Published in Proc Natl Acad Sci U S A on April 02, 2010
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
Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45
Diet rapidly and reproducibly alters the human gut microbiome. Nature (2013) 11.04
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18
Genetics and pathogenesis of inflammatory bowel disease. Nature (2011) 7.79
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
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41
The long-term stability of the human gut microbiota. Science (2013) 5.15
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97
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
How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol (2012) 3.65
Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One (2012) 3.49
Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science (2011) 3.49
Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell (2013) 3.26
Evidence for a core gut microbiota in the zebrafish. ISME J (2011) 3.22
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol (2012) 3.02
Trimethylamine-N-oxide, a metabolite associated with atherosclerosis, exhibits complex genetic and dietary regulation. Cell Metab (2013) 3.01
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci U S A (2010) 2.82
The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect Dis (2013) 2.54
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol (2011) 2.33
Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One (2012) 2.16
Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One (2011) 2.14
Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A (2014) 2.11
Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut (2012) 2.10
Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Res (2012) 2.10
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A (2010) 2.09
Complex carbohydrate utilization by the healthy human microbiome. PLoS One (2012) 2.01
Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol (2012) 1.89
Computational meta'omics for microbial community studies. Mol Syst Biol (2013) 1.84
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J (2012) 1.81
Do interactions between gut ecology and environmental chemicals contribute to obesity and diabetes? Environ Health Perspect (2011) 1.80
Microbes inside--from diversity to function: the case of Akkermansia. ISME J (2012) 1.80
Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis (2012) 1.73
Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci Transl Med (2012) 1.71
Microbiota, disease, and back to health: a metastable journey. Sci Transl Med (2012) 1.70
Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol (2012) 1.69
Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. ISME J (2012) 1.67
Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res (2010) 1.64
Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PLoS One (2011) 1.61
Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME J (2010) 1.60
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therap Adv Gastroenterol (2013) 1.56
The function of our microbiota: who is out there and what do they do? Front Cell Infect Microbiol (2012) 1.54
Our unindicted coconspirators: human metabolism from a microbial perspective. Cell Metab (2010) 1.52
Intestinal microbial diversity during early-life colonization shapes long-term IgE levels. Cell Host Microbe (2013) 1.51
Carbohydrate metabolism in Bifidobacteria. Genes Nutr (2011) 1.50
Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities. PLoS One (2010) 1.49
Gut resistome development in healthy twin pairs in the first year of life. Microbiome (2015) 1.48
Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences. Eur J Clin Invest (2012) 1.43
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS One (2011) 1.39
Impact of the gut microbiota on the development of obesity and type 2 diabetes mellitus. Front Microbiol (2014) 1.35
Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine. PLoS One (2013) 1.34
Sulfatases and a radical S-adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont, Bacteroides thetaiotaomicron. J Biol Chem (2011) 1.34
The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis (2015) 1.33
Oral and airway microbiota in HIV-infected pneumonia patients. J Clin Microbiol (2012) 1.30
Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One (2012) 1.28
Gut microbial gene expression in mother-fed and formula-fed piglets. PLoS One (2010) 1.27
The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One (2012) 1.27
Distribution-based clustering: using ecology to refine the operational taxonomic unit. Appl Environ Microbiol (2013) 1.25
The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? Am J Physiol Gastrointest Liver Physiol (2011) 1.22
Directed culturing of microorganisms using metatranscriptomics. MBio (2011) 1.21
Dietary effects on human gut microbiome diversity. Br J Nutr (2014) 1.21
The mind-body-microbial continuum. Dialogues Clin Neurosci (2011) 1.20
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J (2014) 1.19
Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach. ISME J (2010) 1.19
Sewage reflects the distribution of human faecal Lachnospiraceae. Environ Microbiol (2013) 1.17
Denoising PCR-amplified metagenome data. BMC Bioinformatics (2012) 1.16
The role of mucosal immunity and host genetics in defining intestinal commensal bacteria. Curr Opin Gastroenterol (2010) 1.15
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics (2013) 1.15
Next generation sequencing reveals the hidden diversity of zooplankton assemblages. PLoS One (2013) 1.13
Functional assignment of metagenomic data: challenges and applications. Brief Bioinform (2012) 1.13
A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface. PLoS One (2011) 1.12
Comparison of metagenomic samples using sequence signatures. BMC Genomics (2012) 1.10
Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota. ISME J (2013) 1.10
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. PLoS One (2013) 1.09
Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PLoS One (2013) 1.09
Accurate multiplexing and filtering for high-throughput amplicon-sequencing. Nucleic Acids Res (2015) 1.09
Anaerobic respiration of Escherichia coli in the mouse intestine. Infect Immun (2011) 1.07
The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing. Int J Legal Med (2013) 1.07
The gut microbiome and the brain. J Med Food (2014) 1.06
Inflammation and colorectal cancer, when microbiota-host mutualism breaks. World J Gastroenterol (2014) 1.06
Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 1.03
Engineering ecosystems and synthetic ecologies. Mol Biosyst (2012) 1.02
Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol (2014) 1.01
Pyrosequencing as a tool for better understanding of human microbiomes. J Oral Microbiol (2012) 1.01
Emerging roles of the microbiome in cancer. Carcinogenesis (2013) 1.00
The role of microbial amino acid metabolism in host metabolism. Nutrients (2015) 0.99
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One (2012) 0.99
Improved inference of taxonomic richness from environmental DNA. PLoS One (2013) 0.99
The human gut mobile metagenome: a metazoan perspective. Gut Microbes (2011) 0.99
Bacterial community diversity and variation in spray water sources and the tomato fruit surface. BMC Microbiol (2011) 0.99
ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLoS One (2013) 0.99
Food and the gut microbiota in inflammatory bowel diseases: a critical connection. Curr Opin Gastroenterol (2012) 0.98
Bioinformatics for the Human Microbiome Project. PLoS Comput Biol (2012) 0.97
The altered gut microbiome and necrotizing enterocolitis. Clin Perinatol (2013) 0.97
Discovering new indicators of fecal pollution. Trends Microbiol (2014) 0.96
Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing. PLoS One (2014) 0.96
Maternal influences on fetal microbial colonization and immune development. Pediatr Res (2014) 0.96
Optimizing the analysis of human intestinal microbiota with phylogenetic microarray. FEMS Microbiol Ecol (2010) 0.96
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
Diversity of the human intestinal microbial flora. Science (2005) 49.64
SSAHA: a fast search method for large DNA databases. Genome Res (2001) 48.64
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res (2008) 27.83
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
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
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol (2009) 14.17
Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93
Systematic artifacts in metagenomes from complex microbial communities. ISME J (2009) 8.18
Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A (2008) 6.50
Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol (2008) 6.33
Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. Biotechniques (2009) 4.90
From cellulosomes to cellulosomics. Chem Rec (2008) 2.78
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
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
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
The human microbiome project. Nature (2007) 28.53
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res (2008) 27.83
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
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
GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 18.88
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
Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science (2009) 16.35
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
Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A (2002) 13.58
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
A metagenomic survey of microbes in honey bee colony collapse disorder. Science (2007) 11.72
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
The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res (2013) 10.24
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
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
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
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods (2007) 7.73
A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med (2008) 7.73
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science (2013) 6.98
Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med (2006) 6.96
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