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Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71

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UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics (2006) 25.13

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PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A (2007) 20.60

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

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02

Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods (2009) 15.25

Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One (2008) 14.63

The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99

Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science (2010) 12.54

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

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol (2007) 11.88

Metagenomic biomarker discovery and explanation. Genome Biol (2011) 11.29

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

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

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

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

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Global patterns in bacterial diversity. Proc Natl Acad Sci U S A (2007) 8.00

A diversity profile of the human skin microbiota. Genome Res (2008) 7.65

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Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol (2006) 6.45

UniFrac: an effective distance metric for microbial community comparison. ISME J (2010) 6.43

Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A (2008) 6.42

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics (2010) 5.70

Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol (2006) 5.69

Defining the core Arabidopsis thaliana root microbiome. Nature (2012) 5.56

PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ (2014) 5.52

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Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28

Global diversity in the human salivary microbiome. Genome Res (2009) 5.16

High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08

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Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97

Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell (2012) 4.86

Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med (2011) 4.78

Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol (2014) 4.74

Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol (2006) 4.74

Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A (2010) 4.56

Differential abundance analysis for microbial marker-gene surveys. Nat Methods (2013) 4.49

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol (2011) 4.45

A primer on metagenomics. PLoS Comput Biol (2010) 4.40

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol (2007) 4.32

Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe (2008) 4.14

Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A (2007) 4.06

Bayesian community-wide culture-independent microbial source tracking. Nat Methods (2011) 3.88

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J (2009) 3.84

Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog (2010) 3.75

16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J (2009) 3.75

Colloquium paper: microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci U S A (2008) 3.71

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut. Microbiome (2013) 3.56

Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol (2009) 3.52

Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A (2010) 3.51

Members of the human gut microbiota involved in recovery from Vibrio cholerae infection. Nature (2014) 3.50

Direct sequencing of the human microbiome readily reveals community differences. Genome Biol (2010) 3.34

FXR is a molecular target for the effects of vertical sleeve gastrectomy. Nature (2014) 3.34

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Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24

Diet-induced extinctions in the gut microbiota compound over generations. Nature (2016) 3.13

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature (2015) 3.06

Longitudinal analysis of microbial interaction between humans and the indoor environment. Science (2014) 3.04

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol (2013) 2.96

Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun (2013) 2.95

Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr (2010) 2.93

Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol (2009) 2.92

Cohabiting family members share microbiota with one another and with their dogs. Elife (2013) 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

Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A (2013) 2.88

Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun (2011) 2.87

Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One (2012) 2.77

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

Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis (2010) 2.62

Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J Exp Med (2012) 2.62

Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One (2010) 2.60

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett (2010) 2.57

Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio (2010) 2.53

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe (2012) 2.48

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proc Natl Acad Sci U S A (2011) 2.47

The gut microbiome modulates colon tumorigenesis. MBio (2013) 2.45

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc Natl Acad Sci U S A (2013) 2.44

Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc Natl Acad Sci U S A (2007) 2.38

Meta-analyses of studies of the human microbiota. Genome Res (2013) 2.35

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol (2010) 2.35

The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A (2008) 2.33

454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J (2011) 2.32

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The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst Appl Microbiol (2002) 3.65

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Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl Environ Microbiol (2003) 3.50

Microbial Diversity in Sediments Collected from the Deepest Cold-Seep Area, the Japan Trench. Mar Biotechnol (NY) (1999) 3.02

A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiol Ecol (2001) 2.85

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Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments. Appl Environ Microbiol (2003) 2.23

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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

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71

UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22

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

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

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

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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

The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99

Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science (2010) 12.54

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

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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

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J (2009) 9.71

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

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

Global patterns in bacterial diversity. Proc Natl Acad Sci U S A (2007) 8.00

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

The impact of the gut microbiota on human health: an integrative view. Cell (2012) 6.01

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41

Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J (2010) 5.37

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28

The long-term stability of the human gut microbiota. Science (2013) 5.15

High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08

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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

Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell (2012) 4.86

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci (2010) 4.70

Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61

Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A (2010) 4.56

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol (2007) 4.32

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

Examining the global distribution of dominant archaeal populations in soil. ISME J (2010) 4.24

The Genomic Standards Consortium. PLoS Biol (2011) 3.99

Bayesian community-wide culture-independent microbial source tracking. Nat Methods (2011) 3.88

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J (2009) 3.84

Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A (2010) 3.51

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Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30

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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience (2012) 3.24

Supervised classification of human microbiota. FEMS Microbiol Rev (2010) 3.23

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J (2011) 3.19

The 'rare biosphere': a reality check. Nat Methods (2009) 3.19

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

Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc Natl Acad Sci U S A (2009) 2.91

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol (2010) 2.86

Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol (2012) 2.70

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics (2011) 2.62

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science (2013) 2.62

The Earth Microbiome project: successes and aspirations. BMC Biol (2014) 2.58

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett (2010) 2.57

EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience (2013) 2.54

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe (2012) 2.48

The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem (2011) 2.42

The Western English Channel contains a persistent microbial seed bank. ISME J (2011) 2.37

Meta-analyses of studies of the human microbiota. Genome Res (2013) 2.35

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol (2010) 2.35

Global patterns in the biogeography of bacterial taxa. Environ Microbiol (2011) 2.34

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Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res (2010) 2.21

The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol (2012) 2.17

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab (2013) 2.17

Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics (2011) 2.15

Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05

Microbial biogeography of public restroom surfaces. PLoS One (2011) 2.04

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

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A (2011) 1.96

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe (2012) 1.93

Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol (2010) 1.89

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief Bioinform (2011) 1.87

Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology (2010) 1.87

Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Microbiol (2012) 1.87

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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