Enterotypes of the human gut microbiome.

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

A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68

Diet rapidly and reproducibly alters the human gut microbiome. Nature (2013) 11.04

SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15

Diversity, stability and resilience of the human gut microbiota. Nature (2012) 9.09

Functional interactions between the gut microbiota and host metabolism. Nature (2012) 7.91

The human microbiome: at the interface of health and disease. Nat Rev Genet (2012) 7.54

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One (2013) 7.23

Gut microbiota composition correlates with diet and health in the elderly. Nature (2012) 6.94

Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93

Inflammasomes in health and disease. Nature (2012) 6.75

Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27

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

Gut immune maturation depends on colonization with a host-specific microbiota. Cell (2012) 5.91

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol (2012) 5.66

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

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife (2013) 5.49

Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol (2012) 5.35

Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science (2012) 5.34

Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity (2012) 5.26

Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci (2012) 4.95

The application of ecological theory toward an understanding of the human microbiome. Science (2012) 4.69

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68

Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42

Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38

A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One (2012) 4.35

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

The keystone-pathogen hypothesis. Nat Rev Microbiol (2012) 4.18

The gut microbiota in IBD. Nat Rev Gastroenterol Hepatol (2012) 3.88

The microbiome in infectious disease and inflammation. Annu Rev Immunol (2012) 3.76

How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol (2012) 3.65

Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol (2012) 3.64

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

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

Microbial interactions: from networks to models. Nat Rev Microbiol (2012) 3.28

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science (2015) 3.12

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut (2015) 2.99

NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer. J Clin Invest (2013) 2.96

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

Salivary microbiota reflects changes in gut microbiota in cirrhosis with hepatic encephalopathy. Hepatology (2015) 2.91

Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun (2012) 2.84

Individualized medicine from prewomb to tomb. Cell (2014) 2.76

Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A (2014) 2.65

Intestinal microbiota in functional bowel disorders: a Rome foundation report. Gut (2012) 2.60

The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol (2012) 2.60

A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects. Nat Rev Microbiol (2012) 2.56

Microbial degradation of complex carbohydrates in the gut. Gut Microbes (2012) 2.51

Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51

Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol (2013) 2.46

Role of the commensal microbiota in normal and pathogenic host immune responses. Cell Host Microbe (2011) 2.46

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun (2014) 2.39

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol (2013) 2.36

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

Novel bacterial taxa in the human microbiome. PLoS One (2012) 2.35

Gut dysbiosis promotes M2 macrophage polarization and allergic airway inflammation via fungi-induced PGE₂. Cell Host Microbe (2014) 2.34

The role of diet on intestinal microbiota metabolism: downstream impacts on host immune function and health, and therapeutic implications. J Gastroenterol (2014) 2.32

Dynamics and associations of microbial community types across the human body. Nature (2014) 2.32

Biogeography and individuality shape function in the human skin metagenome. Nature (2014) 2.27

Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol (2015) 2.26

Bambus 2: scaffolding metagenomes. Bioinformatics (2011) 2.24

Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One (2013) 2.24

Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics (2012) 2.19

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

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol (2013) 2.16

Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One (2012) 2.16

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

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa. Nat Rev Microbiol (2011) 2.15

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J (2012) 2.13

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol (2011) 2.11

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

Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation. Proc Natl Acad Sci U S A (2013) 2.10

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

Eating for two: how metabolism establishes interspecies interactions in the gut. Cell Host Microbe (2011) 2.06

Microbes, microbiota, and colon cancer. Cell Host Microbe (2014) 2.06

Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood (2014) 2.04

Composition and similarity of bovine rumen microbiota across individual animals. PLoS One (2012) 2.02

Complex carbohydrate utilization by the healthy human microbiome. PLoS One (2012) 2.01

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nat Biotechnol (2015) 2.01

Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? Brief Bioinform (2012) 2.00

Genomic approaches to studying the human microbiota. Nature (2012) 2.00

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol (2013) 1.97

Country-specific antibiotic use practices impact the human gut resistome. Genome Res (2013) 1.94

Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol (2012) 1.94

The microbiome and rheumatoid arthritis. Nat Rev Rheumatol (2011) 1.91

The intestinal microbiome in early life: health and disease. Front Immunol (2014) 1.90

Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol (2012) 1.89

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun (2014) 1.88

The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol (2013) 1.87

Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. Am J Clin Nutr (2013) 1.87

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

Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One (2013) 1.86

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut (2013) 1.83

New insights in gut microbiota establishment in healthy breast fed neonates. PLoS One (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

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

A core gut microbiome in obese and lean twins. Nature (2008) 52.30

Diversity of the human intestinal microbial flora. Science (2005) 49.64

An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 44.35

A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63

Microbial ecology: human gut microbes associated with obesity. Nature (2006) 36.98

Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76

Bacterial community variation in human body habitats across space and time. Science (2009) 24.84

STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62

Development of the human infant intestinal microbiota. PLoS Biol (2007) 18.91

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol (2008) 16.57

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08

A catalog of reference genomes from the human microbiome. Science (2010) 8.10

Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol Immunol (2002) 6.79

Microbiota and SCFA in lean and overweight healthy subjects. Obesity (Silver Spring) (2009) 6.12

Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol (1997) 6.04

Towards the human intestinal microbiota phylogenetic core. Environ Microbiol (2009) 5.72

Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut (2003) 5.19

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res (2009) 4.55

Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol (2000) 4.49

High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut (2008) 4.10

Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol (2004) 4.05

Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem (2009) 4.05

Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol (2008) 3.95

Prediction of effective genome size in metagenomic samples. Genome Biol (2007) 3.73

Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods (2010) 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

SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics (2010) 3.48

Colonic microbiota signatures across five northern European countries. Appl Environ Microbiol (2005) 2.98

Intestinal bacteria and ageing. J Appl Microbiol (2007) 2.91

Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A (2009) 2.89

Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol (2004) 2.61

Bacterial adhesion: genetics, biogenesis, and role in pathogenesis of fimbrial adhesins of Escherichia coli. Rev Infect Dis (1991) 2.54

Alternative pathways for hydrogen disposal during fermentation in the human colon. Gut (1990) 2.13

The alternative sigma factor sigma(E) plays an important role in intestinal survival and virulence in Vibrio cholerae. Infect Immun (2002) 2.04

Prevotella enzymes involved in mucin oligosaccharide degradation and evidence for a small operon of genes expressed during growth on mucin. FEMS Microbiol Lett (2000) 1.85

Say hello to our little friends. Nat Rev Microbiol (2007) 1.56

Mucosal immunosenescence: new developments and vaccines to control infectious diseases. Trends Immunol (2009) 1.49

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

A method and server for predicting damaging missense mutations. Nat Methods (2010) 78.53

SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13

Differential expression analysis for sequence count data. Genome Biol (2010) 64.56

Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45

Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40

The diploid genome sequence of an Asian individual. Nature (2008) 46.29

De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91

Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19

A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78

SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet (2008) 35.06

SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90

The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48

Comparative metagenomics of microbial communities. Science (2005) 25.88

InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07

Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res (2002) 25.06

The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet (2010) 23.08

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89

Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77

Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med (2013) 20.65

STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62

Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

Multifactorial intervention and cardiovascular disease in patients with type 2 diabetes. N Engl J Med (2003) 20.06

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97

Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50

SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73

Effect of a multifactorial intervention on mortality in type 2 diabetes. N Engl J Med (2008) 18.27

STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet (2010) 17.89

InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53

SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08

SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96

The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (2006) 14.96

Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A (2008) 14.18

InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45

Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34

A variant in CDKAL1 influences insulin response and risk of type 2 diabetes. Nat Genet (2007) 13.28

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08

WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06

Many sequence variants affecting diversity of adult human height. Nat Genet (2008) 12.80