The human microbiome project.

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55

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

Evolution of mammals and their gut microbes. Science (2008) 21.40

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

The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol (2009) 13.87

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

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One (2011) 12.26

Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol (2008) 12.16

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

Detecting novel associations in large data sets. Science (2011) 10.60

Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A (2010) 9.81

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

The case for cloud computing in genome informatics. Genome Biol (2010) 9.20

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res (2008) 9.09

The human oral microbiome. J Bacteriol (2010) 9.00

Integrative analysis of environmental sequences using MEGAN4. Genome Res (2011) 8.60

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A (2010) 8.56

Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol (2009) 8.06

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

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

Necrotizing enterocolitis. N Engl J Med (2011) 6.88

Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature (2010) 6.55

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res (2015) 6.39

Disordered microbial communities in asthmatic airways. PLoS One (2010) 6.35

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

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A (2009) 5.86

What are the consequences of the disappearing human microbiota? Nat Rev Microbiol (2009) 5.62

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

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods (2010) 4.93

Functional characterization of the antibiotic resistance reservoir in the human microflora. Science (2009) 4.78

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford) (2010) 4.66

Microbes in gastrointestinal health and disease. Gastroenterology (2008) 4.65

Homeostasis and inflammation in the intestine. Cell (2010) 4.60

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

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci U S A (2011) 4.53

The core gut microbiome, energy balance and obesity. J Physiol (2009) 4.45

Has the microbiota played a critical role in the evolution of the adaptive immune system? Science (2010) 4.29

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

Assembling the marine metagenome, one cell at a time. PLoS One (2009) 4.10

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

The Genomic Standards Consortium. PLoS Biol (2011) 3.99

Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One (2011) 3.74

Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell (2010) 3.70

Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One (2008) 3.56

The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab (2011) 3.54

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

Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Microbiol (2008) 3.25

Massively parallel sequencing: the next big thing in genetic medicine. Am J Hum Genet (2009) 3.01

Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science (2010) 2.99

Gut microbiome, obesity, and metabolic dysfunction. J Clin Invest (2011) 2.93

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

What would you do if you could sequence everything? Nat Biotechnol (2008) 2.89

Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature (2010) 2.85

Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One (2011) 2.81

Metagenomic pyrosequencing and microbial identification. Clin Chem (2009) 2.81

Temporal response of the human virome to immunosuppression and antiviral therapy. Cell (2013) 2.72

Gut microbiome of the Hadza hunter-gatherers. Nat Commun (2014) 2.72

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

Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system. PLoS Genet (2011) 2.55

From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev (2010) 2.42

The vaginal microbiome: new information about genital tract flora using molecular based techniques. BJOG (2011) 2.41

The immune system and the gut microbiota: friends or foes? Nat Rev Immunol (2010) 2.38

Architectural design influences the diversity and structure of the built environment microbiome. ISME J (2012) 2.36

Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A (2010) 2.34

Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One (2012) 2.34

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

The human intestinal microbiome: a new frontier of human biology. DNA Res (2009) 2.30

Microbial genomics and infectious diseases. N Engl J Med (2011) 2.27

Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection. Infect Immun (2009) 2.26

Intestinal mucosal adherence and translocation of commensal bacteria at the early onset of type 2 diabetes: molecular mechanisms and probiotic treatment. EMBO Mol Med (2011) 2.25

Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis. Arthritis Rheum (2012) 2.24

Principles and clinical implications of the brain-gut-enteric microbiota axis. Nat Rev Gastroenterol Hepatol (2009) 2.24

The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome (2014) 2.24

The oral microbiota: living with a permanent guest. DNA Cell Biol (2009) 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

Hypothesis testing and power calculations for taxonomic-based human microbiome data. PLoS One (2012) 2.15

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

Scaling laws predict global microbial diversity. Proc Natl Acad Sci U S A (2016) 2.10

Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics (2010) 2.04

TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data. PLoS One (2015) 2.04

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

Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing. BMC Microbiol (2011) 2.02

Environmental and gut bacteroidetes: the food connection. Front Microbiol (2011) 2.01

Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC Bioinformatics (2010) 2.01

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

Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology (2009) 1.96

The colibactin warhead crosslinks DNA. Nat Chem (2015) 1.96

Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One (2012) 1.96

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

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

The microbial ocean from genomes to biomes. Nature (2009) 1.91

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95

A haplotype map of the human genome. Nature (2005) 105.70

ARB: a software environment for sequence data. Nucleic Acids Res (2004) 58.27

The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05

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

Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23

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

Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol (2005) 31.06

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

The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A (2004) 26.56

Comparative metagenomics of microbial communities. Science (2005) 25.88

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

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res (2005) 24.85

Java Treeview--extensible visualization of microarray data. Bioinformatics (2004) 24.12

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res (2006) 23.67

Open source clustering software. Bioinformatics (2004) 23.17

An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell (2005) 15.46

HMDB: the Human Metabolome Database. Nucleic Acids Res (2007) 13.38

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

Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science (2006) 9.95

Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93

Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A (2007) 9.73

Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A (2007) 9.71

Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell (2006) 9.64

Environmental exposure to endotoxin and its relation to asthma in school-age children. N Engl J Med (2002) 9.14

Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A (2006) 7.77

Quantitative phylogenetic assessment of microbial communities in diverse environments. Science (2007) 6.35

Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol (2003) 6.17

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

Bacterial biota in the human distal esophagus. Proc Natl Acad Sci U S A (2004) 5.64

Microbes on the human vaginal epithelium. Proc Natl Acad Sci U S A (2005) 5.15

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics (2004) 4.67

Cultivating the uncultured. Proc Natl Acad Sci U S A (2002) 4.03

Community proteomics of a natural microbial biofilm. Science (2005) 3.97

A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol (2007) 3.68

Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol (2007) 3.55

Neutral theory and the evolution of ecological equivalence. Ecology (2006) 3.40

Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol (2001) 3.36

Increased risk of childhood asthma from antibiotic use in early life. Chest (2007) 3.11

Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol (2005) 2.46

Bacteria-induced intestinal cancer in mice with disrupted Gpx1 and Gpx2 genes. Cancer Res (2004) 2.42

Rapid reversal of hyperoxaluria in a rat model after probiotic administration of Oxalobacter formigenes. J Urol (2001) 1.74

Microarray applications in microbial ecology research. Microb Ecol (2006) 1.64

Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. Appl Environ Microbiol (2006) 1.49

Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ Microbiol (2006) 1.49

Tilman's predicted productivity-diversity relationship shown by desert rodents. Nature (1984) 1.29

Oxygen consumption and thyroid hormones in germfree mice fed glucose-amino acid liquid diet. J Nutr (1982) 1.24

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 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

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

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

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

Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19

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

Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature (2008) 5.96

The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94

Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature (2010) 5.92