Published in ISME J on November 13, 2008
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature (2011) 3.80
Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol (2013) 2.73
Microbial control over carbon cycling in soil. Front Microbiol (2012) 2.24
House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A (2013) 1.88
The plant microbiome. Genome Biol (2013) 1.77
Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol (2015) 1.74
Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol (2011) 1.65
Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med (2016) 1.52
Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One (2010) 1.38
PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol (2011) 1.32
Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One (2010) 1.24
Unraveling the plant microbiome: looking back and future perspectives. Front Microbiol (2014) 1.23
Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J (2011) 1.23
Soil microbial community successional patterns during forest ecosystem restoration. Appl Environ Microbiol (2011) 1.05
The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. ISME J (2011) 1.01
Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture. Sci Rep (2015) 0.99
Gut microbiota composition and relapse risk in pediatric MS: A pilot study. J Neurol Sci (2016) 0.96
Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil. Front Microbiol (2015) 0.95
Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS One (2013) 0.95
Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth. PLoS One (2015) 0.93
Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants (2015) 0.92
Temporal variation overshadows the response of leaf litter microbial communities to simulated global change. ISME J (2015) 0.91
Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties. ISME J (2012) 0.90
The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia. PLoS One (2013) 0.90
Plant root-microbe communication in shaping root microbiomes. Plant Mol Biol (2016) 0.89
Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil. Microb Biotechnol (2012) 0.89
Deciphering microbial landscapes of fish eggs to mitigate emerging diseases. ISME J (2014) 0.88
Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS One (2014) 0.88
Role of root microbiota in plant productivity. J Exp Bot (2015) 0.88
Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities. Microb Ecol (2014) 0.87
Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities. Appl Environ Microbiol (2012) 0.85
Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol (2015) 0.84
Diversity of nirK denitrifying genes and transcripts in an agricultural soil. Appl Environ Microbiol (2009) 0.83
The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol (2016) 0.83
Interactions between Bacillus anthracis and plants may promote anthrax transmission. PLoS Negl Trop Dis (2014) 0.82
pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui (Colossoma macropomum). Sci Rep (2016) 0.81
Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes. Microb Ecol (2015) 0.80
Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme. PLoS One (2014) 0.80
Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Sci Rep (2016) 0.80
Reanalysis and simulation suggest a phylogenetic microarray does not accurately profile microbial communities. PLoS One (2012) 0.79
Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site. Environ Sci Technol (2011) 0.79
Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System. Front Plant Sci (2016) 0.79
Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil. Front Microbiol (2016) 0.78
Development of a standardized approach for environmental microbiota investigations related to asthma development in children. J Microbiol Methods (2012) 0.78
Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling. Sci Rep (2015) 0.78
Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons. MBio (2015) 0.78
Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility. Antonie Van Leeuwenhoek (2015) 0.77
Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments. Int J Mol Sci (2016) 0.77
Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions. Microb Ecol (2014) 0.77
Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome (2017) 0.76
Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem. Appl Environ Microbiol (2016) 0.75
Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates. BMC Microbiol (2016) 0.75
Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing. Front Plant Sci (2016) 0.75
Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization. Front Microbiol (2016) 0.75
Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity. Sci Rep (2016) 0.75
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure. Microb Ecol (2016) 0.75
Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell (2009) 20.29
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
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
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res (2008) 9.09
Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science (2010) 6.73
Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science (2011) 5.89
High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol (2002) 4.95
High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol (2007) 4.81
Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci U S A (2006) 4.62
The role of ecological theory in microbial ecology. Nat Rev Microbiol (2007) 4.50
Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol (2010) 4.38
Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol (2006) 4.09
Development of a high-volume aerosol collection system for the identification of air-borne micro-organisms. Lett Appl Microbiol (2002) 4.02
Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet (2012) 3.46
Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiol Lett (2005) 3.42
Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One (2010) 3.38
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci U S A (2005) 2.85
Chronic kidney disease alters intestinal microbial flora. Kidney Int (2012) 2.58
Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol (2010) 2.55
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio (2010) 2.53
Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J (2009) 2.44
A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS (2010) 2.42
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol (2010) 2.41
Cell-cell signaling controls Xylella fastidiosa interactions with both insects and plants. Proc Natl Acad Sci U S A (2004) 2.31
Methods for measuring denitrification: diverse approaches to a difficult problem. Ecol Appl (2006) 2.29
Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol (2006) 2.24
Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol (2006) 2.08
Man's best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol (2010) 2.06
Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl Environ Microbiol (2003) 2.01
Environmental genomics reveals a single-species ecosystem deep within Earth. Science (2008) 1.98
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J (2013) 1.98
Long-term sustainability of a high-energy, low-diversity crustal biome. Science (2006) 1.97
Use of a green fluorescent strain for analysis of Xylella fastidiosa colonization of Vitis vinifera. Appl Environ Microbiol (2003) 1.96
Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities. Oecologia (2003) 1.91
Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. Proc Natl Acad Sci U S A (2012) 1.88
Environmental microarray analyses of Antarctic soil microbial communities. ISME J (2008) 1.84
Genome plasticity in Yersinia pestis. Microbiology (2002) 1.66
Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol (2011) 1.65
Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J (2009) 1.58
Structure of the human gastric bacterial community in relation to Helicobacter pylori status. ISME J (2010) 1.58
Quorum sensing regulates exopolysaccharide production, motility, and virulence in Pseudomonas syringae. Mol Plant Microbe Interact (2005) 1.55
Supervised classification of microbiota mitigates mislabeling errors. ISME J (2010) 1.54
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting. ISME J (2013) 1.53
Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests. Ecology (2011) 1.51
Microbial communities acclimate to recurring changes in soil redox potential status. Environ Microbiol (2010) 1.51
A cell-cell signaling sensor is required for virulence and insect transmission of Xylella fastidiosa. Proc Natl Acad Sci U S A (2008) 1.50
Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J Bacteriol (2005) 1.49
A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. ISME J (2008) 1.48
Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing. Appl Environ Microbiol (2009) 1.41
Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico. Environ Sci Technol (2013) 1.38
Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One (2010) 1.38
Pyrosequencing analysis of bacterial biofilm communities in water meters of a drinking water distribution system. Appl Environ Microbiol (2010) 1.35
Animal-to-animal variation in fecal microbial diversity among beef cattle. Appl Environ Microbiol (2010) 1.33
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. BMC Bioinformatics (2007) 1.33
PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol (2011) 1.32
Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill. PLoS One (2012) 1.32
Effects of selected root exudate components on soil bacterial communities. FEMS Microbiol Ecol (2011) 1.31
Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res (2010) 1.31
Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. Appl Environ Microbiol (2008) 1.31
Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One (2010) 1.24
Utilization of the plant hormone indole-3-acetic acid for growth by Pseudomonas putida strain 1290. Appl Environ Microbiol (2005) 1.24
Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences. FEMS Microbiol Lett (2002) 1.24
Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol Plant Microbe Interact (2004) 1.21
Quorum size of Pseudomonas syringae is small and dictated by water availability on the leaf surface. Proc Natl Acad Sci U S A (2008) 1.21
The "most wanted" taxa from the human microbiome for whole genome sequencing. PLoS One (2012) 1.21
Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree. Appl Environ Microbiol (2011) 1.20
Pseudomonas syringae genes induced during colonization of leaf surfaces. Environ Microbiol (2005) 1.20
Gut microbiota in multiple sclerosis: possible influence of immunomodulators. J Investig Med (2015) 1.18
Regulation of AHL production and its contribution to epiphytic fitness in Pseudomonas syringae. Mol Plant Microbe Interact (2004) 1.16