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An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

Journal Article · · The ISME Journal
 [1];  [2];  [3];  [4];  [5];  [6];  [6];  [7];  [8]
  1. Univ. of Colorado, Boulder, CO (United States). Dept. of Chemistry and Biochemistry. Biofrontiers Inst.; DOE/OSTI
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
  3. Univ. of Colorado, Boulder, CO (United States). Dept. of Chemistry and Biochemistry. Biofrontiers Inst.
  4. Howard Hughes Medical Inst., Ashburn, VA (United States). Janelia Farm Research Campus
  5. Second Genome Inc., San Bruno, CA (United States). Dept. of Bioinformatics
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Center for Environmental Biotechnology
  7. Univ. of Colorado, Boulder, CO (United States). Dept. of Chemistry and Biochemistry. Biofrontiers Inst.; Second Genome Inc., San Bruno, CA (United States). Dept. of Bioinformatics
  8. Australian Centre for Ecogenomics, St Lucia, QLD (Australia). Inst. for Molecular Bioscience. School of Chemistry and Molecular Biosciences
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Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1623754
Journal Information:
The ISME Journal, Journal Name: The ISME Journal Journal Issue: 3 Vol. 6; ISSN 1751-7362
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Temporal Development of Gut Microbiota in Triclocarban Exposed Pregnant and Neonatal Rats journal September 2016
Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics journal February 2017
Kenaf addition has mixed effects on process performance of sequencing batch reactors treating municipal wastewater journal January 2018
Grape seed proanthocyanidins influence gut microbiota and enteroendocrine secretions in female rats journal January 2018
Impact of anaerobic co-digestion between sewage sludge and carbon-rich organic waste on microbial community resilience journal January 2018
Fabrication of a soluble crosslinked corn bran arabinoxylan matrix supports a shift to butyrogenic gut bacteria journal January 2019
Exploiting the real wastewater potential for resource recovery – n -caproate production from acid whey journal January 2018
How do zinc oxide and zero valent iron nanoparticles impact the occurrence of antibiotic resistance genes in landfill leachate? journal January 2019
Protective effect of Bacillus amyloliquefaciens against Salmonella via polarizing macrophages to M1 phenotype directly and to M2 depended on microbiota journal January 2019
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe journal August 2015
Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice journal May 2016
Human and rat gut microbiome composition is maintained following sleep restriction journal February 2017
Caterpillars lack a resident gut microbiome journal August 2017
Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO 2 fixation pathway journal November 2017
Effects of heavy metals on soil microbial community structure and diversity in the rice ( Oryza sativa L. subsp. Japonica, Food Crops Institute of Jiangsu Academy of Agricultural Sciences) rhizosphere journal November 2016
Sphingomonas : from diversity and genomics to functional role in environmental remediation and plant growth journal January 2020
Mucosa-associated microbiota dysbiosis in colitis associated cancer journal October 2017
The ‘ in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice journal June 2019
The lung mycobiome in the next-generation sequencing era journal September 2016
KASpOD—a web service for highly specific and explorative oligonucleotide design journal October 2012
Differences in Clinical Course, Genetics, and the Microbiome Between Familial and Sporadic Inflammatory Bowel Diseases journal November 2017
Microbial diversity in European alpine permafrost and active layers journal January 2016
Changes in the community structure of free-living heterotrophic bacteria in the open tropical Pacific Ocean in response to microalgal lysate-derived dissolved organic matter journal May 2016
Trophic state and geographic gradients influence planktonic cyanobacterial diversity and distribution in New Zealand lakes journal November 2016
Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation–climate gradient journal April 2017
A comparison of prokaryotic symbiont communities in nonnative and native ascidians from reef and harbor habitats journal July 2018
Bacterial community structure and succession in nests of two megachilid bee genera journal October 2018
Bacterial colonization and antimicrobial resistance genes in neonatal enteral feeding tubes journal March 2019
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments journal May 2018
Identification and evaluation of the microbiome in the female and male reproductive tracts journal May 2018
In Silico and Experimental Evaluation of Primer Sets for Species-Level Resolution of the Vaginal Microbiota Using 16S Ribosomal RNA Gene Sequencing journal August 2018
Responses in the rumen microbiome of Bos taurus and indicus steers fed a low-quality rice straw diet and supplemented protein journal March 2018
Effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions, and rumen microbiota in beef heifers1 journal August 2018
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks journal November 2013
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes journal March 2018
Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises journal October 2018
Agarwood wound locations provide insight into the association between fungal diversity and volatile compounds in Aquilaria sinensis journal July 2019
Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally journal November 2014
The ecology of microscopic life in household dust journal September 2015
Temperature-gradient incubation isolates multiple competitive species from a single environmental sample journal March 2020
Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov. journal July 2016
Using MinION ™ to characterize dog skin microbiota through full-length 16S rRNA gene sequencing approach posted_content July 2017
Natural infection with Giardia is associated with altered community structure of the human and canine gut microbiome posted_content January 2020
The urinary microbiome associated with bladder cancer journal November 2017
Taxonomic identification from metagenomic and metabarcoding data using any genetic marker journal January 2018
Diet Modifies Colonic Microbiota and CD4 + T Cell Repertoire to Trigger Flares in a Novel Model of Colitis Induced by IL-23 posted_content January 2018
Altered Fecal Microbiota and Urine Metabolome as Signatures of Soman Poisoning posted_content January 2018
Genetic determinants of gut microbiota composition and bile acid profiles in mice journal January 2019
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms posted_content January 2019
Amplification of the V5 – V8 region of the 16S rRNA gene effectively speciates medically important genital tract Lactobacillus species in the upper female genital tract posted_content January 2019
Impact of Candida auris infection in a neutropenic murine model journal January 2019
A Fast and Memory-Efficient Implementation of the Transfer Bootstrap posted_content January 2019
Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets posted_content March 2020
Pollen-feeding Heliconius butterflies host distinctive adult-stage microbiomes posted_content January 2019
Obligate intracellular bacteria diversity in unfed Leptotrombidium scutellare larvae highlights novel bacterial endosymbionts of mites journal October 2019
Smooth brome invasion increases rare soil bacterial species prevalence, bacterial species richness and evenness journal January 2015
Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3 : Chitinolytic bacterium from the candidate phylum TG3 journal October 2013
Life with compass: diversity and biogeography of magnetotactic bacteria: Magnetotactic bacterial diversity and biogeography journal November 2013
The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey: Microbial community of syntrophic enrichment cultures journal October 2014
Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems: Microbial connectivity and landform structure journal October 2015
Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes: Salmon decomposition and insect microbiomes journal February 2016
Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance's perspective journal June 2017
Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids: Microbial genomics at axial seamount journal December 2017
Field study reveals core plant microbiota and relative importance of their drivers: Core microbiota of field-grown sugarcane and their drivers journal January 2018
Novel bacterial lineages associated with boreal moss species journal July 2018
Temporal and spatial dynamics in microbial community composition within a temperate stream network: Microbial community assembly in streams journal September 2018
Survival in hostile territory: the microbiota of the stomach journal September 2013
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms journal September 2013
Black soldier fly larvae ( Hermetia illucens ) strengthen the metabolic function of food waste biodegradation by gut microbiome journal March 2019
Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing ‘ phyloh ’ as a novel phylogenetic diversity analysis tool journal November 2014
Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types journal February 2018
Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors: Plant-bacteria response to N pollution journal August 2014
Host relatedness influences the composition of aphid microbiomes journal October 2019
Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome journal May 2018
Microbiome changes associated with sustained eradication of Clostridium difficile after single faecal microbiota transplantation in children with and without inflammatory bowel disease journal July 2015
Effects on survival and bacterial community composition of the aquaculture water and gastrointestinal tract of shrimp ( Litopenaeus vannamei ) exposed to probiotic treatments after an induced infection of acute hepatopancreatic necrosis disease: XXXX journal August 2018
Impact of dietary deviation on disease progression and gut microbiome composition in lupus-prone SNF 1 mice: Lupus, diet and gut microbiota journal July 2015
Systemic proinflammation after Mycobacterium tuberculosis infection was correlated to the gut microbiome in HIV‐uninfected humans journal March 2019
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria journal April 2014
Microbial ecosystems are dominated by specialist taxa journal August 2015
Differences in the equine faecal microbiota between horses presenting to a tertiary referral hospital for colic compared with an elective surgical procedure journal September 2018
Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico journal April 2018
Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study journal April 2014
Identifying the microbial taxa that consistently respond to soil warming across time and space journal November 2016
Novel microbial community composition and carbon biogeochemistry emerge over time following saltwater intrusion in wetlands journal December 2018
Nitrate addition stimulates microbial decomposition of organic matter in salt marsh sediments journal July 2019
Potential feedback mediated by soil microbiome response to warming in a glacier forefield journal December 2019
High diversity and variability in the bacterial microbiota of the coffee berry borer ( Coleoptera : Curculionidae), with emphasis on Wolbachia journal May 2018
Exploring oyster mushroom ( Pleurotus ostreatus ) substrate preparation by varying phase I composting time: changes in bacterial communities and physicochemical composition of biomass impacting mushroom yields journal December 2018
Flavin monooxygenase 3, the host hepatic enzyme in the metaorganismal trimethylamine N-oxide-generating pathway, modulates platelet responsiveness and thrombosis risk journal August 2018
Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee journal April 2016
Microbiome changes through ontogeny of a tick pathogen vector journal September 2016
Wolbachia infection alters the relative abundance of resident bacteria in adult Aedes aegypti mosquitoes, but not larvae journal December 2017
Biodiversity-function relationships in methanogenic communities journal November 2018
Antibiotic disturbance affects aquatic microbial community composition and food web interactions but not community resilience journal March 2019
Towards the unification of sequence-based classification and sequence-based identification of host-associated microorganisms journal November 2014
Dynamics of the oral microbiota as a tool to estimate time since death journal August 2017
The skin microbiome in allergen‐induced canine atopic dermatitis journal August 2016
Novel association of Psychrobacter and Pseudomonas with malodour in bloodhound dogs, and the effects of a topical product composed of essential oils and plant-derived essential fatty acids in a randomized, blinded, placebo-controlled study journal September 2018
Physiological Regulation of Drug Metabolism and Transport: Pregnancy, Microbiome, Inflammation, Infection, and Fasting journal March 2018
Variable effects of local management on coral defenses against a thermally regulated bleaching pathogen journal October 2019
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States journal October 2013
Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy journal November 2015
The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients journal January 2018
Host mitochondria influence gut microbiome diversity: A role for ROS journal July 2019
Antibiotics, birth mode, and diet shape microbiome maturation during early life journal June 2016
Metatranscriptomic Evidence for Magnetite Nanoparticle-Stimulated Acetoclastic Methanogenesis under Continuous Agitation journal September 2019
Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom journal May 2018
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3) journal March 2017
The Microbiome of the Red Sea Coral Stylophora pistillata Is Dominated by Tissue-Associated Endozoicomonas Bacteria journal May 2013
Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants journal September 2013
Metagenomic Analyses of Drinking Water Receiving Different Disinfection Treatments journal June 2012
Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes journal October 2019
Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera journal September 2014
“Bowel on the Bench”: Proof of Concept of a Three-Stage, In Vitro Fermentation Model of the Equine Large Intestine journal December 2019
Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment journal November 2015
Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen journal August 2015
From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation journal November 2015
Cell Size Distributions of Soil Bacterial and Archaeal Taxa journal September 2013
Intraspecific Variation in Microbial Symbiont Communities of the Sun Sponge, Hymeniacidon heliophila, from Intertidal and Subtidal Habitats journal November 2015
Microbiome Changes during Tuberculosis and Antituberculous Therapy journal October 2016
Open-Source Sequence Clustering Methods Improve the State Of the Art journal February 2016
The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations journal July 2015
Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption journal May 2015
The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility journal August 2016
Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations journal May 2014
Ecological Analyses of Mycobacteria in Showerhead Biofilms and Their Relevance to Human Health journal November 2018
Prokaryotic Community Structure of Long-Term Fertilization Field Andisols in Central Japan journal January 2019
Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions journal February 2017
The Skin Microbiome of Cohabiting Couples journal July 2017
Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk journal August 2020
Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem journal March 2017
Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem journal February 2019
Using Core Genome Alignments To Assign Bacterial Species journal December 2018
Faecal microbiota study reveals specific dysbiosis in spondyloarthritis journal June 2017
Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention journal July 2017
Effects of bowel cleansing on the intestinal microbiota journal December 2014
Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus journal May 2018
Antibiotics-induced monodominance of a novel gut bacterial order journal January 2019
Lactobacillus iners -dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study journal September 2017
Dietary bovine milk exosomes elicit changes in bacterial communities in C57BL/6 mice journal November 2019
Early gradual feeding with bovine colostrum improves gut function and NEC resistance relative to infant formula in preterm pigs journal September 2015
Associations between the gut microbiota and host responses to high altitude journal December 2018
Treatment with a Monoclonal Anti-IL-12p40 Antibody Induces Substantial Gut Microbiota Changes in an Experimental Colitis Model journal January 2016
Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera) journal January 2018
The Association of Gut Microbiota with Nonalcoholic Steatohepatitis in Thais journal January 2018
Characterization of Microbiota in Endometrial Fluid and Vaginal Secretions in Infertile Women with Repeated Implantation Failure journal May 2019
Intervention with α -Ketoglutarate Ameliorates Colitis-Related Colorectal Carcinoma via Modulation of the Gut Microbiome journal June 2019
Dietary Changes Involving Bifidobacterium longum and Other Nutrients Delays Chronic Kidney Disease Progression journal January 2018
Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12 journal February 2018
Processing faecal samples: a step forward for standards in microbial community analysis journal May 2014
Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis journal November 2012
Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia journal January 2014
EMPeror: a tool for visualizing high-throughput microbial community data journal November 2013
Phylogenetic convolutional neural networks in metagenomics journal March 2018
SAMSA2: a standalone metatranscriptome analysis pipeline journal May 2018
Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data journal September 2019
Joining Illumina paired-end reads for classifying phylogenetic marker sequences journal March 2020
ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins journal November 2016
SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? journal March 2017
Comparative genomics of Bacteria commonly identified in the built environment journal January 2019
Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction journal April 2020
Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile journal January 2016
Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak journal November 2016
Comparison of rumen bacterial communities in dairy herds of different production journal August 2017
Reliability of a participant-friendly fecal collection method for microbiome analyses: a step towards large sample size investigation journal September 2018
Laboratory contamination in airway microbiome studies journal August 2019
Deficiency of Gankyrin in the small intestine is associated with augmented colitis accompanied by altered bacterial composition of intestinal microbiota journal January 2020
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease journal April 2015
Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort journal April 2017
Lessons learned from the microbial ecology resulting from different inoculation strategies for biogas production from waste products of the bioethanol/sugar industry journal July 2016
Upgrading syngas fermentation effluent using Clostridium kluyveri in a continuous fermentation journal March 2017
Enhancing methane production from lignocellulosic biomass by combined steam-explosion pretreatment and bioaugmentation with cellulolytic bacterium Caldicellulosiruptor bescii journal January 2018
Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics journal February 2018
Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas journal February 2017
Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep journal August 2017
The influence of in vitro pectin fermentation on the human fecal microbiome journal June 2018
Microbial shifts in the aging mouse gut journal December 2014
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection journal March 2015
Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data journal May 2015
Collection media and delayed freezing effects on microbial composition of human stool journal August 2015
Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities journal October 2015
Context and the human microbiome journal November 2015
Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut journal November 2015
Composition and dynamics of the respiratory tract microbiome in intubated patients journal February 2016
Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production journal April 2016
Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals journal July 2016
Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis journal March 2017
Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease journal May 2017
Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy journal July 2017
Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken journal August 2017
Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome journal August 2017
Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing journal October 2017
Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River journal January 2018
Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality journal January 2018
Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control journal February 2018
Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner journal July 2018
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men journal November 2018
Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month journal February 2019
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces journal April 2019
Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status journal April 2019
Maize synthesized benzoxazinoids affect the host associated microbiome journal April 2019
Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing journal June 2020
Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand journal December 2019
Bolus Weekly Vitamin D3 Supplementation Impacts Gut and Airway Microbiota in Adults With Cystic Fibrosis: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial journal November 2017
Gut Microbial Diversity in Women With Polycystic Ovary Syndrome Correlates With Hyperandrogenism journal January 2018
Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History journal November 2016
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets journal January 2013
Two dynamic regimes in the human gut microbiome journal February 2017
Genetic effects on the commensal microbiota in inflammatory bowel disease patients journal March 2019
CREST – Classification Resources for Environmental Sequence Tags journal November 2012
In-situ Effects of Eutrophication and Overfishing on Physiology and Bacterial Diversity of the Red Sea Coral Acropora hemprichii journal April 2013
Exploring the Sources of Bacterial Spoilers in Beefsteaks by Culture-Independent High-Throughput Sequencing journal July 2013
Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities journal September 2013
Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton journal January 2014
The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease journal January 2014
Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities journal May 2014
Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species journal June 2014
Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments journal July 2014
Maternal Obesity Is Associated with Alterations in the Gut Microbiome in Toddlers journal November 2014
Microbial Iron Mats at the Mid-Atlantic Ridge and Evidence that Zetaproteobacteria May Be Restricted to Iron-Oxidizing Marine Systems journal March 2015
Altered Microbiomes in Bovine Digital Dermatitis Lesions, and the Gut as a Pathogen Reservoir journal March 2015
The Source of the River as a Nursery for Microbial Diversity journal March 2015
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3) journal June 2015
Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches journal May 2015
Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth journal July 2015
Impact of Water Chemistry, Pipe Material and Stagnation on the Building Plumbing Microbiome journal October 2015
Intestinal Microbiota Is Influenced by Gender and Body Mass Index journal May 2016
Dysbiosis of the Fecal Microbiota in Cattle Infected with Mycobacterium avium subsp. paratuberculosis journal August 2016
Quantifying the Sensitivity of Soil Microbial Communities to Silver Sulfide Nanoparticles Using Metagenome Sequencing journal August 2016
Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer’s Patches journal October 2016
Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals journal December 2017
Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows journal March 2018
A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog journal March 2018
Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens journal August 2018
Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus) journal August 2018
Association between functional lactase variants and a high abundance of Bifidobacterium in the gut of healthy Japanese people journal October 2018
Summer shifts of bacterial communities associated with the invasive brown seaweed Sargassum muticum are location and tissue dependent journal December 2018
Evaluation of the bacterial ocular surface microbiome in clinically normal cats before and after treatment with topical erythromycin journal October 2019
Association between baseline abundance of Peptoniphilus, a Gram-positive anaerobic coccus, and wound healing outcomes of DFUs journal January 2020
A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects journal February 2014
Culture-Independent Analysis of Pediatric Bronchoalveolar Lavage Specimens journal September 2018
Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant journal November 2019
Intestinal Microbiota Protects against MCD Diet-Induced Steatohepatitis text January 2019
The necroptosis-inducing kinase RIPK3 dampens adipose tissue inflammation and glucose intolerance text January 2016
The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis posted_content April 2019
Stress Ulcer Prophylaxis versus Placebo - a Blinded Randomized Control Trial to Evaluate the Safety of Two Strategies in Critically Ill Infants with Congenital Heart Disease (SUPPRESS-CHD) journal June 2020
A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction journal June 2019
Marine Bacterial Diversity in Coastal Sichang Island, the Upper Gulf of Thailand, in 2011 Wet Season journal June 2019
Two distinct microbial communities revealed in the sponge Cinachyrella journal November 2014
Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania journal March 2015
Biosurfactant production from marine hydrocarbon-degrading consortia and pure bacterial strains using crude oil as carbon source journal April 2015
Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows journal July 2015
An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus journal October 2015
Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog journal October 2015
High-Up: A Remote Reservoir of Microbial Extremophiles in Central Andean Wetlands journal December 2015
Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes journal February 2016
Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium journal May 2016
Mississippi River Plume Enriches Microbial Diversity in the Northern Gulf of Mexico journal July 2016
Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method journal August 2016
Niche Filtering of Bacteria in Soil and Rock Habitats of the Colorado Plateau Desert, Utah, USA journal September 2016
Nutritional Models of Experimentally-Induced Subacute Ruminal Acidosis (SARA) Differ in Their Impact on Rumen and Hindgut Bacterial Communities in Dairy Cows journal January 2017
A New Approach to Modify Plant Microbiomes and Traits by Introducing Beneficial Bacteria at Flowering into Progeny Seeds journal January 2017
Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota journal February 2017
The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function journal March 2017
Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs journal July 2017
Antibiotic-Induced Alterations in Gut Microbiota Are Associated with Changes in Glucose Metabolism in Healthy Mice journal November 2017
Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs journal February 2018
Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny journal March 2018
Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility journal July 2018
Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC) journal August 2018
Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking journal October 2018
Role of Probiotics in Mycoplasma pneumoniae Pneumonia in Children: A Short-Term Pilot Project journal January 2019
Potential of Pectins to Beneficially Modulate the Gut Microbiota Depends on Their Structural Properties journal February 2019
Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Fusarium Communities and Their Interactions in Maize Stalks journal February 2019
Darkening of the Greenland Ice Sheet: Fungal Abundance and Diversity Are Associated With Algal Bloom journal March 2019
Long-Term Temperature Stress in the Coral Model Aiptasia Supports the “Anna Karenina Principle” for Bacterial Microbiomes journal May 2019
Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria journal June 2019
Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia journal July 2019
Cross-Regional View of Functional and Taxonomic Microbiota Composition in Obesity and Post-obesity Treatment Shows Country Specific Microbial Contribution journal October 2019
Rates and Microbial Players of Iron-Driven Anaerobic Oxidation of Methane in Methanic Marine Sediments journal January 2020
Effects of Nanoparticles on Plant Growth-Promoting Bacteria in Indian Agricultural Soil journal March 2019
Effect of Supplementing Hydrolysable Tannins to a Grower–Finisher Diet Containing Divergent PUFA Levels on Growth Performance, Boar Taint Levels in Back Fat and Intestinal Microbiota of Entire Males journal December 2019
Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients journal September 2019
Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques journal August 2015
A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice journal September 2018
A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model journal August 2018
Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet journal May 2019
High-throughput biodiversity analysis: Rapid assessment of species richness and ecological interactions of Chrysomelidae (Coleoptera) in the tropics journal June 2016
Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose? journal October 2017
Long Term Diversity and Distribution of Non-photosynthetic Cyanobacteria in Peri-Alpine Lakes text January 2019
Monitoring seasonal changes in winery-resident microbiota text January 2013
mockrobiota: a public resource for microbiome bioinformatics benchmarking text January 2016
Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber journal December 2014
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Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach text January 2013
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Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms posted_content January 2012
Microbial community responses determine how soil–atmosphere exchange of carbonyl sulfide, carbon monoxide, and nitric oxide responds to soil moisture journal January 2019
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Macrophage dysfunction initiates colitis during weaning of infant mice lacking the interleukin-10 receptor journal July 2017
Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature journal November 2018
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A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq journal January 2016
Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients journal January 2017
The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico journal January 2017
CoMiniGut—a small volume in vitro colon model for the screening of gut microbial fermentation processes journal January 2018
Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency journal January 2018
RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments journal January 2014
Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments journal January 2018
Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China journal January 2019
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking journal January 2015
Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens text January 2018

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54 ENVIRONMENTAL SCIENCES
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