Published in Nature on June 13, 2012
Cigarette Smoking and Oral Microbiota | NCT01862809
UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods (2013) 12.05
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
Diversity, stability and resilience of the human gut microbiota. Nature (2012) 9.09
Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science (2013) 8.53
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol (2013) 8.53
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One (2013) 7.23
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol (2013) 6.90
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol (2012) 5.66
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature (2014) 5.51
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
The gut microbiota--masters of host development and physiology. Nat Rev Microbiol (2013) 5.25
The long-term stability of the human gut microbiota. Science (2013) 5.15
The placenta harbors a unique microbiome. Sci Transl Med (2014) 5.10
Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci (2012) 4.95
Human genetics shape the gut microbiome. Cell (2014) 4.91
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68
Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell (2014) 4.25
Compartmentalized control of skin immunity by resident commensals. Science (2012) 4.19
Inflammation-induced cancer: crosstalk between tumours, immune cells and microorganisms. Nat Rev Cancer (2013) 4.02
MR1 presents microbial vitamin B metabolites to MAIT cells. Nature (2012) 3.71
Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med (2013) 3.65
Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol (2012) 3.64
Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. N Engl J Med (2013) 3.39
Microbial interactions: from networks to models. Nat Rev Microbiol (2012) 3.28
Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell (2013) 3.26
Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe (2013) 3.21
Pathogens and host immunity in the ancient human oral cavity. Nat Genet (2014) 3.19
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet (2013) 3.03
The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. MBio (2014) 3.02
Alterations of the human gut microbiome in liver cirrhosis. Nature (2014) 3.02
Colitogenic Bacteroides thetaiotaomicron Antigens Access Host Immune Cells in a Sulfatase-Dependent Manner via Outer Membrane Vesicles. Cell Host Microbe (2015) 2.98
A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell (2014) 2.97
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
Cohabiting family members share microbiota with one another and with their dogs. Elife (2013) 2.92
Salivary microbiota reflects changes in gut microbiota in cirrhosis with hepatic encephalopathy. Hepatology (2015) 2.91
The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J (2013) 2.90
Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol (2013) 2.89
Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A (2013) 2.88
Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. Aliment Pharmacol Ther (2015) 2.87
The microbiome and cancer. Nat Rev Cancer (2013) 2.86
Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun (2012) 2.84
Topographic diversity of fungal and bacterial communities in human skin. Nature (2013) 2.79
Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst (2013) 2.76
The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology (2014) 2.73
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe (2015) 2.58
EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience (2013) 2.54
Fertility and early pregnancy outcomes after treatment for cervical intraepithelial neoplasia: systematic review and meta-analysis. BMJ (2014) 2.50
Biogeography of a human oral microbiome at the micron scale. Proc Natl Acad Sci U S A (2016) 2.46
Temporal Stability of the Human Skin Microbiome. Cell (2016) 2.41
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol (2013) 2.36
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife (2013) 2.36
Meta-analyses of studies of the human microbiota. Genome Res (2013) 2.35
Dynamics and associations of microbial community types across the human body. Nature (2014) 2.32
A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature (2014) 2.29
Biogeography and individuality shape function in the human skin metagenome. Nature (2014) 2.27
Binning metagenomic contigs by coverage and composition. Nat Methods (2014) 2.27
Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One (2013) 2.24
Patterned progression of bacterial populations in the premature infant gut. Proc Natl Acad Sci U S A (2014) 2.20
Bacterial colonization factors control specificity and stability of the gut microbiota. Nature (2013) 2.20
The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol (2012) 2.17
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J (2012) 2.13
Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun (2015) 2.12
Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A (2014) 2.11
Sequence assembly demystified. Nat Rev Genet (2013) 2.09
Intestinal commensal microbes as immune modulators. Cell Host Microbe (2012) 2.07
Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract. Immunity (2015) 2.05
Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring. Cell (2016) 2.05
The microbiome of uncontacted Amerindians. Sci Adv (2015) 2.04
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
Mobile genes in the human microbiome are structured from global to individual scales. Nature (2016) 2.02
Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature (2017) 2.01
Genomic approaches to studying the human microbiota. Nature (2012) 2.00
Country-specific antibiotic use practices impact the human gut resistome. Genome Res (2013) 1.94
Commensal bacteria at the interface of host metabolism and the immune system. Nat Immunol (2013) 1.93
The intestinal microbiome in early life: health and disease. Front Immunol (2014) 1.90
Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection. Sci Transl Med (2013) 1.88
Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One (2013) 1.86
Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun (2016) 1.84
Computational meta'omics for microbial community studies. Mol Syst Biol (2013) 1.84
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc Natl Acad Sci U S A (2013) 1.84
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One (2012) 1.84
Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut (2013) 1.83
How informative is the mouse for human gut microbiota research? Dis Model Mech (2015) 1.79
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science (2015) 1.79
A compositional look at the human gastrointestinal microbiome and immune activation parameters in HIV infected subjects. PLoS Pathog (2014) 1.78
The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics (2013) 1.76
Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A (2015) 1.75
Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. MBio (2014) 1.74
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol (2013) 1.74
Medicines from microbiota. Nat Biotechnol (2013) 1.72
ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol (2015) 1.68
Gut biogeography of the bacterial microbiota. Nat Rev Microbiol (2015) 1.66
Sewage reflects the microbiomes of human populations. MBio (2015) 1.64
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome (2014) 1.63
Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity. ISME J (2014) 1.63
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
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Topographical and temporal diversity of the human skin microbiome. Science (2009) 15.96
Defining the normal bacterial flora of the oral cavity. J Clin Microbiol (2005) 15.75
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
A microbial symbiosis factor prevents intestinal inflammatory disease. Nature (2008) 13.15
Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A (2010) 12.39
Molecular identification of bacteria associated with bacterial vaginosis. N Engl J Med (2005) 11.23
Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods (2012) 8.37
Prevalence of Staphylococcus aureus nasal colonization in the United States, 2001-2002. J Infect Dis (2005) 6.78
Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics (2009) 5.69
Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol (2012) 5.35
Microbiology in the post-genomic era. Nat Rev Microbiol (2008) 4.88
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun (2011) 4.57
A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One (2012) 4.35
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol (2012) 3.02
Analyses of the microbial diversity across the human microbiome. PLoS One (2012) 2.98
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol (2011) 2.54
Novel bacterial taxa in the human microbiome. PLoS One (2012) 2.35
A framework for human microbiome research. Nature (2012) 11.41