Published in Nat Methods on September 01, 2010
Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One (2011) 12.26
UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods (2013) 12.05
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science (2011) 8.88
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41
Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A (2011) 4.85
Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med (2011) 4.78
Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61
Bayesian community-wide culture-independent microbial source tracking. Nat Methods (2011) 3.88
Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One (2012) 3.49
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
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet (2013) 3.03
Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods (2012) 2.77
Diversity of bifidobacteria within the infant gut microbiota. PLoS One (2012) 2.71
Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol (2012) 2.70
Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One (2011) 2.69
Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut (2011) 2.67
Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One (2010) 2.60
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J (2011) 2.48
The Western English Channel contains a persistent microbial seed bank. ISME J (2011) 2.37
The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One (2013) 2.32
PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One (2012) 2.31
Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoS Comput Biol (2013) 2.28
Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One (2012) 1.98
Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One (2013) 1.86
Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A (2013) 1.78
Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide. New Phytol (2013) 1.78
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Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity (Silver Spring) (2011) 1.73
Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J (2013) 1.67
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol (2013) 1.62
Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J (2013) 1.56
Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One (2012) 1.51
Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J (2012) 1.46
Conducting a microbiome study. Cell (2014) 1.46
Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata. PLoS One (2015) 1.39
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Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol (2014) 1.36
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A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing. PLoS One (2013) 1.33
Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One (2013) 1.33
Chemical-biogeographic survey of secondary metabolism in soil. Proc Natl Acad Sci U S A (2014) 1.32
PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol (2011) 1.32
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. MBio (2014) 1.32
Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One (2014) 1.28
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J (2013) 1.28
Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific. PLoS One (2013) 1.27
Strong coupling of plant and fungal community structure across western Amazonian rainforests. ISME J (2013) 1.23
"Remake" by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl Environ Microbiol (2012) 1.23
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. ISME J (2012) 1.23
Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform (2015) 1.22
Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J (2012) 1.22
RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments. PeerJ (2014) 1.21
Biogeography of bacterial communities exposed to progressive long-term environmental change. ISME J (2012) 1.18
A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput Biol (2012) 1.18
Amphibian skin may select for rare environmental microbes. ISME J (2014) 1.17
Upper airways microbiota in antibiotic-naïve wheezing and healthy infants from the tropics of rural Ecuador. PLoS One (2012) 1.17
Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing. PLoS One (2013) 1.16
Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci (2015) 1.16
Denoising PCR-amplified metagenome data. BMC Bioinformatics (2012) 1.16
Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci (2014) 1.15
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Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol (2013) 1.14
Endemism and functional convergence across the North American soil mycobiome. Proc Natl Acad Sci U S A (2014) 1.14
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights (2015) 1.13
Exercise induction of gut microbiota modifications in obese, non-obese and hypertensive rats. BMC Genomics (2014) 1.11
Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer. PLoS One (2012) 1.10
A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: a case study of fungi in indoor dust. Microb Ecol (2013) 1.10
In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes. Microb Ecol (2011) 1.10
Spatial and species variations in bacterial communities associated with corals from the Red Sea as revealed by pyrosequencing. Appl Environ Microbiol (2012) 1.08
Branched chain fatty acids reduce the incidence of necrotizing enterocolitis and alter gastrointestinal microbial ecology in a neonatal rat model. PLoS One (2011) 1.08
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics (2016) 1.06
Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density. Appl Environ Microbiol (2013) 1.04
A selected core microbiome drives the early stages of three popular italian cheese manufactures. PLoS One (2014) 1.02
Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops. PLoS One (2011) 1.02
The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults. PLoS One (2012) 1.01
Pyrosequencing as a tool for better understanding of human microbiomes. J Oral Microbiol (2012) 1.01
When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback. ISME J (2014) 1.01
Diversified pattern of the human colorectal cancer microbiome. Gut Pathog (2013) 1.01
Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. PLoS One (2012) 0.99
Litter quality versus soil microbial community controls over decomposition: a quantitative analysis. Oecologia (2014) 0.99
Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism. Front Microbiol (2015) 0.99
Improved inference of taxonomic richness from environmental DNA. PLoS One (2013) 0.99
Assessing the consequences of denoising marker-based metagenomic data. PLoS One (2013) 0.98
Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform (2013) 0.98
Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest. Sci Rep (2014) 0.98
Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance. Microb Ecol (2012) 0.98
Testing potential effects of maize expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) on mycorrhizal fungal communities via DNA- and RNA-based pyrosequencing and molecular fingerprinting. Appl Environ Microbiol (2012) 0.97
The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue. Microb Ecol (2010) 0.97
Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon. PLoS One (2013) 0.96
Distinctive microbial community structure in highly stratified deep-sea brine water columns. Appl Environ Microbiol (2013) 0.95
Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS One (2012) 0.95
Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning. ISME J (2014) 0.94
A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl Environ Microbiol (2014) 0.94
Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant. ISME J (2014) 0.94
Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides. Appl Environ Microbiol (2014) 0.94
Bacterial endophytic communities in the grapevine depend on pest management. PLoS One (2014) 0.93
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
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
Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol (2007) 23.64
Evolution of mammals and their gut microbes. Science (2008) 21.40
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (2009) 15.93
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
Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol (2010) 13.19
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet (2008) 10.72
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Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
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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
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UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics (2006) 25.13
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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
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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
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
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Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
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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
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41
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Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04
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