Published in BMC Bioinformatics on August 07, 2006
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
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71
The human microbiome project. Nature (2007) 28.53
Evolution of mammals and their gut microbes. Science (2008) 21.40
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
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
Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A (2007) 9.73
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J (2009) 9.71
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
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
Global patterns in bacterial diversity. Proc Natl Acad Sci U S A (2007) 8.00
A diversity profile of the human skin microbiota. Genome Res (2008) 7.65
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
Disordered microbial communities in asthmatic airways. PLoS One (2010) 6.35
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28
Global diversity in the human salivary microbiome. Genome Res (2009) 5.16
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97
Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev (2008) 4.97
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest (2010) 4.95
Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A (2010) 4.56
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature (2013) 4.43
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
Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe (2008) 4.14
Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol (2010) 4.01
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J (2009) 3.84
Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog (2010) 3.75
16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J (2009) 3.75
Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One (2008) 3.56
Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol (2009) 3.52
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A (2010) 3.51
Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J (2010) 3.39
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J (2011) 3.19
Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation. J Exp Med (2012) 3.17
Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature (2015) 3.06
Toward defining the autoimmune microbiome for type 1 diabetes. ISME J (2010) 3.03
Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J Pediatr (2010) 2.93
Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol (2009) 2.92
Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci U S A (2011) 2.92
Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One (2011) 2.81
Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One (2012) 2.77
Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol (2012) 2.75
Diversity of bifidobacteria within the infant gut microbiota. PLoS One (2012) 2.71
Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes (2010) 2.70
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
Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. Gastroenterology (2009) 2.55
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio (2010) 2.53
Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol (2012) 2.50
Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes (2011) 2.46
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
The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A (2008) 2.33
PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One (2012) 2.31
Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease. Am J Respir Crit Care Med (2013) 2.28
An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet (2010) 2.28
Glial-cell-derived neuroregulators control type 3 innate lymphoid cells and gut defence. Nature (2016) 2.23
The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2014) 2.17
Ecosystem-specific selection pressures revealed through comparative population genomics. Proc Natl Acad Sci U S A (2010) 2.12
Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics (2010) 2.04
Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLoS One (2010) 2.02
Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics (2010) 2.01
Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol (2012) 2.01
Bacterial phylogeny structures soil resistomes across habitats. Nature (2014) 1.98
Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol (2013) 1.97
Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol (2011) 1.96
Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infect Immun (2009) 1.91
Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl Environ Microbiol (2007) 1.86
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
Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology (2013) 1.86
Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME J (2010) 1.84
Short-term temporal variability in airborne bacterial and fungal populations. Appl Environ Microbiol (2007) 1.84
Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev (2013) 1.80
Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing. PLoS One (2010) 1.79
Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A (2013) 1.78
Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol (2010) 1.77
Diversity of the human skin microbiome early in life. J Invest Dermatol (2011) 1.77
Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC Gastroenterol (2009) 1.76
Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model. ISME J (2009) 1.74
Influence of fecal sample storage on bacterial community diversity. Open Microbiol J (2009) 1.68
Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J (2013) 1.67
Intercontinental dispersal of bacteria and archaea by transpacific winds. Appl Environ Microbiol (2012) 1.65
Global occurrence of archaeal amoA genes in terrestrial hot springs. Appl Environ Microbiol (2008) 1.65
Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiol (2012) 1.64
Viral communities associated with healthy and bleaching corals. Environ Microbiol (2008) 1.64
Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS One (2012) 1.62
Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol (2012) 1.61
A modified R-type bacteriocin specifically targeting Clostridium difficile prevents colonization of mice without affecting gut microbiota diversity. MBio (2015) 1.59
Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature (2013) 1.59
Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One (2013) 1.56
Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME J (2011) 1.56
Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl Environ Microbiol (2009) 1.53
Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles (2009) 1.51
Cd1d-dependent regulation of bacterial colonization in the intestine of mice. J Clin Invest (2009) 1.49
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res (1997) 175.36
ARB: a software environment for sequence data. Nucleic Acids Res (2004) 58.27
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A (2005) 33.66
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res (2006) 23.67
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol (1998) 21.35
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics (2004) 20.94
Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol (2002) 18.69
The uncultured microbial majority. Annu Rev Microbiol (2003) 17.33
Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol (2001) 16.51
Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol (2004) 12.50
Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol (1995) 11.83
Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol (1999) 6.37
Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol (2006) 5.69
Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci (2004) 4.79
Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science (2003) 4.61
Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J Clin Microbiol (2004) 4.46
FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics (2006) 3.65
Statistical approaches for estimating actinobacterial diversity in marine sediments. Appl Environ Microbiol (2003) 3.39
Comparison of the oral bacterial flora in saliva from a healthy subject and two periodontitis patients by sequence analysis of 16S rDNA libraries. Microbiol Immunol (2000) 3.17
Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains. Appl Environ Microbiol (2004) 3.09
Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance. Can J Microbiol (2002) 2.61
Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase. Appl Environ Microbiol (2004) 2.36
Molecular analysis of carbon monoxide-oxidizing bacteria associated with recent Hawaiian volcanic deposits. Appl Environ Microbiol (2004) 2.10
Microbial community variation in pristine and polluted nearshore Antarctic sediments. FEMS Microbiol Ecol (2003) 2.07
Microbial diversity and functional characterization of sediments from reservoirs of different trophic state. FEMS Microbiol Ecol (2003) 1.90
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
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
The human microbiome project. Nature (2007) 28.53
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
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
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
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
Global patterns in bacterial diversity. Proc Natl Acad Sci U S A (2007) 8.00
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
The impact of the gut microbiota on human health: an integrative view. Cell (2012) 6.01
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
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
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97
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
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci (2010) 4.70
Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61
Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A (2010) 4.56
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
The Genomic Standards Consortium. PLoS Biol (2011) 3.99
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
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A (2010) 3.51
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
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience (2012) 3.24
Supervised classification of human microbiota. FEMS Microbiol Rev (2010) 3.23
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J (2011) 3.19
The 'rare biosphere': a reality check. Nat Methods (2009) 3.19
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
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol (2010) 2.35
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