Published in Curr Opin Biotechnol on December 07, 2011
Fundamentals of microbial community resistance and resilience. Front Microbiol (2012) 2.53
A meta-analysis of changes in bacterial and archaeal communities with time. ISME J (2013) 1.80
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst (2015) 1.73
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci U S A (2014) 1.31
Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. MBio (2014) 1.14
HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats. PLoS One (2014) 1.07
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J (2016) 0.99
GigaDB: promoting data dissemination and reproducibility. Database (Oxford) (2014) 0.95
Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med (2013) 0.93
Co-occurrence patterns of plants and soil bacteria in the high-alpine subnival zone track environmental harshness. Front Microbiol (2012) 0.91
Dynamics in microbial communities: unraveling mechanisms to identify principles. ISME J (2014) 0.89
The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics. PLoS One (2014) 0.84
Microbial community dynamics in the forefield of glaciers. Proc Biol Sci (2014) 0.84
Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover. ISME J (2015) 0.83
Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. Front Microbiol (2015) 0.82
Predicting taxonomic and functional structure of microbial communities in acid mine drainage. ISME J (2016) 0.81
Temporal Study of the Microbial Diversity of the North Arm of Great Salt Lake, Utah, U.S. Microorganisms (2015) 0.80
Flea-Associated Bacterial Communities across an Environmental Transect in a Plague-Endemic Region of Uganda. PLoS One (2015) 0.80
Resilience of aggregated microbial communities subjected to drought--small-scale studies. Microb Ecol (2014) 0.77
Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior. Elife (2017) 0.75
Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds. Front Microbiol (2016) 0.75
Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism. Front Microbiol (2016) 0.75
Bridging the divide: a model-data approach to Polar and Alpine microbiology. FEMS Microbiol Ecol (2016) 0.75
Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major). PLoS One (2017) 0.75
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
The detection of disease clustering and a generalized regression approach. Cancer Res (1967) 39.90
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A (2006) 15.11
Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol (2006) 14.24
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
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
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
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
Moving pictures of the human microbiome. Genome Biol (2011) 6.72
Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science (2003) 6.42
Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature (2010) 5.08
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
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
A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci U S A (2008) 4.00
Colloquium paper: microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci U S A (2008) 3.71
Microbial biogeography: from taxonomy to traits. Science (2008) 3.22
Environmental diversity of bacteria and archaea. Syst Biol (2001) 3.12
Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci U S A (2011) 2.92
Global patterns in belowground communities. Ecol Lett (2009) 2.89
Natural restoration of the species-area relation for a lizard after a hurricane. Science (2001) 2.80
Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J (2011) 2.40
Global patterns in the biogeography of bacterial taxa. Environ Microbiol (2011) 2.34
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics (2006) 2.15
Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05
Spatial scaling of functional gene diversity across various microbial taxa. Proc Natl Acad Sci U S A (2008) 1.95
The microbial ocean from genomes to biomes. Nature (2009) 1.91
Synchrony in aquatic microbial community dynamics. ISME J (2007) 1.83
Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol Ecol (2003) 1.80
Hundred years of genetic structure in a sediment revived diatom population. Proc Natl Acad Sci U S A (2011) 1.65
Sources of bacteria in outdoor air across cities in the midwestern United States. Appl Environ Microbiol (2011) 1.65
Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J (2011) 1.63
Microbes do not follow the elevational diversity patterns of plants and animals. Ecology (2011) 1.54
Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nat Commun (2011) 1.50
Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J (2010) 1.48
The nineteenth century roots of 'everything is everywhere'. Nat Rev Microbiol (2007) 1.41
The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environ Microbiol (2008) 1.31
Biogeography and habitat modelling of high-alpine bacteria. Nat Commun (2010) 1.29
Circumpolar synchrony in big river bacterioplankton. Proc Natl Acad Sci U S A (2009) 1.24
Microbial diversity: the importance of exploration and conservation. J Ind Microbiol Biotechnol (1997) 1.18
Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance. Environ Microbiol (2011) 1.16
Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir. FEMS Microbiol Ecol (2006) 1.12
Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally. Proc Natl Acad Sci U S A (2011) 1.10
Soil microbial community successional patterns during forest ecosystem restoration. Appl Environ Microbiol (2011) 1.05
Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment. Environ Microbiol (2009) 1.03
Functional shifts in unvegetated, perhumid, recently-deglaciated soils do not correlate with shifts in soil bacterial community composition. J Microbiol (2010) 0.96
Web of ecological interactions in an experimental gut microbiota. Environ Microbiol (2010) 0.92
'Candidatus Accumulibacter' gene expression in response to dynamic EBPR conditions. ISME J (2010) 0.88
Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR. Environ Microbiol (2011) 0.86
Phylogeography of microbial phototrophs in the dry valleys of the high Himalayas and Antarctica. Proc Biol Sci (2010) 0.84
Thermophilic microbial mats in a tropical geothermal location display pronounced seasonal changes but appear resilient to stochastic disturbance. Environ Microbiol (2007) 0.83
Bacterial diversity of soil in the vicinity of Pindari glacier, Himalayan mountain ranges, India, using culturable bacteria and soil 16S rRNA gene clones. Extremophiles (2011) 0.79
Development of bacterial community during spontaneous succession on spoil heaps after brown coal mining. FEMS Microbiol Ecol (2011) 0.78
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
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
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
Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A (2013) 5.03
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
Oxygen saturation and outcomes in preterm infants. N Engl J Med (2013) 4.96
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
p62 positive, TDP-43 negative, neuronal cytoplasmic and intranuclear inclusions in the cerebellum and hippocampus define the pathology of C9orf72-linked FTLD and MND/ALS. Acta Neuropathol (2011) 3.73
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
Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science (2013) 2.62
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics (2011) 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
The genetics and neuropathology of amyotrophic lateral sclerosis. Acta Neuropathol (2012) 2.25
Treatment of neonatal sepsis with intravenous immune globulin. N Engl J Med (2011) 2.22
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
An MND/ALS phenotype associated with C9orf72 repeat expansion: abundant p62-positive, TDP-43-negative inclusions in cerebral cortex, hippocampus and cerebellum but without associated cognitive decline. Neuropathology (2011) 2.16
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics (2011) 2.15
A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series. Brain (2008) 2.13
Clinical and neuroanatomical signatures of tissue pathology in frontotemporal lobar degeneration. Brain (2011) 2.13
Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05