Published in ISME J on January 12, 2012
Diversity of bifidobacteria within the infant gut microbiota. PLoS One (2012) 2.71
Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04
A meta-analysis of changes in bacterial and archaeal communities with time. ISME J (2013) 1.80
Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS One (2012) 1.79
Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One (2014) 1.50
Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PLoS One (2012) 1.49
Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities. Appl Environ Microbiol (2013) 1.46
Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One (2013) 1.46
Conducting a microbiome study. Cell (2014) 1.46
Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets. PLoS One (2013) 1.27
Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci (2015) 1.16
The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier. BMC Microbiol (2012) 1.14
Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort. PLoS One (2013) 1.13
Diversity of the vaginal microbiome correlates with preterm birth. Reprod Sci (2013) 1.13
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights (2015) 1.13
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. PLoS One (2013) 1.09
A direct PCR approach to accelerate analyses of human-associated microbial communities. PLoS One (2012) 1.08
HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats. PLoS One (2014) 1.07
The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies. PLoS One (2013) 1.06
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics (2016) 1.06
IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries. PLoS One (2014) 1.05
Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PLoS One (2013) 1.04
High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism. Bioinform Biol Insights (2014) 0.99
Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform (2013) 0.98
Asthma microbiome studies and the potential for new therapeutic strategies. Curr Allergy Asthma Rep (2013) 0.97
Bioinformatics for the Human Microbiome Project. PLoS Comput Biol (2012) 0.97
Impact of logging and forest conversion to oil palm plantations on soil bacterial communities in Borneo. Appl Environ Microbiol (2013) 0.96
Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines. Biomed Res Int (2014) 0.94
Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses. Front Microbiol (2015) 0.93
The poultry-associated microbiome: network analysis and farm-to-fork characterizations. PLoS One (2013) 0.93
The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. PLoS One (2015) 0.88
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics. Front Microbiol (2016) 0.87
Biotic interactions and temporal dynamics of the human gastrointestinal microbiota. ISME J (2014) 0.86
High-resolution phylogenetic microbial community profiling. ISME J (2016) 0.85
Impact of next generation sequencing techniques in food microbiology. Curr Genomics (2014) 0.85
Expansion of Microbial Forensics. J Clin Microbiol (2016) 0.84
Genetic associations and shared environmental effects on the skin microbiome of Korean twins. BMC Genomics (2015) 0.83
The potential of metatranscriptomics for identifying screening targets for bacterial vaginosis. PLoS One (2013) 0.82
Comparing K-mer based methods for improved classification of 16S sequences. BMC Bioinformatics (2015) 0.82
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Front Microbiol (2017) 0.81
A physicians' wish list for the clinical application of intestinal metagenomics. PLoS Med (2014) 0.81
Intricacies of assessing the human microbiome in epidemiologic studies. Ann Epidemiol (2016) 0.80
Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet. Microb Ecol (2016) 0.80
Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes. PLoS One (2015) 0.80
Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions. PLoS One (2015) 0.78
Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples. PLoS One (2016) 0.77
Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes. Front Microbiol (2016) 0.77
Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum. J Microbiol Methods (2016) 0.77
Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods. Sci Rep (2016) 0.77
Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used. Heliyon (2016) 0.76
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the "terroir" Concept. Front Microbiol (2017) 0.76
Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains. Microb Ecol (2012) 0.76
Characterization of Gut Microbiome Dynamics in Developing Pekin Ducks and Impact of Management System. Front Microbiol (2017) 0.75
Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data. PLoS One (2016) 0.75
Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research. Front Microbiol (2017) 0.75
Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys. Front Microbiol (2017) 0.75
Increased water contamination and grow-out Pekin duck mortality when raised with water troughs compared to pin-metered water lines using a United States management system. Poult Sci (2016) 0.75
Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon. Sci Rep (2016) 0.75
Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients. Appl Environ Microbiol (2016) 0.75
How conserved are the conserved 16S-rRNA regions? PeerJ (2017) 0.75
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol (2017) 0.75
Penicillium nalgiovense Laxa isolated from Antarctica is a new source of the antifungal metabolite amphotericin B. Fungal Biol Biotechnol (2015) 0.75
Comparison of antibiotic supplementation versus a yeast-based prebiotic on the cecal microbiome of commercial broilers. PLoS One (2017) 0.75
A clinician's guide to microbiome analysis. Nat Rev Gastroenterol Hepatol (2017) 0.75
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol (2006) 57.72
Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97
Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38
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
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet (2008) 10.72
Fine-scale phylogenetic architecture of a complex bacterial community. Nature (2004) 8.99
Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science (1984) 7.06
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci (2010) 4.70
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods (2009) 4.32
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res (2010) 4.17
Illumina-based analysis of microbial community diversity. ISME J (2011) 3.13
Bacterial flora-typing with targeted, chip-based Pyrosequencing. BMC Microbiol (2007) 2.51
Regulation of surface architecture by symbiotic bacteria mediates host colonization. Proc Natl Acad Sci U S A (2008) 1.79
An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One (2008) 1.53
Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS (2002) 1.52
Effects of experimental choices and analysis noise on surveys of the "rare biosphere". Appl Environ Microbiol (2009) 1.51
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
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
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
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
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
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
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
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
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
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
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
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
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A (2002) 10.28
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
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
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 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
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
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature (2007) 7.12
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
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 impact of structural genomics: expectations and outcomes. Science (2006) 5.30
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
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
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
ASTRAL compendium enhancements. Nucleic Acids Res (2002) 4.43
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
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
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
Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol (2005) 3.14
The evolving roles of alternative splicing. Curr Opin Struct Biol (2004) 2.99
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
SCOR: a Structural Classification of RNA database. Nucleic Acids Res (2002) 2.79
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
Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43
The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem (2011) 2.42