancient history, modern implications. , 2009, The Journal of clinical investigation.

[76]  Patrick J. Lindsey,et al.  Butyrate-Induced Transcriptional Changes in Human Colonic Mucosa , 2009, PloS one.

[77]  Dan R. Littman,et al.  Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria , 2009, Cell.

[78]  Vincent Wai-Sun Wong,et al.  Bacterial Microbiota Profiling in Gastritis without Helicobacter pylori Infection or Non-Steroidal Anti-Inflammatory Drug Use , 2009, PloS one.

[79]  M. Blaser,et al.  What are the consequences of the disappearing human microbiota? , 2009, Nature Reviews Microbiology.

[80]  R. Knight,et al.  Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.

[81]  J. Doré,et al.  The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age , 2009, BMC Microbiology.

[82]  R. Knight,et al.  The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice , 2009, Science Translational Medicine.

[83]  Cynthia L Sears,et al.  A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses , 2009, Nature Medicine.

[84]  J. Ravel,et al.  Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota , 2009, PloS one.

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

[86]  Evan S Snitkin,et al.  Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response , 2010, Proceedings of the National Academy of Sciences.

[87]  E. Quigley,et al.  The role of the gut microbiota in nonalcoholic fatty liver disease , 2010, Nature Reviews Gastroenterology &Hepatology.

[88]  M. Kalliomäki,et al.  The impact of perinatal probiotic intervention on the development of overweight and obesity: follow-up study from birth to 10 years , 2010, International Journal of Obesity.

[89]  Courtney J. Robinson,et al.  Antibiotic administration alters the community structure of the gastrointestinal microbiota , 2010, Gut microbes.

[90]  K. McColl.  Clinical practice. Helicobacter pylori infection. , 2010, The New England journal of medicine.

[91]  P. Gajer,et al.  Vaginal microbiome of reproductive-age women , 2010, Proceedings of the National Academy of Sciences.

[92]  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.

[93]  Min Zhang,et al.  Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors , 2010, Proceedings of the National Academy of Sciences.

[94]  J. Flynn,et al.  Infection with Helicobacter pylori Is Associated with Protection against Tuberculosis , 2010, PloS one.

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

[96]  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.

[97]  S. Mazmanian,et al.  Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota , 2010, Proceedings of the National Academy of Sciences.

[98]  Henrik Svanström,et al.  Antibiotic use and inflammatory bowel diseases in childhood , 2010, Gut.

[99]  S. Fukudo,et al.  Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome , 2009, Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society.

[100]  D. Segal,et al.  Commensal bacteria play a role in mating preference of Drosophila melanogaster , 2010, Proceedings of the National Academy of Sciences.

[101]  Maria Karlsson,et al.  Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. , 2010, Cell host & microbe.

[102]  Rob Knight,et al.  Direct sequencing of the human microbiome readily reveals community differences , 2010, Genome Biology.

[103]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[104]  P. Hugenholtz,et al.  Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities , 2010, PLoS biology.

[105]  Bernard Henrissat,et al.  The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins , 2011, Science Translational Medicine.

[106]  Sharon I. Greenblum,et al.  Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease , 2011, Proceedings of the National Academy of Sciences.

[107]  T. Sørensen,et al.  Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics , 2011, International Journal of Obesity.

[108]  Colin G Fink,et al.  A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of type I cell surface-associated antigens. , 2011, Microbiology.

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

[110]  S. Dusko Ehrlich,et al.  MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract , 2011 .

[111]  Jose U. Scher,et al.  The microbiome and rheumatoid arthritis , 2011, Nature Reviews Rheumatology.

[112]  Baoli Zhu,et al.  Characterization of fecal microbial communities in patients with liver cirrhosis , 2011, Hepatology.

[113]  H. Ashrafian,et al.  Metabolic surgery profoundly influences gut microbial–host metabolic cross-talk , 2011, Gut.

[114]  S. Dowd,et al.  Comparative Analysis of Salivary Bacterial Microbiome Diversity in Edentulous Infants and Their Mothers or Primary Care Givers Using Pyrosequencing , 2011, PloS one.

[115]  M. Lebwohl,et al.  In the clinic. Psoriasis. , 2011, Annals of internal medicine.

[116]  Ateequr Rehman,et al.  Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. , 2011, Gastroenterology.

[117]  Otto X. Cordero,et al.  Ecology drives a global network of gene exchange connecting the human microbiome , 2011, Nature.

[118]  Elizabeth A. Grice,et al.  The skin microbiome , 2020, Nature.

[119]  B. Finlay,et al.  Antibiotic Treatment Alters the Colonic Mucus Layer and Predisposes the Host to Exacerbated Citrobacter rodentium-Induced Colitis , 2011, Infection and Immunity.

[120]  J. Doré,et al.  Highlighting new phylogenetic specificities of Crohn's disease microbiota , 2011, Inflammatory bowel diseases.

[121]  A. Morgun,et al.  Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut , 2011, Nature Medicine.

[122]  Eoin L Brodie,et al.  Structure of the human gastric bacterial community in relation to Helicobacter pylori status , 2011, The ISME Journal.

[123]  E. Pamer,et al.  Role of the commensal microbiota in normal and pathogenic host immune responses. , 2011, Cell host & microbe.

[124]  Karen E. Nelson,et al.  Metagenomics of the human body , 2011 .

[125]  Brian J. Bennett,et al.  Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease , 2011, Nature.

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

[127]  V. Tremaroli,et al.  Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88 , 2011, Gut.

[128]  William A. Walters,et al.  Experimental and analytical tools for studying the human microbiome , 2011, Nature Reviews Genetics.

[129]  Manolito Torralba,et al.  Enteric dysbiosis associated with a mouse model of alcoholic liver disease , 2011, Hepatology.

[130]  M. Blaser,et al.  Antibiotic overuse: Stop the killing of beneficial bacteria , 2011, Nature.

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

[132]  Min Zhang,et al.  Prior Helicobacter pylori infection ameliorates Salmonella typhimurium‐induced colitis: Mucosal crosstalk between stomach and distal intestine , 2011, Inflammatory bowel diseases.

[133]  M. Blaser,et al.  Microbiome and malignancy. , 2011, Cell host & microbe.

[134]  Michael Mitzenmacher,et al.  Detecting Novel Associations in Large Data Sets , 2011, Science.

[135]  Sebastian Reuter,et al.  Helicobacter pylori infection prevents allergic asthma in mouse models through the induction of regulatory T cells. , 2011, The Journal of clinical investigation.

[136]  Susan M. Huse,et al.  Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis , 2011, PloS one.

[137]  L. Meza-Zepeda,et al.  Depletion of Murine Intestinal Microbiota: Effects on Gut Mucosa and Epithelial Gene Expression , 2011, PloS one.

[138]  V. Tybulewicz,et al.  Genomically humanized mice: technologies and promises , 2011, Nature Reviews Genetics.

[139]  B. Birren,et al.  Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. , 2012, Genome research.

[140]  Richard A. Moore,et al.  Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. , 2012, Genome research.