Published in Nat Methods on February 10, 2008
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
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
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
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol (2008) 16.57
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One (2011) 15.19
The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99
Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A (2010) 12.39
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
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
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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
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res (2008) 9.09
Target-enrichment strategies for next-generation sequencing. Nat Methods (2010) 8.78
Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods (2008) 7.50
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One (2013) 7.23
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Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol (2011) 6.03
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
Natural mutagenesis of human genomes by endogenous retrotransposons. Cell (2010) 5.50
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res (2008) 5.00
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
Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol (2014) 4.74
Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A (2010) 4.56
Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe (2010) 4.54
BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J (2010) 4.52
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res (2010) 4.17
Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe (2008) 4.14
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J (2009) 3.84
Statistical design and analysis of RNA sequencing data. Genetics (2010) 3.56
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A (2010) 3.51
FXR is a molecular target for the effects of vertical sleeve gastrectomy. Nature (2014) 3.34
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J (2011) 3.33
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
Illumina-based analysis of microbial community diversity. ISME J (2011) 3.13
DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res (2009) 3.05
Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr (2010) 2.93
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
Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol (2009) 2.91
Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One (2011) 2.81
Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. PLoS One (2012) 2.79
A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol (2010) 2.79
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics (2009) 2.78
Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One (2012) 2.77
Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci U S A (2011) 2.71
Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol (2012) 2.70
Reproducibility and quantitation of amplicon sequencing-based detection. ISME J (2011) 2.64
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics (2011) 2.62
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci U S A (2012) 2.59
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett (2010) 2.57
Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol (2011) 2.52
Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes (2011) 2.46
Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res (2010) 2.46
The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem (2011) 2.42
Architectural design influences the diversity and structure of the built environment microbiome. ISME J (2012) 2.36
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol (2010) 2.35
Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J (2010) 2.33
PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One (2012) 2.31
A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Res (2011) 2.23
Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res (2010) 2.20
Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One (2012) 2.16
The importance of a multifaceted approach to characterizing the microbial flora of chronic wounds. Wound Repair Regen (2011) 2.09
Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS One (2011) 2.09
AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition. Gut (2013) 2.08
Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood (2010) 2.05
Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05
PANGEA: pipeline for analysis of next generation amplicons. ISME J (2010) 2.05
Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics (2010) 2.04
Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04
The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS One (2012) 2.03
Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics (2010) 2.01
Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells. Mol Ther (2009) 1.97
Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infect Immun (2009) 1.91
Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour (2009) 1.88
Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol Motil (2012) 1.87
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
Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One (2008) 1.86
Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J (2010) 1.85
Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis. J Clin Microbiol (2010) 1.82
Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut (2014) 1.82
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2011) 1.81
Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments. ISME J (2010) 1.79
Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS One (2012) 1.79
Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res (2013) 1.78
Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol (2010) 1.77
Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants. PLoS One (2012) 1.74
Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model. ISME J (2009) 1.74
Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances. PLoS One (2011) 1.74
Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity (Silver Spring) (2011) 1.73
Influence of fecal sample storage on bacterial community diversity. Open Microbiol J (2009) 1.68
Spatial organization of intestinal microbiota in the mouse ascending colon. ISME J (2010) 1.66
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinformatics (2011) 1.62
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UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
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UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics (2006) 25.13
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res (2006) 23.67
Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol (2007) 23.64
Microbial population structures in the deep marine biosphere. Science (2007) 14.61
Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J (2007) 13.95
Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol (1998) 10.17
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17
Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics (2006) 6.99
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res (2007) 6.89
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
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
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
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
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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
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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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Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev (2008) 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
Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol (2006) 4.74
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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
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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
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Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A (2010) 3.51
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Direct sequencing of the human microbiome readily reveals community differences. Genome Biol (2010) 3.34
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
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Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J (2011) 3.19
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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
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Global patterns in the biogeography of bacterial taxa. Environ Microbiol (2011) 2.34
The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A (2008) 2.33
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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
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol (2008) 2.12
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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