The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
2012/11/27 by Christian Quast, Elmar Pruesse, Pelin Yilmaz +5 · 365 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology #RNA modifications and cancer
paper · pdf · doi:10.1093/nar/gks1219
Abstract
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Cited by
- Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland
- Obstructive sleep apnea and primary snoring in children are associated with oropharyngeal dysbiosis and a mild compositional imbalance in the gastrointestinal tract
- Endemic within endemics: the microbiota of the Galapagos marine iguanas
- The marine microbiome can accurately predict its chemical and biological environment
- Conventional and biodegradable microplastics elicit contrasting taxon-level responses in rhizosphere microbiomes of maize and strawberry
- Gut microbiome of New Zealand abalone ( <i>Haliotis iris</i> ): a Chatham Islands case study
- An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection
- Diet and gut microbiome of skipjack tuna (Katsuwonus pelamis) as indicators of environmental changes
- Lateral Coastal Blue Carbon Export Fuels a Deep‐Ocean Carbon Sink in an Oligotrophic Warm Pool
- <i>Desulfatiglans-</i> related bacteria associated with conductive mineral particles in marine subsurface sediments
- Planting food forests can increase soil biodiversity in agricultural landscapes of Northwest Europe
- Intestinal epithelial TLR5 signaling promotes barrier-supportive macrophages
- Functional Stability and the Limits of <scp>16S</scp> ‐Based Inference in Serpentine Biocrusts
- Sulfoquinovose degradation by cow rumen microbiota
- Association between the gut microbiome and neurodevelopmental outcomes in infants with congenital heart disease: A prospective cohort study
- Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
- Repetition and order of exposure to salinization and nutrient enrichment drive freshwater microbial community responses
- Shifts and rebound in microbial community function following repeated introduction of a novel species
- Increased Transmission of Antibiotic Resistance Occurs in a Soil Food Chain under Pesticide Stress
- A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity
- Gut microbial diversity and inferred capacity to produce short-chain fatty acids are associated with acute stress reactivity in healthy adults
- Soil Microbial Diversity and Network Organization Respond to Land Use and Agricultural Inputs Worldwide
- AliFilter: a machine learning approach to alignment filtering
- Protist-dominated hard substrate faunas thrive at the deepest ocean depths
- Impact of changed c-di-AMP levels and hypoosmotic stress on the transcriptome of <i>Haloferax volcanii</i> and on RCK domain-containing proteins
- Temporal transcriptional rhythms govern coral-symbiont function and microbiome dynamics
- Urea use drives niche separation between dominant marine ammonia oxidizing archaea
- Segmented filamentous bacteria are worldwide human gut commensals
- Ontogenetic variation in the gut microbiota of <i>Kyphosus sydneyanus</i> : a comparative analysis
- Limited microbial community responses of marine macroalgae to artificial light at night and moderate warming conditions
- Microbiome Composition in a Common Mediterranean Bryozoan Following an Unprecedented Marine Heatwave
- Functional redundancy enables emergent metabolic dynamics in marine microbiomes
- Effects of parental care on skin microbial community composition in poison frogs
- The genetic basis of microbiome recruitment in grapevine and its association with fermentative and pathogenic taxa
- Soil functions are shaped by aridity through soil properties and the microbial community structure
- Cross Sequencing Integration of Compositional Microbiome Data in Cancer
- Acute exposure to high-fat diet impairs ILC3 functions and gut homeostasis
- Dual nomenclature in organic-walled dinoflagellate cysts I: concepts, methods and applications
- Bacterial inoculation elicits changes to the coral epigenome
- Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance
- Bacillus amyloliquefaciens FG14 as a potential biocontrol strain against rusty root rot of Panax ginseng, and its impact on the rhizosphere microbial community
- Effects of different disinfectants on bacterial reduction and microbial diversity of contact surfaces during beef production
- Seasonal and spatial transitions in phytoplankton assemblages spanning estuarine to open ocean waters of the tropical Pacific
- Gut microbiome and body composition with sorbitol intake during early lifespan
- Groundcovers Alter Vineyard Soil Microbiomes Within and Beyond Their Rooting Zones
- Diatoms (Bacillariophyta) of the Salish Sea, Northeast Pacific: annotated checklist and new species reports
- A 16S rRNA amplicon dataset of Las Tablas de Daimiel National Park, Spain
- FERONIA Kinase-Interacting Cell Wall Sensors LRX1/2 Regulate the Plant Rhizosphere Microbiome
- Sediment microbial communities in long‐term wetland restorations within the Prairie Pothole Region of the United States
- Herbivore Dung inputs mainly drive copiotrophic bacterial contributions to soil nutrient pool turnover in alpine grasslands
- Exploring the lichenization continuum through the marine tripartite symbiosis of <i>Collemopsidium pelvetiae</i>
- Dissolved Organic Carbon Shapes Sediment Bacterial Diversity in Continental Lakes
- Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., halophilic archaea from a coastal saline-alkali land and two saline lakes
- A defined microbial community reproduces attributes of fine flavour chocolate fermentation
- A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on Hyphomicrobiales dark matter
- Legacy Effects of Cropping System and Precipitation Influence the Core <i>Camelina sativa</i> Microbiome
- Community of arbuscular mycorrhizal fungi in a broad-leaved forest in the Fukiage Garden of the Imperial Palace, Tokyo Japan
- Shifts and critical periods in coral metabolism reveal energetic vulnerability during development
- Potential relationship between clinical symptoms and the root canal microbiomes of root filled teeth based on the next‐generation sequencing
- Removal of organic biomass in Eucalyptus plantations has a greater impact on fungal than on bacterial networks
- Blurred Lines Between Determinism and Stochasticity in an Amphibian Phylosymbiosis Under Pathogen Infection
- Evolution of Wolbachia male-killing mechanism within a host species
- Revealing Elasmobranch Distributions in Turbid Coastal Waters: Insights From Environmental <scp>DNA</scp> and Particle Tracking
- Metabolic complexities and heterogeneity in quorum sensing signaling molecules in bacteria isolated from black band disease in a Caribbean coral
- Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function
- The immunotranscriptome of the Caribbean reef-building coral Pseudodiploria strigosa
- Morphological and taxonomic diversity of mesozooplankton is an important driver of carbon export fluxes in the ocean
- A Conserved Ribosomal Protein Has Entirely Dissimilar Structures in Different Organisms
- Environmental Drivers on Blue Tit Nest Microbiome: An Experimental Study
- Toll-like receptor 5 protects against murine lung fibrosis through reduced dysbiosis, and <i>TLR5</i> deficiency is associated with human IPF
- DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification
- Microbial growth rates captured using Raman-SIP reveal a highly active subsurface biosphere fueled by serpentinization
- <i>RBL1</i> Shapes Phyllosphere Microbial Structure to Enhance Disease Resistance in Rice
- The impact of short‐term flooding on soil microbial communities, soil nitrogen and maize productivity in clay loam soils of Ohio, United States
- Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization
- Mucospheres produced by a mixotrophic protist impact ocean carbon cycling
- Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes
- Bacterial Composition of <i>Meloidogyne exigua</i> Egg Masses from Symptomatic and Asymptomatic Coffee Plants
- Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics
- Nutrient competition predicts gut microbiome restructuring under drug perturbations
- Pollutant biodegradation profile mediated by multi-trophic microbial dynamics in rivers
- Nitrification potential and ammonia-oxidizing archaeal diversity in three contrasting acidic soils of eastern China
- Microbial community response to temperature in microcosm incubations and their associated changes in branched glycerol dialkyl glycerol tetraether distribution
- Profiling the eukaryotic diversity over a year in a lake ecosystem through short- and long-read metabarcoding
- Field dynamics of the root endosphere microbiome assembly in paddy rice cultivated under no fertilizer input
- Sex-Biased Gene Expression Under Sexually Antagonistic and Sex-Limited Selection
- Nontuberculous mycobacteria remodel lung microbiota in cystic fibrosis-associated respiratory infections
- Sulfur-rich deposits associated with the deep submarine volcano Fani Maoré support broad microbial sulfur cycling communities
- Phosphorus-transforming microbes enhance phosphatase catalytic efficiency to alleviate phosphorus limitation under nitrogen and phosphorus additions in subtropical forest soil
- Connectivity and Adaptation Patterns of the Deep-Sea Ground-Forming Sponge <i>Geodia hentscheli</i> Across Its Entire Distribution
- Novel cross-feeding human gut microbes metabolizing tryptophan to indole-3-propionate
- Fish are poor sentinels for surveillance of riverine antimicrobial resistance
- Sex-related gut microbiota in three geographically separated Norway lobster ( <i>Nephrops norvegicus</i> ) populations
- Polyethylene mulching film degrading bacteria within the plastisphere: Co-culture of plastic degrading strains screened by bacterial community succession
- Methanotrophic flexibility of ‘ <i>Ca</i> . Methanoperedens’ and its interactions with sulfate-reducing bacteria in the sediment of meromictic Lake Cadagno
- The putative immune recognition repertoire of the model cnidarian Hydractinia symbiolongicarpus is large and diverse
- Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection
- Seasonality drives temporal niche partitioning of pelagic prokaryotes
- Patterns of microbial diversity in three aquatic ecosystems of a Caribbean island
- Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton
- Circulatory dietary and gut-derived metabolites predict early cognitive decline
- Elevated microbial network complexity and enriched methanogens contribute to higher methanogenic potential in hollows than in hummocks in alpine meadows
- Genomic insights into the functional and metabolic versatility of gut microbiome Anaerostipes species
- Guidance and best practices for species identification using eDNA metabarcoding – When do you call a cod a cod?
- Nitrification CouplesMicrobial CO2 Fixationto Warming and Drought Responses in Alpine Grassland Soils
- An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut
- Leucogemmata humicola gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadota isolated from soil
- Carbon monoxide oxidizers in soils of different ages from Piton de la Fournaise volcano
- MitoNGS: an online platform to analyze fish metabarcoding data in high resolution
- Caldifarcimen microaerophilum gen. nov., sp. nov., a facultatively anaerobic, thermophilic bacterium of a novel bacterial phylum, Caldifarciminota phyl. nov., formerly called candidate phylum WOR-3, description of Caldifarciminaceae fam. nov., Caldifarciminales ord. nov. and Caldifarciminia classis nov.
- Greengenes2 unifies microbial data in a single reference tree
- Cycles of contamination and recovery: Combined sewer overflows drive acute but transient antimicrobial resistance exposure in an urban stream
- Multi-host and multi-taxon experiment reveals the overlooked importance of small-sized carrion for biodiversity
- The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly
- Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing
- Incorporating mitogenome sequencing into integrative taxonomy: The multidisciplinary redescription of the ciliate Thuricola similis (Peritrichia, Vaginicolidae) provides new insights into the evolutionary relationships among Oligohymenophorea subclasses
- 25 years of serving the community with ribosomal RNA gene reference databases and tools
- Rapid detection of RNase‐based self‐incompatibility in <i>Lysimachia monelli</i> (Primulaceae)
- Design, delivery and evaluation of a bioinformatics education workshop for 13-16-year-olds
- Next-Generation Sequencing Technology: Current Trends and Advancements
- A Comparative Analysis of <scp>DNA</scp> Metabarcoding and Morphological Identification in Diatoms Reveals Similar Patterns of Environmental Response
- Experimental evidence for the absence of a functional gut microbiome in the solitary bee <i>Megachile tosticauda</i>
- Traditional fermented foods of Indonesia harbour functionally redundant but phylogenetically diverse taxa
- Monitoring Cross-Border Dissemination of Antimicrobial Resistance (AMR) via Air Travel to Saudi Arabia: Formulation of Monitoring Strategies to Mitigate AMR Concerns
- Frozen in time: using museomics to investigate the gut bacteriome of fish from the <scp>Gulf</scp> of <scp>Carpentaria</scp>
- Efficient methane removal by thermophilic methanotrophs in a compost biofilter
- Metabolic capacities of large “pillotinaceous” spirochetes from termite guts and their placement among Breznakiellaceae
- Acidithiobacillus sibiricus sp. nov., a novel extremely acidophilic sulfur-oxidizing bacterium isolated from a magmatic sulfide-rich ore deposit
- Investigating the potential for redox-active organic matter reduction in high elevation wetlands of the Colorado Rocky Mountains, USA
- Microbial network stability, not diversity, drives colonization resistance against Borrelia afzelii in Ixodes ricinus ticks
- Pushing the upper temperature limit of methanotrophy in continental hydrothermal ecosystems, active biological methane oxidation in hot springs of Yellowstone National Park
- Desulfurivibrio nitratireducens sp. nov. and Desulfurivibrio modestus sp. nov., two novel alkaliphilic anaerobes isolated from terrestrial mud volcanoes
- Cultivation in a Natural Microbial Community Enhances the Industrial Performance of a Genetically Engineered Cyanobacterium for Bioplastic Production
- Microbial nitrogen removal and recycling in the redox transition zone of a meromictic lake and its coupling to sulfur cycling
- Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments
- Percent‐Level Copper Mineralisation Promoted by Copper‐Tolerant Iron‐Oxidising Bacteria in Circumneutral Mine Drainage
- Prokaryotic communities as proxies for eukaryotic soil beta diversity in forest ecosystems
- Impact of rising temperatures on the bacterial communities of <i>Aphaenogaster</i> ants
- Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities
- Forest conversion in subtropical ecosystems reduces soil microbial phosphorus potential
- Plant defense metabolite detoxification by a pathogenic fungus opens necrotic tissue to diverse bacteria in <i>Arabidopsis thaliana</i>
- Patterns, Processes, and Predictions: Soil bacteria unique habitats along a megametre transect in Eastern Australia
- Larval density drives thermogenesis and affects microbiota and substrate properties in black soldier fly trials
- <i>Endogonales</i> fungi associated with understory herbaceous plants in Japanese temperate forests
- The neuroactive potential of the human gut microbiota in quality of life and depression
- Transcriptomic evidence of cytokine storm and sepsis in little brown bats exposed to white-nose syndrome
- Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane seep <i>Sericosura</i>
- Microbial starch degradation in arid soil: Community dynamics, environmental influences, and archaeological implications
- Characterization of transcriptional and metabolic responses to a complex plant growth‐promoting soil inoculum
- Next Generation Sequencing Improves Diagnostic 16<scp>S</scp> r<scp>RNA</scp> Amplicon‐Based Microbiota Analyses of Clinical Samples Compared to Sanger Sequencing
- Gut microbiome communities demonstrate fine-scale spatial variation in a closed, island bird population
- Co-occurrence network and predicted functions of bacterial community in soil from Brazilian Cerrado under distinct types of vegetation cover
- Does the host matter? Testing the impact of host identity on the microbiome of a trematode parasite
- GTP before ATP: The energy currency at the origin of genes
- Cover crop monocultures and mixtures enhance bacterial abundance and functionality in the maize root zone
- Fluorescence in situ hybridization, a complementary molecular tool for the clinical diagnosis of infectious diseases by intracellular and fastidious bacteria
- Effects of Soluble Electron Shuttles on Microbial Iron Reduction and Methanogenesis
- Reverse microdialysis of sucrose stimulates soil fungal and bacterial growth at the microscale
- Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France)
- Mung bean seed coat extract modulates gut microbiota and inflammatory markers in high-fat fed rats
- Microbial scents: Soil microbial Volatile Organic Compounds (mVOCs) as biomarkers for grasslands across a land use gradient
- The effect of seed bacterization with Bacillus paralicheniformis 2R5 on bacterial and fungal communities in the canola rhizosphere
- Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer
- Deciphering the interaction of bacteria inoculants with the recipient endophytic community in grapevine micropropagated plants
- Parasitoid venom alters the lipid composition and development of microorganisms on the wax moth cuticle
- Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts
- Fur microbiome as a putative source of symbiotic bacteria in sucking lice
- RiboSnake – a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis
- Microbial Community Structure in Soilless Substrates Used for Nursery Crops
- Illegal dumping of oil and gas wastewater alters arid soil microbial communities
- Global mesozooplankton communities show lower connectivity in deep oceanic layers
- Core Microbiota Drives Host-Specific Growth Enhancement: Evidence in a Harmful Algal Bloom Causing Dinoflagellate <i>Prorocentrum lima</i>
- Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular anaerobic digestion sludges
- Emergence of community behaviors in the gut microbiota upon drug treatment
- The Oral Microbiota May Have Influence on Oral Cancer
- Mechanisms of carbon sequestration via interactions between dissolved organic matter (DOM) and bacteria during floating-leaf macrophyte decline
- <i>Pantoea</i> -Induced Interveinal Chlorosis (PIC): A New Bacterial Disease of Corn and Sorghum Caused by <i>Pantoea agglomerans</i> Identified in the Texas Panhandle
- Interactions between urbanization, malaria infection and avian cloacal microbiome
- Potential for Manganese Oxide Driven Anaerobic Methane Oxidation in Sediments of a Seasonally Euxinic Coastal Basin
- Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments
- Straw Mulching Differentially Shapes the Structure and Function of Below‐Ground Bacterial Communities in Potato Depending on <scp>eDNA</scp> Source and Cultivar
- Applying machine learning to classify table olives using bacterial metataxonomic data
- Characterization of the Core Microbiome Associated with Table Beet Production in New York
- Omics-Based Insights into Microbial Community Changes and Pathogen Identification in Strawberries Under Continuous Cropping
- Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams
- Sea urchin holobionts: microbiome variation across species, compartments and locations in Paracentrotus lividus and Arbacia lixula
- Dispersal shapes compositional and functional diversity in aquatic microbial communities
- Investigating microbiota differences across chronic pancreatitis, influenced by lifestyle and genetic determinants
- RETRACTED ARTICLE: Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing
- Inside the Atacama Desert: uncovering the living microbiome of an extreme environment
- Ecosystem retrogression enhances cross‐domain microbial stability and increases the genetic potential for nutrient cycling
- Precipitation Modulates the Impact of Human Activities on Riverine Food Webs Revealed by Environmental <scp>DNA</scp>
- Urban soil Gammaproteobacteria diversity, shaped by biodiverse land use, predicts a lower risk of developing allergy in children
- Methanotrophs and methanogens are differently affected by small-scale heterogeneities in transiently flooded kettle holes
- A comparison of deep multiomics profiles across ethnicity, geography, and age
- Interactive effects of biochar types and <i>Bacillus velezensis</i> inoculation on soil properties, microbial communities and wheat performance under greenhouse conditions
- Sediments From a Seasonally Euxinic Coastal Ecosystem Show High Nitrogen Cycling Potential
- Anaeroglomus insulsum gen. nov., sp. nov., anaerobic planctomycete, isolated from a thermal water stream
- Microbial communities and biogeochemistry of a melting Rocky Mountain glacier
- Structure of the Prokaryotic Community in Bottom Sediments of the Alginsky Hydro-Mineral Natural Complex (Barguzin Depression, Russia)
- Fine-scale differences in feeding ecology of three tropical euphausiid species revealed using 18S V9 metabarcoding and stable isotope analysis
- Heterotrophic lifestyle in the phylum Thermodesulfobiota revealed by physiological and genomic characterization of the acidophilic sulfate-reducing bacterium Thermodesulfobium fumaratoxidans sp. nov.
- Comparison of bacterial and diatom diversity patterns from waterbodies across two Antarctic Peninsula island groups
- Gut feeling: host and habitat as drivers of the microbiome in blackbuck <i>Antilope cervicapra</i>
- The facultative intracellular symbiont Lariskella is neutral for lifetime fitness and spreads through cytoplasmic incompatibility in the leaffooted bug, Leptoglossus zonatus
- The hidden life of <i>Xylella</i> : mining the NCBI Sequence Read Archive reveals potential new species, host plants, and infected areas for this elusive bacterial plant pathogen
- Concomitant COX-1 and COX-2 suppression is not sufficient to induce enteropathy associated with chronic NSAID use
- Exploring key factors in anaerobic syntrophic interactions: Biomass activity, microbial community, and morphology
- Resource landscape shapes the composition and stability of the human vaginal microbiota
- Imposing primary colonisation success of wood‐decomposing fungi in birch wood alters microbiome composition and carbon release rates
- Impact of Low-Starch Dietary Modifications on Faecal Microbiota Composition and Gastric Disease Scores in Performance Horses
- Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice
- Environmental microbiomes drive chemotactile sensation in octopus
- Comparative Three‐Barcode Phylogenetics and Soil Microbiomes of Planted and Wild <i>Arbutus</i> Strawberry Trees
- Marine invasive alien species in Europe: 9 years after the IAS Regulation
- Microbiome transplants may not improve health and longevity in <i>Drosophila melanogaster</i>
- Robust prediction of colorectal cancer via gut microbiome 16S rRNA sequencing data
- Local microbial yield-associating signatures largely extend to global differences in plant growth
- Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.
- Single-cell imaging reveals efficient nutrient uptake and growth of microalgae darkening the Greenland Ice Sheet
- Shotgun metagenomics reveals the flexibility and diversity of Arctic marine microbiomes
- Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of <i>Methylobacterium</i> and lack of support for <i>Methylorubrum</i> as a genus
- Use of FISH‐FLOW as a Method for the Identification and Quantification of Bacterial Populations
- Subtle diurnal microbial rhythms in a large mammalian carnivore
- Metabarcoding of protozoa and helminth in black-necked cranes: a high prevalence of parasites and free-living amoebae
- Potential postmortem microbial biomarkers of infant and younger children death investigation
- The NEREA Augmented Observatory: an integrative approach to marine coastal ecology
- Picky eaters: Selective microbial diet of avian ectosymbionts
- Microbial genetic potential differs among cryospheric habitats of the Damma glacier
- Transient hypoxia drives soil microbial community dynamics and biogeochemistry during human decomposition
- Microbiome turnover during offspring development varies with maternal care, but not moult, in a hemimetabolous insect
- Are plant traits drivers of endophytic communities in seasonally flooded tropical forests?
- Host population crashes disrupt the diversity of associated marine microbiomes
- Cultivation potential of Vanilla crop wild relatives in two contrasting land use systems
- Solving a Bloody Mess: B-Vitamin Independent Metabolic Convergence among Gammaproteobacterial Obligate Endosymbionts from Blood-Feeding Arthropods and the Leech<i>Haementeria officinalis</i>
- Tree tissues and species traits modulate the microbial methane-cycling communities of the tree phyllosphere
- Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study
- Integrated Multi-Omics Analysis Provides Insights into the Rhizosphere Microbial Dynamics in Soybean– <i>Fusarium virguliforme</i> Interaction
- Microbial community succession on submerged vertebrate carcasses in a tidal river habitat: Implications for aquatic forensic investigations
- Effects of coenzyme M and methyl-coenzyme M on the efficacy of inhibitors of methanogenesis in rumen cultures
- Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth
- The hydrocarbon-degrading bacteria and fungi in oil contaminated soils of Kazakhstan: microbiome composition, enrichment, isolation and bioremediation potential
- Multiple dimensions of plant diversity predict microbial community composition in grassland soils
- Microbial efficiency enhancement drives carbon sequestration in long-term organic farming systems: linking taxonomic succession to carbon use efficiency
- Predator-mediated local convergence fosters global microbial community divergence
- The hidden role of rhizospheric viruses in promoting nitrogen fixation in soils
- Intestinal interoceptive dysfunction drives age-associated cognitive decline
- Microbiome analysis of groundwaters in the Slovenian Dinaric Karst, a recognized biodiversity hotspot
- Evolutionary Analysis of Trehalose Breakdown Pathways
- Does Emerald Ash Borer Infestation Alter Ash Phloem Microbial Communities over Time?
- Diet chemistry and cross-kingdom microbiota associate with black soldier fly larvae performance on regional side streams
- Fluctuations in Ammonia-Oxidizing Bacteria Biomass Density as a Potential Driver of Seasonal Variations in N <sub>2</sub> O Emissions from Activated Sludge Nitrification
- Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems
- Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences
- Feeding habits and ecological roles of marine cladocerans in offshore zooplankton food-web in Suruga Bay, Japan
- Intraspecific microbiome dynamics across the life cycle of the milkweed bug Oncopeltus fasciatus
- Stage-Specific Microbiota Transitions Throughout Black Soldier Fly Ontogeny
- Shifts in seed‐associated endophytic bacterial communities from parental lines to advanced generations in lima bean
- A matter of salt: Global assessment of the effect of salt ionic composition as a driver of aquatic bacterial diversity
- The tomato seed microbiome is mainly shaped by host genotype and production site
- Bacterial Assembly in the Switchgrass Rhizosphere Is Shaped by Phylogeny, Host Genotype, and Growing Site
- Phylogenomic Analysis of Deep-Branching Telonemid
- Comparing apples and apples; evaluating the impact of conventional and organic management on the soil microbial communities of apple orchards
- Barley Rhizosphere Bacteriome Dynamics under Organic and Mineral Inputs: The importance of intercropping predecessor
- River biofilm bacteria as sentinels of national-scale freshwater ecosystems
- Dupilumab Treatment Is Associated With Clinical Improvement and a Shift Toward a Health‐Associated Nasal Passage Microbiota in Diffuse Type 2 Chronic Rhinosinusitis
- Urocanase-Positive Skin-Resident Bacteria Metabolize cis-Urocanic Acid and in Turn Reduce the Immunosuppressive Properties of UVR
- Microbial ecology applied to fuel ethanol production from sugarcane
- New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the <i>Pelagibacterales</i>
- Coupled Phylogenetic and Functional Enrichment in the Tomato Rhizosphere Microbiome
- Distinct compositional changes but shared quantitative microbiome and anti-inflammatory modulations by diet
- The <i>ATO</i> gene family governs <i>Candida albicans</i> colonization in the dysbiotic gastrointestinal tract
- Colony-level food storage and microbial predigestion shape nutrient acquisition in the termite Velocitermes heteropterus (Isoptera: Termitidae)
- The Impact of Whole‐Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research
- Biofilms on plastic litter in an urban river: Community composition and activity vary by substrate type
- Exploring the visual system of the black grouse ( <i>Lyrurus tetrix</i> ): combining experimental and molecular approaches to inform strategies for reducing collisions
- Predicting resting metabolic rate in healthy adults: a comparative analysis using the <i>enable</i> cohort
- Interactive effects of warming and iron supplementation on O2 dynamics, trace metal content, and microbial diversity within different compartments of two Mediterranean corals
- Peatland Pond Microbiome and Biogeochemical Responses to Solar Radiation Extremes in a High-Altitude Wetland, Salar de Huasco, Chile
- Pregnancy influences on the rumen environment of Angus heifers differing in feed efficiency
- Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition
- Freeze-thaw cycles and biodegradable microplastics alter the microbial degradation of atrazine in mollisols
- StrainInfo—the central database for linked microbial strain identifiers
- Family life and cadmium ingestion independently shape offspring microbiomes in a subsocial insect
- Effect of sweeteners and sweetness enhancers on weight management and gut microbiota composition in individuals with overweight or obesity: the SWEET study
- Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints
- A quartet-based approach for inferring phylogenetically informative features from genomic and phenomic data
- A novel method to assess the integrity of frozen archival <scp>DNA</scp> samples: Alpha‐diversity ratios of short‐ and long‐read <scp>16S rRNA</scp> gene sequences
- The role of different exogenous NO concentrations on C and N biogeochemistry of an agricultural soil
- Reducing skin microbiome exposure impacts through swine farm biosecurity
- Establishing microbial communities to promote the growth of <i>Pleurotus ostreatus</i> through a top-down approach is hindered by the dominance of antagonistic interactions
- Dissecting multitrophic interactions: The relationships among Entomophthora, their dipteran hosts, and associated bacteria
- Contamination-controlled upper gastrointestinal microbiota profiling reveals salivary-duodenal community types linked to opportunistic pathogen carriage and inflammation
- Gut microbiota composition is related to anxiety and aggression scores in companion dogs
- Holobiont Traits Shape Climate Change Responses in Cryptic Coral Lineages
- Indirect effects of soil amendments on plant traits and the microbiome in post-wildfire forest recovery
- Impacts of diverse undersown cover crops on seasonal soil microbial properties
- Chromosome-level genome assembly and transcriptome analysis of the Ural owl, <i>Strix uralensis</i> Pallas, 1771
- Defining the cultured and uncultured bacterial fractions in Cannabis seeds
- Two decades long-term field trial data on fertilization, tillage, and crop rotation focusing on soil microbes
- An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota
- Genital microbiota in infertile couples
- Organ structure and bacterial microbiogeography in a reproductive organ of the Hawaiian bobtail squid reveal dimensions of a defensive symbiosis
- A novel cable bacteria species with a distinct morphology and genomic potential
- The archaeal class <i>Nitrososphaeria</i> is a key component of the reproductive microbiome in sponges during gametogenesis
- Honey wasps differ from other wasps in possessing large gut communities dominated by host-restricted bacteria
- Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes
- The impact of management on the fecal microbiome of endangered greater sage-grouse (<i>Centrocercus urophasianus</i>) in a zoo-based conservation program
- Gut Colonization With Vancomycin-Resistant <i>Enterococcus</i> Shapes the Gut Microbiome in the Intensive Care Unit
- Inoculation of wild type or EPS mutant Bacillus subtilis does not alter rhizocompetence, soil EPS, and tomato growth in the absence of stress
- The abundance of microbial "specific groups" significantly influences downed log respiration
- Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice
- Sedimentary indicators of anthropogenic impact in Fildes Peninsula lakes (King George Island, Maritime Antarctica)
- Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice
- Environmentally dependent interactions shape patterns in gene content across natural microbiomes
- Persistent Gaps and Errors in Reference Databases Impede Ecologically Meaningful Taxonomy Assignments in <scp>18S rRNA</scp> Studies: A Case Study of Terrestrial and Marine Nematodes
- Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)
- Transcriptomic response of the picoalga <i>Pelagomonas calceolata</i> to nitrogen availability: new insights into cyanate lyase function
- Plant-Guided Microbiome Selection Produces Transient Effects on Insect Performance and Rhizosphere Community Assembly
- Skyglow increases cyanobacteria abundance and organic matter cycling in lakes
- Microbial metabolism of food allergens determines the severity of IgE-mediated anaphylaxis
- Carbon and energy utilization in microbial cell extracts from soil
- Oronasal mucosal melanoma is defined by two transcriptional subtypes in humans and dogs with implications for diagnosis and therapy
- Effects of turbulence on diatoms of the genus <i>Pseudo-nitzschia</i> spp. and associated bacteria
- Cross-domain diversity effects: linking diatom species richness, intraspecific richness, and biomass production to host-associated bacterial diversity
- Garden fruit chafer (Pachnoda sinuata L.) accelerates recycling and bioremediation of animal waste
- Microbial Diversity Limits Belowground Colonization of <i>Sphaerulina musiva</i>
- The blood metabolome of brain health in midlife and influences of genes, microbiome and exposome
- Sulfide-oxidizing potential and hypersalinity tolerance strategies in salt-crust covered coastal microbial mats
- Exposure of termites and associated prokaryotes to soil mercury in a tropical rainforest (French Guiana)
- Methanotrophy under extreme alkalinity in a serpentinizing system
- Spatiotemporal dynamics of benthic Microcoleus in a Swiss lotic system
- Functional biogeography of marine microbial heterotrophs
- Assessment of the Endophytic Microbiome of Soybean Seeds Under the Agricultural Ecosystem in Mississippi, U.S.A.
- Characterization of Ornithobacterium hominis colonization dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort
- User Guided Selection and Alignment of Sequence Data by GeneMatrix
- Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants
- Microbial oxidation significantly reduces methane export from global groundwaters
- Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia
- Archaea show different geographical distribution patterns compared to bacteria and fungi in Arctic marine sediments
- The lipid transfer protein STARD7 controls intestinal tumor development in a context-dependent manner
- Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses
- IGFBP3 repression driven by inflammation links air pollution to placental and developmental defects
- Spatial heterogeneity of soil organic matter and microbial community composition across ice-wedge polygons and soil layers in Arctic lowland tundra
- Effects of Acid Rock Drainage on Microbial Communities in Alpine Streams of the Pyrenees
- Do honey phytochemicals modulate forager aggression and the gut microbiome in the honey bee ( <i>Apis mellifera</i> L.)?
- Engineering orthogonal ribosomes for real-time monitoring using fluorescence
- Large-scale association analyses identify host factors influencing human gut microbiome composition
- Microplastics habituated with biofilm change decabrominated diphenyl ether degradation products and thyroid endocrine toxicity
- Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits
- CLAE: A High‐Fidelity Nanopore Sequencing Strategy for Read‐Level Viral Variant Detection and Environmental RNA Virus Discovery
- Best practices in metabarcoding of fungi: From experimental design to results
- Arctic sea-ice ridges are biomass hotspots harboring diverse microbial communities
- Functional group of grassland plants affects their fungal symbionts more than long-term fertilisation in a field experiment
- Soil type and precipitation level have a greater influence on fungal than bacterial diversity in serpentine and non‐serpentine biological soil crusts
- Vibrio pectenicida strain FHCF-3 is a causative agent of sea star wasting disease
- RNA secondary structures are conserved but random
- Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats
- Enhanced methane cycling across the Laptev Sea signaled by time-integrated biomarkers of aerobic methane oxidation
- Towards Functional Fertilisers: Feed Composition Shapes Microbial Community Structure and Viability in Black Soldier Fly ( <scp> <i>Hermetia illucens</i> </scp> ) Frass
- Pathway-specific bulk and clumped isotope signatures of methane production in marine sediment incubations
- The Microflora Danica atlas of Danish environmental microbiomes
- Estimating the size of a set using cascading exclusion
- Microbiological Characteristics of Sapropel and the Possibility of Its Application for Enhanced Oil Recovery from Carbonate Reservoirs
- SILVA ribosomal RNA database [wikipedia]
Related