Published in Science on May 22, 2008
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell (2009) 20.29
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A (2010) 19.48
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
The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol (2009) 13.87
Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol (2008) 12.16
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A (2010) 11.21
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
Detecting novel associations in large data sets. Science (2011) 10.60
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J (2009) 9.71
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med (2013) 9.44
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18
Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity (2010) 8.90
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science (2011) 8.88
Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature (2009) 8.71
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun (2009) 7.48
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67
UniFrac: an effective distance metric for microbial community comparison. ISME J (2010) 6.43
Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A (2011) 6.16
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
Gut immune maturation depends on colonization with a host-specific microbiota. Cell (2012) 5.91
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe (2008) 5.39
The gut microbiota--masters of host development and physiology. Nat Rev Microbiol (2013) 5.25
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods (2010) 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
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68
Homeostasis and inflammation in the intestine. Cell (2010) 4.60
Multilocus sequence typing of Clostridium difficile. J Clin Microbiol (2009) 4.16
Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med (2013) 4.15
Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol (2009) 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
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem (2009) 4.05
Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A (2009) 4.03
Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol (2010) 4.01
Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol (2011) 3.97
The population genetics of commensal Escherichia coli. Nat Rev Microbiol (2010) 3.78
Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun (2009) 3.36
Direct sequencing of the human microbiome readily reveals community differences. Genome Biol (2010) 3.34
Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc Natl Acad Sci U S A (2010) 3.30
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
Epithelial antimicrobial defence of the skin and intestine. Nat Rev Immunol (2012) 3.21
The 'rare biosphere': a reality check. Nat Methods (2009) 3.19
Stepwise development of MAIT cells in mouse and human. PLoS Biol (2009) 3.18
Illumina-based analysis of microbial community diversity. ISME J (2011) 3.13
NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer. J Clin Invest (2013) 2.96
The gut microbiota regulates bone mass in mice. J Bone Miner Res (2012) 2.92
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc Natl Acad Sci U S A (2009) 2.91
Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS One (2011) 2.84
Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog (2010) 2.79
The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology (2014) 2.73
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
The gut microbiota modulates host energy and lipid metabolism in mice. J Lipid Res (2009) 2.59
Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system. PLoS Genet (2011) 2.55
Microbial degradation of complex carbohydrates in the gut. Gut Microbes (2012) 2.51
From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev (2010) 2.42
Outer membrane vesicles of a human commensal mediate immune regulation and disease protection. Cell Host Microbe (2012) 2.41
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife (2013) 2.36
The human plasma lipidome. N Engl J Med (2011) 2.35
Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One (2012) 2.34
Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection. PLoS Pathog (2012) 2.30
Threatened corals provide underexplored microbial habitats. PLoS One (2010) 2.29
An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet (2010) 2.28
Cospeciation of gut microbiota with hominids. Science (2016) 2.28
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res (2010) 2.21
Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont. J Biol Chem (2009) 2.21
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol (2009) 2.20
The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog (2010) 2.17
Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J Bacteriol (2009) 2.15
Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice. PLoS One (2010) 2.14
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J (2012) 2.13
Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients (2012) 2.10
Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol (2012) 2.08
Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol (2009) 2.07
Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04
Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol (2012) 2.01
Evidence of cellulose metabolism by the giant panda gut microbiome. Proc Natl Acad Sci U S A (2011) 2.00
Lymphotoxin regulates commensal responses to enable diet-induced obesity. Nat Immunol (2012) 1.99
Exploitation of the intestinal microflora by the parasitic nematode Trichuris muris. Science (2010) 1.98
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One (2012) 1.98
Significance of the microbiome in obstructive lung disease. Thorax (2012) 1.97
Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol (2012) 1.94
Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe (2012) 1.93
Establishment of characteristic gut bacteria during development of the honeybee worker. Appl Environ Microbiol (2012) 1.92
Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infect Immun (2009) 1.91
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A (2010) 1.89
Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiol (2011) 1.89
Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol (2012) 1.89
Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One (2013) 1.86
Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei. Appl Environ Microbiol (2009) 1.86
Alteration of the murine gut microbiota during infection with the parasitic helminth Heligmosomoides polygyrus. Inflamm Bowel Dis (2010) 1.85
Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J (2010) 1.85
Genomic insights into the marine sponge microbiome. Nat Rev Microbiol (2012) 1.83
Bacteria from diverse habitats colonize and compete in the mouse gut. Cell (2014) 1.83
Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut (2014) 1.82
Microbes inside--from diversity to function: the case of Akkermansia. ISME J (2012) 1.80
Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing. PLoS One (2010) 1.79
Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A (2013) 1.78
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol (2006) 57.72
UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
Diversity of the human intestinal microbial flora. Science (2005) 49.64
Microbial ecology: human gut microbes associated with obesity. Nature (2006) 36.98
Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A (2005) 33.66
The human microbiome project. Nature (2007) 28.53
UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics (2006) 25.13
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics (2004) 18.87
Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell (2006) 18.83
An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature (2007) 10.92
Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell (2006) 9.64
Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol Immunol (2002) 6.79
Marked decline in atmospheric carbon dioxide concentrations during the Paleogene. Science (2005) 4.37
Symbiosis. Curr Biol (2006) 3.72
Mammalian mitogenomic relationships and the root of the eutherian tree. Proc Natl Acad Sci U S A (2002) 3.38
Factors that alter rumen microbial ecology. Science (2001) 2.87
Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation. Microbiol Immunol (2002) 2.66
Carbon dioxide starvation, the development of C4 ecosystems, and mammalian evolution. Philos Trans R Soc Lond B Biol Sci (1998) 2.66
Climate change as the dominant control on glacial-interglacial variations in C3 and C4 plant abundance. Science (2001) 2.46
Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP. Microbiol Immunol (2003) 2.22
The impact of Quaternary Ice Ages on mammalian evolution. Philos Trans R Soc Lond B Biol Sci (2004) 2.02
Fecal bacterial diversity in a wild gorilla. Appl Environ Microbiol (2006) 1.70
Culture-independent phylogenetic analysis of the faecal flora of the rat. Can J Microbiol (2003) 1.69
Culture-independent analysis of fecal microbiota in cattle. Biosci Biotechnol Biochem (2005) 1.67
Vertebrate ecology and evolution in 'Deep Time'. Trends Ecol Evol (2005) 1.40
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
UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
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
Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A (2005) 33.66
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
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
Host-bacterial mutualism in the human intestine. Science (2005) 26.39
UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics (2006) 25.13
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A (2010) 19.48
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
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J (2012) 16.84
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (2009) 15.93
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45
The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99
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
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
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
Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol (2007) 11.88
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A (2010) 11.21
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature (2012) 10.74
Detecting novel associations in large data sets. Science (2011) 10.60
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
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J (2009) 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
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18
Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res (2007) 9.15
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res (2008) 9.09
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
Global patterns in bacterial diversity. Proc Natl Acad Sci U S A (2007) 8.00
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
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
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
UniFrac: an effective distance metric for microbial community comparison. ISME J (2010) 6.43
The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci (2010) 6.30
Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol (2003) 6.17
The impact of the gut microbiota on human health: an integrative view. Cell (2012) 6.01
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
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