Published in Science on March 25, 2005
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A (2005) 33.66
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A (2007) 20.60
Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell (2009) 20.29
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol (2008) 16.57
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A (2010) 15.22
Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One (2008) 14.63
Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature (2011) 13.53
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08
Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol (2008) 12.16
Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe (2008) 11.08
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet (2008) 10.72
Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A (2007) 9.71
Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell (2006) 9.64
Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity (2010) 8.90
Inflammatory bowel disease. N Engl J Med (2009) 8.62
Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell (2007) 8.42
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun (2009) 7.48
The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci U S A (2008) 7.43
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature (2012) 6.37
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A (2009) 5.86
Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. Immunity (2008) 5.82
Peripheral education of the immune system by colonic commensal microbiota. Nature (2011) 5.80
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A (2006) 5.19
Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract. Infect Immun (2007) 5.06
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest (2010) 4.95
Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci (2012) 4.95
RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol (2006) 4.93
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One (2009) 4.93
Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol (2006) 4.74
Microbes in gastrointestinal health and disease. Gastroenterology (2008) 4.65
p38 MAPK regulates expression of immune response genes and contributes to longevity in C. elegans. PLoS Genet (2006) 4.47
The core gut microbiome, energy balance and obesity. J Physiol (2009) 4.45
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature (2013) 4.43
Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38
The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc Natl Acad Sci U S A (2010) 4.35
The keystone-pathogen hypothesis. Nat Rev Microbiol (2012) 4.18
Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med (2013) 4.15
Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev (2007) 4.13
Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol (2010) 4.01
Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A (2013) 3.86
Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol (2011) 3.81
Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell (2010) 3.70
A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol (2007) 3.68
Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev (2007) 3.61
The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol (2009) 3.58
Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol (2009) 3.57
Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Microbiol (2008) 3.25
Evidence for a core gut microbiota in the zebrafish. ISME J (2011) 3.22
Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev (2008) 3.12
Metformin retards aging in C. elegans by altering microbial folate and methionine metabolism. Cell (2013) 3.10
Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature (2015) 3.06
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure (2008) 3.02
NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer. J Clin Invest (2013) 2.96
Gut microbiome, obesity, and metabolic dysfunction. J Clin Invest (2011) 2.93
Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J Clin Microbiol (2006) 2.93
The microbiome and cancer. Nat Rev Cancer (2013) 2.86
Intestinal bacteria and the regulation of immune cell homeostasis. Annu Rev Immunol (2010) 2.85
Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun (2012) 2.84
Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep (2012) 2.83
The alpha7 nicotinic acetylcholine receptor as a pharmacological target for inflammation. Br J Pharmacol (2007) 2.82
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res (2012) 2.81
Metagenomic pyrosequencing and microbial identification. Clin Chem (2009) 2.81
Diversity of bifidobacteria within the infant gut microbiota. PLoS One (2012) 2.71
Antigen-independent differentiation and maintenance of effector-like resident memory T cells in tissues. J Immunol (2012) 2.70
Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes (2010) 2.70
Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity (2014) 2.69
Gut commensal bacteria direct a protective immune response against Toxoplasma gondii. Cell Host Microbe (2009) 2.67
Interplay between the TH17 and TReg cell lineages: a (co-)evolutionary perspective. Nat Rev Immunol (2009) 2.65
The gastrointestinal mucus system in health and disease. Nat Rev Gastroenterol Hepatol (2013) 2.65
The gut microbiota modulates host energy and lipid metabolism in mice. J Lipid Res (2009) 2.59
Innate immune mechanisms of colitis and colitis-associated colorectal cancer. Nat Rev Immunol (2010) 2.58
Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A (2008) 2.53
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol (2006) 2.50
Fecal microbiota transplantation and emerging applications. Nat Rev Gastroenterol Hepatol (2011) 2.47
Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis (2009) 2.44
Intestinal crosstalk: a new paradigm for understanding the gut as the "motor" of critical illness. Shock (2007) 2.37
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife (2013) 2.36
Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl Environ Microbiol (2009) 2.34
The human intestinal microbiome: a new frontier of human biology. DNA Res (2009) 2.30
Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol (2008) 2.28
Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection. Infect Immun (2009) 2.26
The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases. Cell Mol Immunol (2011) 2.26
Intestinal mucosal adherence and translocation of commensal bacteria at the early onset of type 2 diabetes: molecular mechanisms and probiotic treatment. EMBO Mol Med (2011) 2.25
The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome (2014) 2.24
Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One (2007) 2.22
The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models. Nat Rev Microbiol (2010) 2.22
Asthma and allergic inflammation. Cell (2010) 2.21
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res (2010) 2.21
The oral microbiota: living with a permanent guest. DNA Cell Biol (2009) 2.19
Bacterial biogeography of the human digestive tract. Sci Rep (2011) 2.18
Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol Syst Biol (2008) 2.17
The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog (2010) 2.17
The effects of circumcision on the penis microbiome. PLoS One (2010) 2.15
Selective antimicrobial action is provided by phenol-soluble modulins derived from Staphylococcus epidermidis, a normal resident of the skin. J Invest Dermatol (2010) 2.13
Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol (2011) 2.11
Tuning microenvironments: induction of regulatory T cells by dendritic cells. Immunity (2008) 2.09
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 44.35
Microbial ecology: human gut microbes associated with obesity. Nature (2006) 36.98
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Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
The human microbiome project. Nature (2007) 28.53
The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A (2004) 26.56
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Evolution of mammals and their gut microbes. Science (2008) 21.40
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell (2006) 18.83
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science (2003) 12.57
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science (2010) 12.54
Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature (2008) 12.45
Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol (2008) 12.16
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe (2008) 11.97
Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature (2012) 10.74
Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci U S A (2002) 9.78
NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell (2011) 9.75
Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A (2007) 9.71
Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell (2006) 9.64
Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A (2010) 9.57
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics (2010) 9.47
Diversity, stability and resilience of the human gut microbiota. Nature (2012) 9.09
Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science (2005) 9.08
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science (2011) 8.88
Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr (2002) 8.31
Human nutrition, the gut microbiome and the immune system. Nature (2011) 7.77
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science (2013) 6.98
Moving pictures of the human microbiome. Genome Biol (2011) 6.72
Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67
Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol (2003) 6.17
Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A (2010) 6.10
Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature (2010) 5.92
Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc Natl Acad Sci U S A (2004) 5.89
Peripheral education of the immune system by colonic commensal microbiota. Nature (2011) 5.80
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
Honor thy symbionts. Proc Natl Acad Sci U S A (2003) 5.72
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe (2008) 5.39
IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe (2007) 5.18
Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A (2004) 5.16
The long-term stability of the human gut microbiota. Science (2013) 5.15
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A (2006) 5.13
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A (2006) 5.04
Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell (2012) 4.86
Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A (2011) 4.85
Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr (2011) 4.60
Homeostasis and inflammation in the intestine. Cell (2010) 4.60
Getting a grip on things: how do communities of bacterial symbionts become established in our intestine? Nat Immunol (2004) 4.58
Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe (2010) 4.54
Immunoproliferative small intestinal disease associated with Campylobacter jejuni. N Engl J Med (2004) 4.47
The core gut microbiome, energy balance and obesity. J Physiol (2009) 4.45
Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Natl Acad Sci U S A (2008) 4.45
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature (2013) 4.43
Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol (2006) 4.27
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med (2011) 4.24
Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe (2008) 4.14
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Division-coupled astrocytic differentiation and age-related depletion of neural stem cells in the adult hippocampus. Cell Stem Cell (2011) 4.08
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem (2009) 4.05
Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol (2011) 3.97
Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell (2010) 3.70
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A (2010) 3.51
Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science (2011) 3.49
Direct sequencing of the human microbiome readily reveals community differences. Genome Biol (2010) 3.34
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc Natl Acad Sci U S A (2006) 3.07
Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host Microbe (2013) 3.05
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure (2008) 3.02
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol (2013) 2.96
Cohabiting family members share microbiota with one another and with their dogs. Elife (2013) 2.92
Manipulation of a nuclear NAD+ salvage pathway delays aging without altering steady-state NAD+ levels. J Biol Chem (2002) 2.91
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc Natl Acad Sci U S A (2009) 2.91
Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A (2013) 2.88
Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A (2007) 2.79
Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut (2011) 2.67
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett (2010) 2.57
Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches. J Biol Chem (2006) 2.49
Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe (2012) 2.48
Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem (2006) 2.43
Dissecting the in vivo metabolic potential of two human gut acetogens. J Biol Chem (2010) 2.42
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol (2013) 2.36
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife (2013) 2.36