Published in Nature on July 29, 2004
UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell (2006) 9.64
The biodiversity of the Mediterranean Sea: estimates, patterns, and threats. PLoS One (2010) 6.77
PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol (2005) 5.97
Overview of the marine roseobacter lineage. Appl Environ Microbiol (2005) 5.79
Multivariate analyses in microbial ecology. FEMS Microbiol Ecol (2007) 5.65
Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol (2009) 4.79
Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol (2008) 4.58
Microbial community structure and its functional implications. Nature (2009) 4.23
Recombination and the nature of bacterial speciation. Science (2007) 3.98
Explaining microbial population genomics through phage predation. Nat Rev Microbiol (2009) 3.87
Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol (2005) 3.39
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res (2008) 3.37
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J (2011) 3.33
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A (2009) 3.11
Independently evolving species in asexual bdelloid rotifers. PLoS Biol (2007) 3.05
Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci U S A (2007) 2.78
Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol (2006) 2.76
Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci U S A (2008) 2.44
Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Syst Biol (2013) 2.36
A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc Natl Acad Sci U S A (2008) 2.23
Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl Environ Microbiol (2005) 2.06
Coevolutionary arms races between bacteria and bacteriophage. Proc Natl Acad Sci U S A (2005) 2.03
Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J (2009) 1.94
E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol (2005) 1.93
Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean. Appl Environ Microbiol (2005) 1.88
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J (2012) 1.86
Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Philos Trans R Soc Lond B Biol Sci (2006) 1.80
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol (2008) 1.80
Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics (2006) 1.80
Diversity and dynamics of a north atlantic coastal Vibrio community. Appl Environ Microbiol (2004) 1.79
Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome. Appl Environ Microbiol (2009) 1.76
Genomics and the bacterial species problem. Genome Biol (2006) 1.76
Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A (2007) 1.68
Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc Lond B Biol Sci (2006) 1.65
Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J (2011) 1.63
Seasonal variations in the contributions of different bacterial groups to the uptake of low-molecular-weight compounds in northwestern Mediterranean coastal waters. Appl Environ Microbiol (2007) 1.63
Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A (2010) 1.58
Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol (2005) 1.52
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res (2008) 1.50
Low intraspecific diversity in a polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond. Appl Environ Microbiol (2005) 1.49
Microeukaryote community patterns along an O2/H2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway). Appl Environ Microbiol (2006) 1.45
Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies. Appl Environ Microbiol (2006) 1.44
Global extent of horizontal gene transfer. Proc Natl Acad Sci U S A (2007) 1.43
The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev (2008) 1.42
Assimilation of polysaccharides and glucose by major bacterial groups in the Delaware Estuary. Appl Environ Microbiol (2005) 1.42
Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol (2007) 1.38
Bacterial and fungal microbiota in relation to probiotic therapy (VSL#3) in pouchitis. Gut (2006) 1.36
Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl Environ Microbiol (2007) 1.35
The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol (2006) 1.35
Captured diversity in a culture collection: case study of the geographic and habitat distributions of environmental isolates held at the american type culture collection. Appl Environ Microbiol (2005) 1.35
Patterns of gene flow define species of thermophilic Archaea. PLoS Biol (2012) 1.33
Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Microb Ecol (2007) 1.31
Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucleic Acids Res (2013) 1.27
Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. PLoS One (2011) 1.27
Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One (2010) 1.24
Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl Environ Microbiol (2006) 1.22
Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microb Ecol (2005) 1.20
Using population genetic theory and DNA sequences for species detection and identification in asexual organisms. PLoS One (2010) 1.20
RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities. Bioinformatics (2009) 1.20
Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol Mol Biol Rev (2005) 1.18
Environmental rRNA inventories miss over half of protistan diversity. BMC Microbiol (2008) 1.18
Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data. Biol Lett (2009) 1.18
Ecology of speciation in the genus Bacillus. Appl Environ Microbiol (2010) 1.16
Miniprimer PCR, a new lens for viewing the microbial world. Appl Environ Microbiol (2007) 1.16
Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora. Appl Environ Microbiol (2005) 1.16
Phylogenetic diversity, localization, and cell morphologies of members of the candidate phylum TG3 and a subphylum in the phylum Fibrobacteres, recently discovered bacterial groups dominant in termite guts. Appl Environ Microbiol (2006) 1.15
Biogeography and landscape-scale diversity of the dominant Crenarchaeota of soil. Microb Ecol (2006) 1.15
Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria. J Mol Evol (2007) 1.13
Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. Appl Environ Microbiol (2005) 1.12
Cultivation and ecosystem role of a marine roseobacter clade-affiliated cluster bacterium. Appl Environ Microbiol (2008) 1.11
Extensive variation in intracellular symbiont community composition among members of a single population of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). Appl Environ Microbiol (2006) 1.11
The dynamics of microbial partnerships in the coral Isopora palifera. ISME J (2010) 1.11
Diversity of basidiomycetes in michigan agricultural soils. Appl Environ Microbiol (2006) 1.10
Bacterial community associated with healthy and diseased reef coral Mussismilia hispida from eastern Brazil. Microb Ecol (2010) 1.10
Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters. Appl Environ Microbiol (2012) 1.10
Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters. Philos Trans R Soc Lond B Biol Sci (2008) 1.09
Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil. Microb Ecol (2007) 1.09
Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environ Microbiol (2008) 1.09
The native bacterioplankton community in the central baltic sea is influenced by freshwater bacterial species. Appl Environ Microbiol (2007) 1.07
Recombination shapes the structure of an environmental Vibrio cholerae population. Appl Environ Microbiol (2010) 1.06
Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. ISME J (2012) 1.05
High temporal but low spatial heterogeneity of bacterioplankton in the Chesapeake Bay. Appl Environ Microbiol (2007) 1.05
Evolving entities: towards a unified framework for understanding diversity at the species and higher levels. Philos Trans R Soc Lond B Biol Sci (2010) 1.04
Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev (2014) 1.04
Evolutionary biology: oceans of bacteria. Nature (2004) 1.04
Structuring of bacterioplankton diversity in a large tropical bay. PLoS One (2012) 1.02
The oral microbiome and the immunobiology of periodontal disease and caries. Immunol Lett (2014) 1.01
Euxinic freshwater hypolimnia promote bacterial endemicity in continental areas. Microb Ecol (2010) 1.01
Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto. PLoS One (2008) 1.00
The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments. BMC Genomics (2009) 1.00
Bacterial profile of dentine caries and the impact of pH on bacterial population diversity. PLoS One (2014) 1.00
Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques. Environ Microbiol (2013) 0.98
A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microb Ecol (2007) 0.97
Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle. ISME J (2013) 0.97
Testing for differentiation of microbial communities using phylogenetic methods: accounting for uncertainty of phylogenetic inference and character state mapping. Microb Ecol (2006) 0.96
Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proc Natl Acad Sci U S A (2006) 0.95
Low taxon richness of bacterioplankton in high-altitude lakes of the eastern tibetan plateau, with a predominance of Bacteroidetes and Synechococcus spp. Appl Environ Microbiol (2009) 0.95
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol (2004) 7.98
Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res (2002) 6.07
PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol (2005) 5.97
Population genomics of early events in the ecological differentiation of bacteria. Science (2012) 4.67
Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol (2002) 4.35
Genotypic diversity within a natural coastal bacterioplankton population. Science (2005) 4.06
Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science (2008) 3.46
Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science (2007) 3.36
The bacterial species challenge: making sense of genetic and ecological diversity. Science (2009) 2.88
Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc Natl Acad Sci U S A (2008) 2.70
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio (2010) 2.53
Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J (2010) 2.33
Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance. Science (2012) 2.28
High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ Microbiol (2004) 2.15
Diversity and dynamics of a north atlantic coastal Vibrio community. Appl Environ Microbiol (2004) 1.79
DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A (2011) 1.69
Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc Lond B Biol Sci (2006) 1.65
A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ Microbiol Rep (2011) 1.64
Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc Natl Acad Sci U S A (2012) 1.62
Phenazine content in the cystic fibrosis respiratory tract negatively correlates with lung function and microbial complexity. Am J Respir Cell Mol Biol (2012) 1.52
Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio (2011) 1.47
Effects of temperature and salinity on Vibrio vulnificus population dynamics as assessed by quantitative PCR. Appl Environ Microbiol (2004) 1.45
Spatial distribution and stability of the eight microbial species of the altered schaedler flora in the mouse gastrointestinal tract. Appl Environ Microbiol (2004) 1.45
Conservation of the chitin utilization pathway in the Vibrionaceae. Appl Environ Microbiol (2007) 1.40
Phylogenetic analysis implicates birds as a source of Cryptosporidium spp. oocysts in agricultural watersheds. Environ Sci Technol (2007) 1.37
Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environ Microbiol (2010) 1.34
Colonization dynamics of altered Schaedler flora is influenced by gender, aging, and Helicobacter hepaticus infection in the intestines of Swiss Webster mice. Appl Environ Microbiol (2006) 1.29
Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Environ Microbiol (2009) 1.29
The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One (2009) 1.28
Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl Environ Microbiol (2006) 1.22
Solar disinfection (SODIS): simulation of solar radiation for global assessment and application for point-of-use water treatment in Haiti. Water Res (2003) 1.22
Molecular and functional analysis of an interferon gene from the zebrafish, Danio rerio. J Virol (2003) 1.19
The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs. Environ Health (2008) 1.18
Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc Natl Acad Sci U S A (2011) 1.14
Differences in bacterial saliva profile between periodontitis patients and a control cohort. J Clin Periodontol (2013) 1.14
Merging taxonomy with ecological population prediction in a case study of Vibrionaceae. Appl Environ Microbiol (2011) 1.14
Extensive variation in intracellular symbiont community composition among members of a single population of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). Appl Environ Microbiol (2006) 1.11
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
Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas. ISME J (2007) 1.06
Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. ISME J (2012) 1.05
Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations. Proc Natl Acad Sci U S A (2014) 1.05
Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers. Appl Environ Microbiol (2002) 1.02
Endodontic photodynamic therapy ex vivo. J Endod (2011) 1.01
Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ Microbiol (2005) 1.00
Microbial community succession on developing lesions on human enamel. J Oral Microbiol (2012) 1.00
Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO. Arch Microbiol (2004) 0.96
Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proc Natl Acad Sci U S A (2006) 0.95
Vibrio chromosomes share common history. BMC Microbiol (2010) 0.95
O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates. Environ Microbiol (2010) 0.94
ACID: annotation of cassette and integron data. BMC Bioinformatics (2009) 0.93
Phylogenetic analysis of the hypervariable region of the 18S rRNA gene of Cryptosporidium oocysts in feces of Canada geese (Branta canadensis): evidence for five novel genotypes. Appl Environ Microbiol (2004) 0.93
A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment. BMC Genomics (2009) 0.93
Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME J (2010) 0.90
Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol (2014) 0.90
Protistan grazing analysis by flow cytometry using prey labeled by in vivo expression of fluorescent proteins. Appl Environ Microbiol (2003) 0.90
Emerging contaminant or an old toxin in disguise? Silver nanoparticle impacts on ecosystems. Environ Sci Technol (2014) 0.89
Porphyromonas gingivalis: keeping the pathos out of the biont. J Oral Microbiol (2013) 0.89
Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria. Environ Microbiol Rep (2013) 0.88
High frequency of a novel filamentous phage, VCY φ, within an environmental Vibrio cholerae population. Appl Environ Microbiol (2011) 0.86
Association between upper digestive tract microbiota and cancer-predisposing states in the esophagus and stomach. Cancer Epidemiol Biomarkers Prev (2014) 0.85
CelAB, a multifunctional cellulase encoded by Teredinibacter turnerae T7902T, a culturable symbiont isolated from the wood-boring marine bivalve Lyrodus pedicellatus. Appl Environ Microbiol (2007) 0.85
Shape and evolution of the fundamental niche in marine Vibrio. ISME J (2012) 0.83
Microbial distribution and abundance in the digestive system of five shipworm species (Bivalvia: Teredinidae). PLoS One (2012) 0.83
Turnerbactin, a novel triscatecholate siderophore from the shipworm endosymbiont Teredinibacter turnerae T7901. PLoS One (2013) 0.77
Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits. ISME J (2013) 0.77
Genetic differentiation among isolates of Teredinibacter turnerae, a widely occurring intracellular endosymbiont of shipworms. Mol Ecol (2014) 0.77
Detection of the oyster parasite Bonamia ostreae by fluorescent in situ hybridization. Dis Aquat Organ (2003) 0.77
Binding of harvested bacterial exopolymers to the surface of calcite. Environ Sci Technol (2005) 0.76
Association between tobacco use and the upper gastrointestinal microbiome among Chinese men. Cancer Causes Control (2015) 0.75
Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index. Obesity (Silver Spring) (2015) 0.75
The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China. BMC Public Health (2014) 0.75
Annual community patterns are driven by seasonal switching between closely related marine bacteria. ISME J (2017) 0.75
Antimicrobial action of minocycline microspheres versus 810-nm diode laser on human dental plaque microcosm biofilms. J Periodontol (2013) 0.75