Published in BMC Microbiol on May 24, 2013
The soil microbiome influences grapevine-associated microbiota. MBio (2015) 2.03
The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev (2015) 1.51
Unraveling the plant microbiome: looking back and future perspectives. Front Microbiol (2014) 1.23
Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci (2014) 1.15
A Vavilovian approach to discovering crop-associated microbes with potential to enhance plant immunity. Front Plant Sci (2014) 0.96
Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea). PLoS One (2015) 0.92
Xanthomonas perforans colonization influences Salmonella enterica in the tomato phyllosphere. Appl Environ Microbiol (2014) 0.90
Phyllosphere microbiota composition and microbial community transplantation on lettuce plants grown indoors. MBio (2014) 0.88
Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One (2016) 0.86
Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing. BMC Microbiol (2015) 0.84
Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. Front Microbiol (2015) 0.83
Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities. PeerJ (2015) 0.82
The impact of systemic and copper pesticide applications on the phyllosphere microflora of tomatoes. J Sci Food Agric (2014) 0.82
Avoiding Pandemic Fears in the Subway and Conquering the Platypus. mSystems (2016) 0.82
Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase. Hortic Res (2016) 0.80
Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System. Front Plant Sci (2016) 0.79
Microbial interactions: ecology in a molecular perspective. Braz J Microbiol (2016) 0.79
Development of Culture Medium for the Isolation of Flavobacterium and Chryseobacterium from Rhizosphere Soil. Microbes Environ (2016) 0.78
The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility. MBio (2016) 0.77
Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome (2017) 0.76
Environmental Metabolomics of the Tomato Plant Surface Provides Insights on Salmonella enterica Colonization. Appl Environ Microbiol (2016) 0.76
Recent and emerging innovations in Salmonella detection: a food and environmental perspective. Microb Biotechnol (2016) 0.76
Using a Control to Better Understand Phyllosphere Microbiota. PLoS One (2016) 0.76
Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes. Front Plant Sci (2017) 0.75
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
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics (2003) 53.11
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res (2001) 43.17
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics (2008) 29.20
FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One (2010) 26.15
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Topographical and temporal diversity of the human skin microbiome. Science (2009) 15.96
Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One (2008) 14.63
Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes (2007) 10.11
Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One (2011) 6.75
Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res (2008) 4.71
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics (2011) 3.64
Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol (1999) 2.89
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol (2010) 2.35
Survival of salmonellae on and in tomato plants from the time of inoculation at flowering and early stages of fruit development through fruit ripening. Appl Environ Microbiol (2001) 1.53
Colonization of tomato plants by Salmonella enterica is cultivar dependent, and type 1 trichomes are preferred colonization sites. Appl Environ Microbiol (2010) 1.38
Chromosomal evolution in the plant family Solanaceae. BMC Genomics (2010) 1.29
Divergent regulation of terpenoid metabolism in the trichomes of wild and cultivated tomato species. Plant Physiol (2008) 1.11
Plant-endophyte interplay protects tomato against a virulent Verticillium. Planta (2008) 1.08
SitePainter: a tool for exploring biogeographical patterns. Bioinformatics (2011) 1.01
Bacterial community diversity and variation in spray water sources and the tomato fruit surface. BMC Microbiol (2011) 0.99
Impact of organic and conventional management on the phyllosphere microbial ecology of an apple crop. J Food Prot (2009) 0.92
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
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
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
The physics of optimal decision making: a formal analysis of models of performance in two-alternative forced-choice tasks. Psychol Rev (2006) 7.93
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
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
Epithelial to mesenchymal transition is a determinant of sensitivity of non-small-cell lung carcinoma cell lines and xenografts to epidermal growth factor receptor inhibition. Cancer Res (2005) 5.33
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
Berberine is a novel cholesterol-lowering drug working through a unique mechanism distinct from statins. Nat Med (2004) 3.92
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
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics (2011) 3.64
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
flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinformatics (2009) 3.33
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
Identification of a salmonellosis outbreak by means of molecular sequencing. N Engl J Med (2011) 2.81
Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol (2012) 2.70
Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1. Nat Neurosci (2003) 2.66
Feedback mechanisms promote cooperativity for small molecule inhibitors of epidermal and insulin-like growth factor receptors. Cancer Res (2008) 2.62
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
Investigation of the safety of irreversible electroporation in humans. J Vasc Interv Radiol (2011) 2.55
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
Genome-wide association identifies a susceptibility locus for coronary artery disease in the Chinese Han population. Nat Genet (2011) 2.32
Rapamycin synergizes with the epidermal growth factor receptor inhibitor erlotinib in non-small-cell lung, pancreatic, colon, and breast tumors. Mol Cancer Ther (2006) 2.25
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res (2010) 2.21
The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol (2012) 2.17
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab (2013) 2.17
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics (2011) 2.15