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2025
Synergistic pathogenicity between Herpesvirus and Vibrio aestuarianus in killing juvenile oysters during spring in natural conditions
Science of The Total Environment
2025
Spatial and Seasonal Biodiversity Variation in a Large Mediterranean Lagoon Using Environmental DNA Metabarcoding Through Sponge Tissue Collection
Environmental DNA
2025
The immune response modulated by inoculation of commensal bacteria at birth impacts the gut microbiota and prevents Salmonella colonization
Gut Microbes
2025
Benchmarking metabarcode sequence denoisers for improved invertebrate community diversity estimates
Methods in Ecology and Evolution
2025
Integrative approach to the systematics of the endemic Svalbard aphid specis Macrosiphum calvulum (Hemiptera, Aphididae) using molecular morphological and reproductive system analysis
Scientific Reports
2025
Ultrasensitive Sequencing (SiMSen‐Seq) for Environmental DNA Applications
Environmental DNA
2025
Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring
Ecology and Evolution
2025
Ecology of vertical tumor transmission in the freshwater cnidarian Hydra oligactis
Scientific Reports
2025
Variation in diet concentration and bacterial inoculum size in larval habitats shapes the performance of the Asian tiger mosquito, Aedes albopictus
Microbiome
2025
The best of two worlds: toward large‐scale monitoring of biodiversity combining COI metabarcoding and optimized parataxonomic validation
Ecography
2025
Exploring riverine aquatic animal diversity and establishing aquatic ecological monitoring approaches tailored to the Qinling region via eDNA technology
Integrative Zoology
2025
Bat things come in threes: within-host dynamics of herpesvirus triple infection in bats
Journal of Virology
2025
Experimental assessment of antibiotic resistance in a Biofilm – Grazer system
Environmental Pollution
2025
The pitfalls of rDNA‐based AMF identification: a comparative analysis of rDNA and protein‐coding genes
New Phytologist
2025
High-throughput biodiversity surveying sheds new light on the brightest of insect taxa
Proceedings of the Royal Society B: Biological Sciences
2025
Uncovering diversity and abundance patterns of CO2-fixing microorganisms in peatlands
npj Biodiversity
2025
Pink discoloration defects associated with microbial structure and metabolome changes in commercial bloomy cheeses
International Journal of Food Microbiology
2025
A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed
PeerJ
2025
Co‐occurrence and successional patterns among diatoms, dinoflagellates, and potential parasites in a coastal upwelling experiment
Limnology and Oceanography
2025
Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar
Scientific Data
2025
New insights into the cultivability of human milk bacteria from ingestion to digestion and implications for their Immunomodulatory properties
Scientific Reports
2025
Functional Characterisation of Microbial Communities Related to Black Stain Formation in Lascaux Cave
Environmental Microbiology Reports
2025
Interdisciplinary approaches at early invasion stages maximise the evidence on human-induced and climate-driven fish dispersal
Hydrobiologia
2025
Angelica cultivation and mycorrhizal inoculation improve microbial diversity, functions and network complexity of trace elements-polluted soil: A three-year field study
Applied Soil Ecology
2025
High-performance protocol for ultra-short DNA sequencing using Oxford Nanopore Technology (ONT)
PLOS One
2025
Combining environmental DNA and remote sensing variables to model fish biodiversity in tropical river ecosystems
Ecological Informatics
2025
Phototrophic periphyton tolerance reflects in situ exposure to pharmaceuticals overtime – A translocation study using a pollution-induced community approach (PICT)
Journal of Hazardous Materials
2025
The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis
Biology
2025
Advancing Marine Conservation: Metabarcoding and Metaphylogeography for a Multi‐Year Biomonitoring of Benthic Communities of National Parks Across Two Seas
Diversity and Distributions
2025
Cobalt induces the set-up of new structural networks in river biofilms: Impairment of autotrophic-heterotrophic coupling
Environmental Pollution
2025
Insight into how fermentation might contribute to the distinctiveness of Australian coffee
Food Chemistry
2025
Comparing the spring diet of buff-tailed bumble bees and honey bees (Hymenoptera: Apidae) in a forest landscape: a metabarcoding approach
Journal of Insect Science
2025
HAPP: High-accuracy pipeline for processing deep metabarcoding data
PLOS Computational Biology
2025
Response of Montane Fish Biodiversity to Landscape and Anthropogenic Activity Under Potential Water Quality Pathways
Ecology and Evolution
2025
Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology
Environmental Microbiome
2025
Microbial and bryospheric photosynthesis of boreal peatlands have peatland‐type‐specific responses to long‐term drying
New Phytologist
2025
Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France
Biodiversity Data Journal
2025
Independent transitions to fully planktonic life cycles shaped the global distribution of medusozoans in the epipelagic zone
Proceedings of the National Academy of Sciences
2025
The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities
BMC Microbiology
2025
Plant taxa visited by the European orchard bee Osmia cornuta (Latreille, 1805) analyzed by metabarcoding through nesting residuals (Hymenoptera, Anthophila, Megachilidae)
Bulletin de la Société entomologique de France
2025
Comparison between Ribosomal Assembly and Machine Learning Tools for Microbial Identification of Organisms with Different Characteristics
Current Bioinformatics
2024
Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae
Communications Earth & Environment
2024
Prophylactic phage administration reduces Salmonella Enteritidis infection in newly hatched chicks
MicrobiologyOpen
2024
Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage
Microbiome
2024
On the role of niche specialization in the geographic distribution of aphid asexual lineages: a case study using the leaf‐curl plum aphid superclones
Oikos
2024
Introduced fish reduce the occurrence of shrews in alpine lakes
Biological Conservation
2024
Global mesozooplankton communities show lower connectivity in deep oceanic layers
Molecular Ecology
2024
Prediction of learning outcomes with a machine learning algorithm based on online learning behavior data in blended courses
Asia Pacific Education Review
2024
Microbial community structure in recovering forests of Mount St. Helens
Frontiers in Microbiomes
2024
Milk replacer feeding once or twice a day did not change the ruminal metabolomic profile and the microbial diversity of dairy calves from birth to weaning
Journal of Dairy Science
2024
Impact of the Biocontrol Product, Esquive® WP, on the Indigenous Grapevine Wood Microbiome after a 6-Year Application Period
Journal of Fungi
2024
The rootstock modifies the arbuscular mycorrhizal community of the root system, while the influence of the scion is limited in grapevines
Environmental Microbiology Reports
2024
Predicting trawl catches using environmental DNA
ICES Journal of Marine Science
2024
V9 Hypervariable Region Metabarcoding Primers for Euglenozoa and Metamonada
Environmental DNA
2024
Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding
Food Research International
2024
Overview of microbial communities in the surface water of the Seine River to understand their response to climate change and human activities
Aquatic Ecology
2024
Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection in Crassostrea gigas
Scientific Reports
2024
Plant diversity and functional identity drive grassland rhizobacterial community responses after 15 years of CO2 and nitrogen enrichment
Journal of Ecology
2024
Ecological impact of mechanical cleaning method to curb black stain alterations on Paleolithic cave walls
International Biodeterioration & Biodegradation
2024
Using meta‐analysis to understand the impacts of dietary protein and fat content on the composition of fecal microbiota of domestic dogs (Canis lupus familiaris): A pilot study
MicrobiologyOpen
2024
Radioactivity as a driver of bacterial community composition in naturally radioactive mineral springs in the French Massif Central
Frontiers in Microbiology
2024
Nutritional and microbial profiles of ripened plant-based cheese analogs collected from the European market
Food Research International
2024
Urbanization impoverishes taxonomic but not functional diversity of the gut microbiota in a forest specialist ground beetle, Carabus convexus
Scientific Reports
2024
Detecting the invisible through DNA metabarcoding: The role of gelatinous taxa in the diet of two demersal Antarctic key stone fish species (Notothenioidei)
Environmental DNA
2024
Determining growth rates of heterotrophic bacteria from 16S rRNA gene sequence-based analyses of dilution experiments
Aquatic Microbial Ecology
2024
A spatial matrix factorization method to characterize ecological assemblages as a mixture of unobserved sources: An application to fish eDNA surveys
Methods in Ecology and Evolution
2024
Temporal and Spatial eDNA Analysis of Fish Assemblages in Postindustrial, Urban Coastal Habitats
Environmental DNA
2024
Accurately clustering biological sequences in linear time by relatedness sorting
Nature Communications
2024
Cobalt effects on prokaryotic communities of river biofilms: Impact on their colonization kinetics, structure and functions
Science of The Total Environment
2024
Pollution gradients shape microbial communities associated with Ae. albopictus larval habitats in urban community gardens
FEMS Microbiology Ecology
2024
Hydrothermal vents supporting persistent plumes and microbial chemoautotrophy at Gakkel Ridge (Arctic Ocean)
Frontiers in Microbiology
2024
Evidencing the influence of temperature and mineralogy on microbial competition for hydrogen consumption: Implications for underground hydrogen storage (UHS)
International Journal of Hydrogen Energy
2024
Maximizing sampling efficiency to detect differences in fish community composition using environmental DNA metabarcoding in subarctic fjords
Environmental DNA
2024
Mapping Biodiversity Coast‐to‐Coast‐to‐Coast Across Canada's Three Oceans Using eDNA Metabarcoding
Environmental DNA
2024
Alteration of Rice Root Endophytic Bacterial Community Composition by Meloidogyne graminicola and Identification of Potential Biocontrol Agent
Annals of Microbiology
2024
Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave
mSystems
2024
Calcium-rich dairy matrix protects better than mineral calcium against colonic luminal haem-induced alterations in male rats
npj Science of Food
2024
The abundance of snail hosts mediates the effects of antagonist interactions between trematodes on the transmission of human schistosomes
Infectious Diseases of Poverty
2024
Soil Horizons Harbor Differing Fungal Communities
Diversity
2024
D genome acquisition and breeding have had a significant impact on interaction of wheat with ACC deaminase producers in soil or ACC deaminase potential activity in the rhizosphere
Soil Biology and Biochemistry
2024
Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact
Environmental Microbiome
2024
Assessing the chronic effect of the bioavailable fractions of radionuclides and heavy metals on stream microbial communities: A case study at the Rophin mining site
Science of The Total Environment
2024
Deviation from neutral species abundance distributions unveils geographical differences in the structure of diatom communities
Science Advances
2024
Temporal and spatial dynamics within the fungal microbiome of grape fermentation
Environmental Microbiology
2024
CRISPR-Cas in Pseudomonas aeruginosa provides transient population-level immunity against high phage exposures
The ISME Journal
2024
The gut microbiota and its metabolite butyrate shape metabolism and antiviral immunity along the gut-lung axis in the chicken
Communications Biology
2024
Simple approaches for evaluation of OTU quality based on dissimilarity arrays
Metabarcoding and Metagenomics
2024
Assessing patterns of metazoans in the global ocean using environmental DNA
Royal Society Open Science
2024
Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years
mSystems
2024
Distinct anal microbiome is correlated with anal cancer precursors in MSM with HIV
AIDS
2024
A DNA‐based evaluation of North American river otter diet with respect to fishes: Implications for the conservation of aquatic predators and their prey
Aquatic Conservation: Marine and Freshwater Ecosystems
2024
Applications of Metagenomics
2024
Variations in the root mycobiome and mycorrhizal fungi between different types of Vanilla forest farms on Réunion Island
Mycorrhiza
2024
Benchmarking three DNA metabarcoding technologies for efficient detection of non-native cerambycid beetles in trapping collections
NeoBiota
2024
The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data
PeerJ
2024
Seasonality of primary production explains the richness of pioneering benthic communities
Nature Communications
2024
2024
eDNA Metabarcoding, a Promising Tool for Monitoring Aquatic Biodiversity in the Estuaries of Reunion Island (South‐West Indian Ocean)
Environmental DNA
2024
Assessing the response of an urban stream ecosystem to salinization under different flow regimes
Science of The Total Environment
2024
Towards eDNA informed biodiversity studies – Comparing water derived molecular taxa with traditional survey methods
Progress in Oceanography
2024
Phytoplankton growth and grazing dynamics during anomalous heat wave and suppressed upwelling conditions in the southern California Current
Deep Sea Research Part I: Oceanographic Research Papers
2024
Development of an in vitro biofilm model for the study of the impact of fluoroquinolones on sewer biofilm microbiota
Frontiers in Microbiology
2024
Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions
Frontiers in Plant Science
2024
Increasing marine trophic web knowledge through DNA analyses of fish stomach content: a step towards an ecosystem‐based approach to fisheries research
Journal of Fish Biology
2024
Effect of an organophosphorus insecticide, soil texture and earthworm species on the turnover of soil, gut and cast microbiota during the earthworm's gut transit
Soil Biology and Biochemistry
2024
Seismic events as potential drivers of the microbial community structure and evolution in a paleo-ocean analog
Communications Earth & Environment
2024
The lost generation of Pemphigus populiglobuli (Hemiptera, Aphididae): exploring the taxonomy of the Svalbard aphids of genus Pemphigus
Zoological Letters
2024
Niche partitioning and plastisphere core microbiomes in the two most plastic polluted zones of the world ocean
Environmental Science and Pollution Research
2024
Spatial and temporal characteristics of microbial communities in the Seine river in the greater Paris area under anthropogenic perturbation
Heliyon
2024
Multiple nutrient limitation of the soil micro-food web in a tropical grassland revealed by nutrient-omission fertilization
Applied Soil Ecology
2023
The phyto-bacterioplankton couple in a shallow freshwater ecosystem: Who leads the dance?
Harmful Algae
2023
Culturing the desert microbiota
Frontiers in Microbiology
2023
Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs
Microbial Ecology
2023
Bioinformatic and Statistical Analysis of Microbiome Data
2023
Phytobiotic-Prebiotic Feed Additive Containing a Combination of Carob Pulp, Chicory, and Fenugreek Improve Growth Performance, Carcass Traits, and Fecal Microbiota of Fattening Pigs
Animals
2023
Drivers of pelagic and benthic microbial communities on Central Arctic seamounts
Frontiers in Marine Science
2023
Inulin increases the beneficial effects of rhubarb supplementation on high-fat high-sugar diet-induced metabolic disorders in mice: impact on energy expenditure, brown adipose tissue activity, and microbiota
Gut Microbes
2023
DNA metabarcoding of mock communities highlights potential biases when assessing Neotropical fish diversity
Environmental DNA
2023
Human Microbiomes and Disease for the Biomedical Data Scientist
Annual Review of Biomedical Data Science
2023
Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome
Molecular Ecology
2023
Consortia cultivation of the Desulfobacterota from macrophyte periphyton: tool for increasing the cultivation of microorganisms involved in mercury methylation
Microbiological Research
2023
Contemporary issues, current best practice and ways forward in soil protist ecology
Molecular Ecology Resources
2023
A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes
Nature Microbiology
2023
Microbiota Profile of the Nasal Cavity According to Lifestyles in Healthy Adults in Santiago, Chile
Microorganisms
2023
Coriander (Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning
Plants
2023
Effects of metal contamination with physicochemical properties on the sediment microbial communities in a tropical eutrophic-hypereutrophic urban reservoir in Brazil
Environmental Science and Pollution Research
2023
Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea
Marine Pollution Bulletin
2023
Dark-zone alterations expand throughout Paleolithic Lascaux Cave despite spatial heterogeneity of the cave microbiome
Environmental Microbiome
2023
A toolbox of machine learning software to support microbiome analysis
Frontiers in Microbiology
2023
Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages
Peer Community Journal
2023
A deep continental aquifer downhole sampler for microbiological studies
Frontiers in Microbiology
2023
Evaluation of 16S rRNA gene primer pairs for bacterial community profiling in an across soil and ryegrass plant study
Journal of Sustainable Agriculture and Environment
2023
Ecological corridors homogenize plant root endospheric mycobiota
New Phytologist
2023
Discrete patterns of microbiome variability across timescales in a wild rodent population
BMC Microbiology
2023
Microevolutionary Processes in a Foundation Tree Inform Macrosystem Patterns of Community Biodiversity and Structure
Forests
2023
Diversity of DNA Sequences from Pathogenic and Potentially Pathogenic Eukaryotic Microorganisms in Protected Granite Mountain Rocks
Diversity
2023
Impact of Norway spruce pre-degradation stages induced by Gloeophyllum trabeum on fungal and bacterial communities
Fungal Ecology
2023
Biogeography of microbial communities in high‐latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes
Environmental Microbiology
2023
In grapevine decline, microbiomes are affected differently in symptomatic and asymptomatic soils
Applied Soil Ecology
2023
Exploring macroinvertebrate biodiversity in the dynamic southern Balkan stream network of the Vjosa using preservative-based DNA metabarcoding
Aquatic Sciences
2023
Bio-precipitation of arsenic and antimony in a sulfate-reducing bioreactor treating real acid mine drainage water
FEMS Microbiology Ecology
2023
VTAM: A robust pipeline for validating metabarcoding data using controls
Computational and Structural Biotechnology Journal
2023
PGPR-Soil Microbial Communities’ Interactions and Their Influence on Wheat Growth Promotion and Resistance Induction against Mycosphaerella graminicola
Biology
2023
Occurrence of biogenic amines and their correlation with bacterial communities in the Ivorian traditional fermented fish adjuevan during the storage
Folia Microbiologica
2023
Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield
Microbial Ecology
2023
Controlled natural selection of soil microbiome through plant-soil feedback confers resistance to a foliar pathogen
Plant and Soil
2023
Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach
Scientific Reports
2023
Multi-Omic Profiling, Structural Characterization, and Potent Inhibitor Screening of Evasion-Related Proteins of a Parasitic Nematode, Haemonchus contortus, Surviving Vaccine Treatment
Biomedicines
2023
DNA metabarcoding reveals the dietary profiles of a benthic marine crustacean, Nephrops norvegicus
PLOS ONE
2023
Effects of sodium nitrite reduction, removal or replacement on cured and cooked meat for microbiological growth, food safety, colon ecosystem, and colorectal carcinogenesis in Fischer 344 rats
npj Science of Food
2023
Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs
Peer Community Journal
2023
Methods in Molecular Biology
2023
Evaluation of 96‐well high‐throughput DNA extraction methods for 16S rRNA gene metabarcoding
Molecular Ecology Resources
2023
A longitudinal survey in the wild reveals major shifts in fish host microbiota after parasite infection
Molecular Ecology
2023
Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys
Scientific Reports
2023
Ectomycorrhizal (dipterocarp) and arbuscular mycorrhizal (non‐dipterocarp) tree hosts and their relative distribution in a tropical forest predict soil bacterial communities
Journal of Ecology
2023
Homogeneity in terrestrial land cover is reflected in fish diversity patterns in a Chinese river system
Environmental DNA
2023
A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification
Journal of Fungi
2023
Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird
Molecular Ecology
2023
First report of ectomycorrhizae in Prunus serotina in the exotic range
Plant and Soil
2023
The diet of commensal Crocidura olivieri (Soricomorpha: Soricidae): predation on co-existing invasive Mus musculus suggested by DNA metabarcoding data
Mammalia
2023
A special drop: Characterising yeast isolates associated with fermented beverages produced by Australia's indigenous peoples
Food Microbiology
2023
Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations
Peer Community Journal
2023
Microscale dynamics of dark zone alterations in anthropized karstic cave shows abrupt microbial community switch
Science of The Total Environment
2023
Inflammatory Responses Induced by the Monophasic Variant of Salmonella Typhimurium in Pigs Play a Role in the High Shedder Phenotype and Fecal Microbiota Composition
mSystems
2023
Microbiome analysis in Lascaux Cave in relation to black stain alterations of rock surfaces and collembola
Environmental Microbiology Reports
2023
Sediment and bottom water eDNA metabarcoding to support coastal management
Ocean & Coastal Management
2023
Bioinformatic and Statistical Analysis of Microbiome Data
2023
Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota
Environmental Microbiology
2023
Habitat partitioning of soil microbial communities along an elevation gradient: from plant root to landscape scale
Oikos
2023
ITS alchemy: On the use of ITS as a DNA marker in fungal ecology
Fungal Ecology
2023
Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus
Applied and Environmental Microbiology
2023
Urinary Metabolome Analysis Reveals Potential Microbiota Alteration and Electrophilic Burden Induced by High Red Meat Diet: Results from the French NutriNet‐Santé Cohort and an In Vivo Intervention Study in Rats
Molecular Nutrition & Food Research
2023
Microbiota of the Digestive Glands and Extrapallial Fluids of Clams Evolve Differently Over Time Depending on the Intertidal Position
Microbial Ecology
2023
Quantification of diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media using 16S amplicon barcoding
PLOS ONE
2023
Single-celled bioturbators: benthic foraminifera mediate oxygen penetration and prokaryotic diversity in intertidal sediment
Biogeosciences
2022
Prey size is more representative than prey taxa when measuring dietary overlap in sympatric forest bats
Environmental DNA
2022
Maternal heme-enriched diet promotes a gut pro-oxidative status associated with microbiota alteration, gut leakiness and glucose intolerance in mice offspring
Redox Biology
2022
Seawater copper content controls biofilm bioaccumulation and microbial community on microplastics
Science of The Total Environment
2022
A carvacrol-based product reduces Campylobacter jejuni load and alters microbiota composition in the caeca of chickens
Journal of Applied Microbiology
2022
Temporal changes of genetic structure and diversity in a marine diatom genus discovered via metabarcoding
Environmental DNA
2022
Lake Sediments From Littoral and Profundal Zones are Heterogeneous but Equivalent Sources of Methane Produced by Distinct Methanogenic Communities—A Case Study From Lake Remoray
Journal of Geophysical Research: Biogeosciences
2022
Caecal microbiota composition of experimental inbred MHC-B lines infected with IBV differs according to genetics and vaccination
Scientific Reports
2022
A combined microbial and biogeochemical dataset from high-latitude ecosystems with respect to methane cycle
Scientific Data
2022
Effect of live yeast supplementation in sow diet during gestation and lactation on sow and piglet fecal microbiota, health, and performance
Journal of Animal Science
2022
Light and freshwater discharge drive the biogeochemistry and microbial ecology in a sub-Arctic fjord over the Polar night
Frontiers in Marine Science
2022
Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics
Food Research International
2022
EdClust: A heuristic sequence clustering method with higher sensitivity
Journal of Bioinformatics and Computational Biology
2022
Regional factors as major drivers for microbial community turnover in tropical cascading reservoirs
Frontiers in Microbiology
2022
Host identity and neighborhood trees affect belowground microbial communities in a tropical rainforest
Tropical Ecology
2022
Catching change in microbial diversity indicators under different soil organic matter managements: Higher taxonomic resolution, better discrimination?
Ecological Indicators
2022
Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions
mSystems
2022
The relationship between land cover and microbial community composition in European lakes
Science of The Total Environment
2022
Glyphosate-based herbicide exposure: effects on gill microbiota of rainbow trout (Oncorhynchus mykiss) and the aquatic bacterial ecosystem
FEMS Microbiology Ecology
2022
Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions
Ecography
2022
Combination of High-Pressure Treatment at 500 MPa and Biopreservation with a Lactococcus lactis Strain for Lowering the Bacterial Growth during Storage of Diced Cooked Ham with Reduced Nitrite Salt
Microorganisms
2022
Microbes on decomposing litter in streams: entering on the leaf or colonizing in the water?
The ISME Journal
2022
Plant genetic effects on microbial hubs impact host fitness in repeated field trials
Proceedings of the National Academy of Sciences
2022
Shared and contrasting associations in the dynamic nano‐ and picoplankton communities of two close but contrasting sites from the Bay of Biscay
Environmental Microbiology
2022
Agglomerative Clustering with Threshold Optimization via Extreme Value Theory
Algorithms
2022
Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area
Current Microbiology
2022
Niche separation between two dominant crustacean predators in European estuarine soft-bottom habitats
Ecological Indicators
2022
Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies
Environmental DNA
2022
Taming DNA clustering in massive datasets with SLYMFAST
ACM SIGAPP Applied Computing Review
2022
Invasive and native grasses exert negative plant–soil feedbacks on the woody shrub Artemisia tridentata
Oecologia
2022
Applications of Machine Learning Models to Predict and Prevent Obesity: A Mini-Review
Frontiers in Nutrition
2022
Seasonal dynamics of marine protist communities in tidally mixed coastal waters
Molecular Ecology
2022
The impacts of bovine milk, soy beverage, or almond beverage on the growing rat microbiome
PeerJ
2022
Gut Microbiota Diversity of Preterm Neonates Is Associated With Clostridioides Difficile Colonization
Frontiers in Cellular and Infection Microbiology
2022
Phylogenetic and functional diversity of Chrysophyceae in inland waters
Organisms Diversity & Evolution
2022
Insights of Host Physiological Parameters and Gut Microbiome of Indian Type 2 Diabetic Patients Visualized via Metagenomics and Machine Learning Approaches
Frontiers in Microbiology
2022
Methodology for fish biodiversity monitoring with environmental DNA metabarcoding: The primers, databases and bioinformatic pipelines
Water Biology and Security
2022
Gut content metabarcoding of three widespread Iberian ant‐eating spiders reveals specialisation on the same abundant harvester ants
Ecological Entomology
2022
Microbiome Analysis of New, Insidious Cave Wall Alterations in the Apse of Lascaux Cave
Microorganisms
2022
Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities
Frontiers in Microbiology
2022
Root‐associated fungi not tree density influences stand nitrogen dynamics at the larch forest–tundra ecotone
Journal of Ecology
2022
Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling
Frontiers in Bioinformatics
2022
Do microbial planktonic communities reflect the ecological changes of Glorieuses coral reefs (Iles Eparses, Western Indian Ocean)?
Marine Pollution Bulletin
2022
Rhizophere analysis of auxin producers harboring the phenylpyruvate decarboxylase pathway
Applied Soil Ecology
2022
Alternative to ZnO to establish balanced intestinal microbiota for weaning piglets
PLOS ONE
2022
Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding
Ecology and Evolution
2022
Organic agriculture and field edges uphold endospheric wheat microbiota at field and landscape scale
FEMS Microbiology Ecology
2022
Impact of preservation method and storage period on ribosomal metabarcoding of marine microbes: Implications for remote automated samplings
Frontiers in Microbiology
2022
Advances in Phytoplankton Ecology
2022
Influence of Sharklet‐Inspired Micropatterned Polymers on Spatio‐Temporal Variations of Marine Biofouling
Macromolecular Bioscience
2022
Gut-content analysis in four species, combined with comparative analysis of trophic traits, suggests an araneophagous habit for the entire family Palpimanidae (Araneae)
Organisms Diversity & Evolution
2022
Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion
Scientific Reports
2022
Seaweeds influence oyster microbiota and disease susceptibility
Journal of Animal Ecology
2022
Fellfields of the Kerguelen Islands harbour specific soil microbiomes and rhizomicrobiomes of an endemic plant facing necrosis
Frontiers in Soil Science
2022
Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals
Peer Community Journal
2022
Frontloading of stress response genes enhances robustness to environmental change in chimeric corals
BMC Biology
2022
Development of colorectal cancer detection and prediction based on gut microbiome big-data
Medicine in Microecology
2022
Ecological indices from environmental DNA to contrast coastal reefs under different anthropogenic pressures
Ecology and Evolution
2022
Evaluating bioinformatics pipelines for population‐level inference using environmental DNA
Environmental DNA
2022
Does clustering of DNA barcodes agree with botanical classification directly at high taxonomic levels? Trees in French Guiana as a case study
Molecular Ecology Resources
2022
Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens
Genetics Selection Evolution
2022
LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis
Microbiome
2022
Make visible the invisible: Optimized development of an environmental DNA metabarcoding tool for the characterization of trematode parasitic communities
Environmental DNA
2022
Analysis of Microbiota Persistence in Quebec’s Terroir Cheese Using a Metabarcoding Approach
Microorganisms
2022
Saccharomyces cerevisiae boulardiiCNCM I-1079 supplementation in finishing male pigs helps to cope with heat stress through feeding behaviour and gut microbiota modulation
British Journal of Nutrition
2021
Temporal Comparison of Microbial Community Structure in an Australian Winery
Fermentation
2021
Multi-marker DNA metabarcoding reflects tardigrade diversity in different habitats
Genome
2021
A multicriteria approach for assessing the recovery of soil functions following high-temperature remediation of hydrocarbons
Science of The Total Environment
2021
Effect of Aeration on Yeast Community Structure and Volatile Composition in Uninoculated Chardonnay Wines
Fermentation
2021
Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes
Environmental DNA
2021
Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA
Biotropica
2021
Temporal differences in microbial composition of Époisses cheese rinds during ripening and storage
Journal of Dairy Science
2021
A pilot experiment to assess the efficiency of pharmaceutical plant wastewater treatment and the decreasing effluent toxicity to periphytic biofilms
Journal of Hazardous Materials
2021
On the use of sequence-quality information in OTU clustering
PeerJ
2021
Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding
Science of The Total Environment
2021
Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia – a biogeographical study on Lake Remoray (France)
FEMS Microbiology Ecology
2021
A correlational study of Weifuchun and its clinical effect on intestinal flora in precancerous lesions of gastric cancer
Chinese Medicine
2021
Global drivers of eukaryotic plankton biogeography in the sunlit ocean
Science
2021
Perinatal Administration of C-Phycocyanin Protects Against Atherosclerosis in apoE-Deficient Mice by Modulating Cholesterol and Trimethylamine-N-Oxide Metabolisms
Arteriosclerosis, Thrombosis, and Vascular Biology
2021
Environmental vulnerability of the global ocean epipelagic plankton community interactome
Science Advances
2021
Plant neighbours shape fungal assemblages associated with plant roots: A new understanding of niche‐partitioning in plant communities
Functional Ecology
2021
Temporal recovery of soil biological activity and diversity after 915-MHz microwave treatments
Biology and Fertility of Soils
2021
Microbial Diversity and Activity During the Biodegradation in Seawater of Various Substitutes to Conventional Plastic Cotton Swab Sticks
Frontiers in Microbiology
2021
Large-scale geography survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa
Peer Community Journal
2021
Microbial Communities of the Drinking Water With Gradient Radon Concentration Are Primarily Contributed by Radon and Heavy Metal Content
Frontiers in Environmental Science
2021
Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia)
Ecology and Evolution
2021
Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves
Microorganisms
2021
Quantification of the covariation of lake microbiomes and environmental variables using a machine learning‐based framework
Molecular Ecology
2021
Influence of stormwater infiltration systems on the structure and the activities of groundwater biofilms: Are the effects restricted to rainy periods?
Science of The Total Environment
2021
Saccharomyces Cerevisiae Var Boulardii CNCM I–1079 Reduces Expression of Genes Involved in Inflammatory Response in Porcine Cells Challenged by Enterotoxigenic E. Coli and Influences Bacterial Communities in an In Vitro Model of the Weaning Piglet Colon
Antibiotics
2021
Early spring subglacial discharge plumes fuel under-ice primary production at a Svalbard tidewater glacier
The Cryosphere
2021
Environmental and Microbial Biotechnology
2021
Graphene-Based Nanomaterials Modulate Internal Biofilm Interactions and Microbial Diversity
Frontiers in Microbiology
2021
DNA metabarcoding improves the detection of multiple stressor responses of stream invertebrates to increased salinity, fine sediment deposition and reduced flow velocity
Science of The Total Environment
2021
Phylogenetic diversity and dominant ecological traits of freshwater Antarctic Chrysophyceae
Polar Biology
2021
16S rRNA Gene Amplicon Profiling of the New Zealand Parasitic Blowfly Calliphora vicina
Microbiology Resource Announcements
2021
Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs
Frontiers in Microbiology
2021
Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study
Environmental Microbiology
2021
Contribution of microbial photosynthesis to peatland carbon uptake along a latitudinal gradient
Journal of Ecology
2021
Peatland microhabitat heterogeneity drives phototrophic microbe distribution and photosynthetic activity
Environmental Microbiology
2021
Endurance Training in Humans Modulates the Bacterial DNA Signature of Skeletal Muscle
Biomedicines
2021
SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements
Molecular Ecology Resources
2021
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
BMC Bioinformatics
2021
The Influence of Above-Ground Herbivory on the Response of Arctic Soil Methanotrophs to Increasing CH4 Concentrations and Temperatures
Microorganisms
2021
Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing
Microbiology Resource Announcements
2021
Metabarcoding analysis suggests that flexible food web interactions in the eukaryotic plankton community are more common than specific predator–prey relationships at Helgoland Roads, North Sea
ICES Journal of Marine Science
2021
An accurate and exact clustering algorithm for next generation sequencing metagenomic sequences
Mathematical Methods in the Applied Sciences
2021
Metagenomic Analysis of Bacterial Communities in Agricultural Soils from Vietnam with Special Attention to Phosphate Solubilizing Bacteria
Microorganisms
2021
Effect of the Manufacturing Process on the Microbiota, Organoleptic Properties and Volatilome of Three Salmon-Based Products
Foods
2021
The microbial community associated with pea seeds (Pisum sativum) of different geographical origins
Plant and Soil
2021
Volatile aroma composition and sensory profile of Shiraz and Cabernet Sauvignon wines produced with novelMetschnikowia pulcherrimayeast starter cultures
Australian Journal of Grape and Wine Research
2021
Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood
Soil Biology and Biochemistry
2021
Environmental DNA effectively captures functional diversity of coastal fish communities
Molecular Ecology
2021
Biodegradation of Fipronil: Transformation Products, Microbial Characterisation and Toxicity Assessment
Water, Air, & Soil Pollution
2021
Medium-term effects of Ag supplied directly or via sewage sludge to an agricultural soil on Eisenia fetida earthworm and soil microbial communities
Chemosphere
2021
DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions
Microorganisms
2021
Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences
Frontiers in Microbiology
2021
Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts
Journal of Fungi
2021
The food web in a subterranean ecosystem is driven by intraguild predation
Scientific Reports
2021
Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities
Environmental Microbiology
2021
The microbial profile of a tissue necrosis affecting the Atlantic invasive coral Tubastraea tagusensis
Scientific Reports
2021
Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics
Genes
2021
Testing small‐scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding
Molecular Ecology
2021
Effects of the Denitrification Inhibitor “Procyanidins” on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome
Microorganisms
2021
eDNA in a bottleneck: Obstacles to fish metabarcoding studies in megadiverse freshwater systems
Environmental DNA
2021
Guide RNA Repertoires in the Main Lineages of Trypanosoma cruzi: High Diversity and Variable Redundancy Among Strains
Frontiers in Cellular and Infection Microbiology
2021
Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them?
PLOS ONE
2021
Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities
Scientific Reports
2021
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts
Microbial Genomics
2021
Pathogen Challenge and Dietary Shift Alter Microbiota Composition and Activity in a Mucin-Associated in vitro Model of the Piglet Colon (MPigut-IVM) Simulating Weaning Transition
Frontiers in Microbiology
2021
Management of biofloc concentrations as an ecological strategy for microbial control in intensive shrimp culture
Aquaculture
2021
Biodiversity monitoring using environmental DNA
Molecular Ecology Resources
2021
Proceedings of the 36th Annual ACM Symposium on Applied Computing
2021
A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis
Frontiers in Marine Science
2021
Ecotoxicological assessment of commercial boron nitride nanotubes toward Xenopus laevis tadpoles and host-associated gut microbiota
Nanotoxicology
2021
Composition and functional comparison of vetiver root endophytic microbiota originating from different geographic locations that show antagonistic activity towards Fusarium graminearum
Microbiological Research
2021
Swarm v3: towards tera-scale amplicon clustering
Bioinformatics
2021
Links between fecal microbiota and the response to vaccination against influenza A virus in pigs
npj Vaccines
2021
Pollutant removal, electricity generation and microbial community in an electrochemical membrane bioreactor during co-treatment of sewage and landfill leachate
Journal of Environmental Chemical Engineering
2021
The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms
Molecular Ecology Resources
2021
eDNA metabarcoding reveals a core and secondary diets of the greater horseshoe bat with strong spatio‐temporal plasticity
Environmental DNA
2021
Microbiome Preprocessing Machine Learning Pipeline
Frontiers in Immunology
2021
Multiple Selection Criteria for Probiotic Strains with High Potential for Obesity Management
Nutrients
2021
An investigation into the anaerobic spoilage microbiota of beef carcass and rump steak cuts using high- throughput sequencing
FEMS Microbiology Letters
2021
Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM)
Journal of Animal Science and Biotechnology
2021
Impact of Soil-Applied Microbial Inoculant and Fertilizer on Fungal and Bacterial Communities in the Rhizosphere of Robinia sp. and Populus sp. Plantations
Forests
2021
Effects of silver nanoparticles on performance of anaerobic digestion of sewage sludge and associated microbial communities
Renewable Energy
2020
Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes
Microbial Ecology
2020
Microbial Communities of the Shallow-Water Hydrothermal Vent Near Naples, Italy, and Chemosynthetic Symbionts Associated With a Free-Living Marine Nematode
Frontiers in Microbiology
2020
Taxonomic differences shape the responses of freshwater aerobic anoxygenic phototrophic bacterial communities to light and predation
Molecular Ecology
2020
Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes
The ISME Journal
2020
Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location
Molecular Ecology
2020
Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software
Ecological Indicators
2020
Exploring the Role of Macroalgal Surface Metabolites on the Settlement of the Benthic Dinoflagellate Ostreopsis cf. ovata
Frontiers in Marine Science
2020
Evolution of gut microbial community through reproductive life in female rabbits and investigation of the link with offspring survival
Animal
2020
Implications of increasing Atlantic influence for Arctic microbial community structure
Scientific Reports
2020
Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations
Scientific Reports
2020
DNA Metabarcoding as a Tool for Disentangling Food Webs in Agroecosystems
Insects
2020
Alterations in Yeast Species Composition of Uninoculated Wine Ferments by the Addition of Sulphur Dioxide
Fermentation
2020
Modulation of pathogenic oral biofilms towards health with nisin probiotic
Journal of Oral Microbiology
2020
High Diversity of Testate Amoebae (Amoebozoa, Arcellinida) Detected by HTS Analyses in a New England Fen using Newly Designed Taxon‐specific Primers
Journal of Eukaryotic Microbiology
2020
No ontogenetic shift in the realised trophic niche but in Batesian mimicry in an ant-eating spider
Scientific Reports
2020
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
IMA Fungus
2020
Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss)
Frontiers in Microbiology
2020
Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects
Biodiversity and Conservation
2020
A Landscape of Opportunities for Microbial Ecology Research
Frontiers in Microbiology
2020
Persistence of plastic debris and its colonization by bacterial communities after two decades on the abyssal seafloor
Scientific Reports
2020
Arbuscular mycorrhizal fungi in roots and soil respond differently to biotic and abiotic factors in the Serengeti
Mycorrhiza
2020
Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages
FEMS Microbiology Ecology
2020
Effect of Litter Treatment on Campylobacter jejuni in Broilers and on Cecal Microbiota
Pathogens
2020
The role of sedimentation in the structuring of microbial communities in biofloc-dominated aquaculture tanks
Aquaculture
2020
Novel Rickettsia genotypes in ticks in French Guiana, South America
Scientific Reports
2020
Initial Sequencing and Characterization of the Gastrointestinal and Oral Microbiota in Urban Pakistani Adults
Frontiers in Cellular and Infection Microbiology
2020
Ant‐eating spider maintains specialist diet throughout its ontogeny
Journal of Zoology
2020
Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients
Frontiers in Microbiology
2020
Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme
PLOS ONE
2020
CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
PLOS ONE
2020
Tropical forest type influences community assembly processes in arbuscular mycorrhizal fungi
Journal of Biogeography
2020
Detection and spread of Phytophthora austrocedri within infected Juniperus communis woodland and diversity of co‐associated Phytophthoras as revealed by metabarcoding
Forest Pathology
2020
Alpine Snow Algae Microbiome Diversity in the Coast Range of British Columbia
Frontiers in Microbiology
2020
Nitrifying and Denitrifying Microbial Communities in Centralized and Decentralized Biological Nitrogen Removing Wastewater Treatment Systems
Water
2020
Gut microbiome composition and risk factors in a large cross-sectional IBS cohort
BMJ Open Gastroenterology
2020
Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible
The ISME Journal
2020
Methanotroph populations and CH4 oxidation potentials in high-Arctic peat are altered by herbivory induced vegetation change
FEMS Microbiology Ecology
2020
Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel
The ISME Journal
2020
Dataset of foraminiferal sedimentary DNA (sedDNA) sequences from Svalbard
Data in Brief
2020
The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth)
Biogeosciences
2020
Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences
Ecography
2020
Soil P reduces mycorrhizal colonization while favors fungal pathogens: observational and experimental evidence in Bipinnula (Orchidaceae)
FEMS Microbiology Ecology
2020
Effects of a Low-Fat Vegan Diet on Gut Microbiota in Overweight Individuals and Relationships with Body Weight, Body Composition, and Insulin Sensitivity. A Randomized Clinical Trial
Nutrients
2020
Assessment of graphene oxide ecotoxicity at several trophic levels using aquatic microcosms
Carbon
2020
Impact of sampling and DNA extraction methods on skin microbiota assessment
Journal of Microbiological Methods
2020
Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back
Frontiers in Microbiology
2020
Methods to Study Litter Decomposition
2020
Large microbiota survey reveals how the microbial ecology of cooked ham is shaped by different processing steps
Food Microbiology
2020
Who is eating fructose within the Aedes albopictus gut microbiota?
Environmental Microbiology
2020
Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
Animal Microbiome
2020
Identifying Mechanisms for Successful Ecological Restoration with Salvaged Topsoil in Coastal Sage Scrub Communities
Diversity
2020
Two ectomycorrhizal truffles, Tuber melanosporum and T. aestivum, endophytically colonise roots of non‐ectomycorrhizal plants in natural environments
New Phytologist
2020
Local oral and nasal microbiome diversity in age-related macular degeneration
Scientific Reports
2020
Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area
Frontiers in Marine Science
2020
Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effects
Scientific Reports
2020
Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing
PeerJ
2020
A Multi-Omics Analysis Suggests Links Between the Differentiated Surface Metabolome and Epiphytic Microbiota Along the Thallus of a Mediterranean Seaweed Holobiont
Frontiers in Microbiology
2020
Characterization of the microbial community composition in Italian Cinta Senese sausages dry-fermented with natural extracts as alternatives to sodium nitrite
Food Microbiology
2020
Effect of floristic composition and configuration on plant root mycobiota: a landscape transposition at a small scale
New Phytologist
2020
Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes
Science of The Total Environment
2020
Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area
Ecology and Evolution
2020
Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding
PLOS ONE
2020
Factors shaping community patterns of protists and bacteria on a European scale
Environmental Microbiology
2020
Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments
Ecology and Evolution
2020
Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome
Microbiome
2020
Rhubarb Supplementation Prevents Diet-Induced Obesity and Diabetes in Association with Increased Akkermansia muciniphila in Mice
Nutrients
2020
Ectomycorrhizal and Dark Septate Fungal Associations of Pinyon Pine Are Differentially Affected by Experimental Drought and Warming
Frontiers in Plant Science
2020
ReClustOR: a re‐clustering tool using an open‐reference method that improves operational taxonomic unit definition
Methods in Ecology and Evolution
2020
Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean
Global Ecology and Biogeography
2020
Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity
Environmental Microbiology
2020
Protistan and fungal diversity in soils and freshwater lakes are substantially different
Scientific Reports
2020
A Conserved TCRβ Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection
Frontiers in Immunology
2020
Influence of Macrophyte and Gut Microbiota on Mercury Contamination in Fish: A Microcosms Study
Applied Sciences
2020
Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos
Metabarcoding and Metagenomics
2020
Early Introduction of Solid Feeds: Ingestion Level Matters More Than Prebiotic Supplementation for Shaping Gut Microbiota
Frontiers in Veterinary Science
2020
Multiproxy evidence of the Neoglacial expansion of Atlantic Water to eastern Svalbard
Climate of the Past
2020
Gut microbiota composition before infection determines the Salmonella super‐ and low‐shedder phenotypes in chicken
Microbial Biotechnology
2020
Sensory ecology of the frog-eating bat, Trachops cirrhosus, from DNA metabarcoding and behavior
Behavioral Ecology
2020
Fat‐Shaped Microbiota Affects Lipid Metabolism, Liver Steatosis, and Intestinal Homeostasis in Mice Fed a Low‐Protein Diet
Molecular Nutrition & Food Research
2020
Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking
Frontiers in Microbiology
2020
Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota
Childhood Obesity
2020
Glucose triggers strong taxon‐specific responses in microbial growth and activity: insights from DNA and RNA qSIP
Ecology
2020
Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle
Proceedings of the Royal Society B: Biological Sciences
2020
Exploring Environmental DNA (eDNA) to Assess Biodiversity of Hard Substratum Faunal Communities on the Lucky Strike Vent Field (Mid-Atlantic Ridge) and Investigate Recolonization Dynamics After an Induced Disturbance
Frontiers in Marine Science
2020
The marine intertidal zone shapes oyster and clam digestive bacterial microbiota
FEMS Microbiology Ecology
2020
Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data
Frontiers in Genetics
2020
Environmental DNA reveals seasonal shifts and potential interactions in a marine community
Nature Communications
2020
Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Scientific Reports
2020
Salmon Gravlax Biopreservation With Lactic Acid Bacteria: A Polyphasic Approach to Assessing the Impact on Organoleptic Properties, Microbial Ecosystem and Volatilome Composition
Frontiers in Microbiology
2020
Antibiotic-induced microbiome perturbations are associated with significant alterations to colonic mucosal immunity in rhesus macaques
Mucosal Immunology
2020
Coexistence of two termite‐eating specialists (Araneae)
Ecological Entomology
2020
Estimation of trophic niches in myrmecophagous spider predators
Scientific Reports
2020
Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern
Frontiers in Microbiology
2020
In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses
Ecology and Evolution
2020
Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis
Animal Microbiome
2020
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
GigaScience
2020
The influence of host‐plant connectivity on fungal assemblages in the root microbiota of Brachypodium pinnatum
Ecology
2020
Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea
Journal of Plankton Research
2019
The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills
Environmental Microbiology
2019
Global Trends in Marine Plankton Diversity across Kingdoms of Life
Cell
2019
Effect of sodium chloride reduction or partial substitution with potassium chloride on the microbiological, biochemical and sensory characteristics of semi-hard and soft cheeses
Food Research International
2019
Current practice in plankton metabarcoding: optimization and error management
Journal of Plankton Research
2019
Metabarcoding reveals a high diversity of woody host-associatedPhytophthoraspp. in soils at public gardens and amenity woodlands in Britain
PeerJ
2019
Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
PLOS ONE
2019
Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta)
Microbial Ecology
2019
Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments
Nature Protocols
2019
Photoperiod modulates the gut microbiome and aggressive behavior in Siberian hamsters
Journal of Experimental Biology
2019
Contrasted Micro-Eukaryotic Diversity Associated with Sphagnum Mosses in Tropical, Subtropical and Temperate Climatic Zones
Microbial Ecology
2019
How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation
Mycorrhiza
2019
Design of microbial consortia for the fermentation of pea-protein-enriched emulsions
International Journal of Food Microbiology
2019
Host genetics and geography influence microbiome composition in the spongeIrcinia campana
Journal of Animal Ecology
2019
Mycobiome diversity: high-throughput sequencing and identification of fungi
Nature Reviews Microbiology
2019
Anaerobic Degradation of Non-Methane Alkanes by “ Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico
mBio
2019
Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river
Environmental DNA
2019
Microbiome Variation in an Intertidal Sea Anemone Across Latitudes and Symbiotic States
Frontiers in Marine Science
2019
Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms
PLOS ONE
2019
Haem iron reshapes colonic luminal environment: impact on mucosal homeostasis and microbiome through aldehyde formation
Microbiome
2019
Global distribution of Trebouxiophyceae diversity explored by high‐throughput sequencing and phylogenetic approaches
Environmental Microbiology
2019
Responses of arbuscular mycorrhizal fungi to multiple coinciding global change drivers
Fungal Ecology
2019
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2019
Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves
Molecular Ecology
2019
Dehydrated Alfalfa and Fresh Grass Supply in Young Rabbits: Effect on Performance and Caecal Microbiota Biodiversity
Animals
2019
FACEPAI: a script for fast and consistent environmental DNA processing and identification
BMC Ecology
2019
Hydrocarbon-Degrading Microbial Communities Are Site Specific, and Their Activity Is Limited by Synergies in Temperature and Nutrient Availability in Surface Ocean Waters
Applied and Environmental Microbiology
2019
Dispersant Enhances Hydrocarbon Degradation and Alters the Structure of Metabolically Active Microbial Communities in Shallow Seawater From the Northeastern Gulf of Mexico
Frontiers in Microbiology
2019
Communications in Computer and Information Science
2019
Surface sterilization methods impact measures of internal microbial diversity in ticks
Parasites & Vectors
2019
The composition and abundance of bacterial communities residing in the gut of Glossina palpalis palpalis captured in two sites of southern Cameroon
Parasites & Vectors
2019
Biodiversity of leaf litter fungi in streams along a latitudinal gradient
Science of The Total Environment
2019
The fecal resistome of dairy cattle is associated with diet during nursing
Nature Communications
2019
Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets
Microorganisms
2019
A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA
Molecular Ecology Resources
2019
Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities
PLOS ONE
2019
Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants
Environmental Microbiology
2019
Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse
Scientific Reports
2019
Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean
The ISME Journal
2019
Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring
Molecular Ecology Resources
2019
Aedes albopictus mosquitoes host a locally structured mycobiota with evidence of reduced fungal diversity in invasive populations
Fungal Ecology
2019
Chemosynthetic ectosymbionts associated with a shallow-water marine nematode
Scientific Reports
2019
Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits
Frontiers in Microbiology
2019
Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding
Ecology and Evolution
2019
Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems
Molecular Ecology Resources
2019
Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP
Frontiers in Microbiology
2019
Rapid alignment-free phylogenetic identification of metagenomic sequences
Bioinformatics
2019
Coupling between taxonomic and functional diversity in protistan coastal communities
Environmental Microbiology
2019
Behavior of two-chamber microbial electrochemical systems started-up with different ion-exchange membrane separators
Bioresource Technology
2019
A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis
PLOS ONE
2019
DNAmetabarcoding unveils multiscale trophic variation in a widespread coastal opportunist
Molecular Ecology
2019
A Bioinformatics Guide to Plant Microbiome Analysis
Frontiers in Plant Science
2019
Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding
Scientific Reports
2019
Hydrogen production in reactors: The influence of organic loading rate, inoculum and support material
International Journal of Hydrogen Energy
2019
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Genome Biology
2019
Microbial community composition of sediments influenced by intensive mariculture activity
FEMS Microbiology Ecology
2019
Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single‐cell high‐throughput DNA sequencing
Limnology and Oceanography: Methods
2019
Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring
Environmental Science & Technology
2019
What Can Environmental Sequences Tell Us About the Distribution of Low‐Rank Taxa? The Case of Euplotes (Ciliophora, Spirotrichea), Including a Description of Euplotes enigma sp. nov.
Journal of Eukaryotic Microbiology
2019
Temporal development of the oral microbiome and prediction of early childhood caries
Scientific Reports
2019
Influence of feed temperature to biofouling of ultrafiltration membrane during skim milk processing
International Dairy Journal
2019
Anthocyanins protect the gastrointestinal tract from high fat diet-induced alterations in redox signaling, barrier integrity and dysbiosis
Redox Biology
2019
A critical analysis of state-of-the-art metagenomics OTU clustering algorithms
Journal of Biosciences
2019
Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks
Frontiers in Plant Science
2019
rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing
BMC Microbiology
2019
A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data
Journal of Computational Biology
2019
Evolution of intestinal microbiota and body compartments during spontaneous hyperphagia in the Greylag goose
Poultry Science
2019
Is It First the Egg or the Shrimp? – Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development
Frontiers in Microbiology
2019
Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments
Environmental Microbiology
2019
Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front
Frontiers in Microbiology
2019
The prebiotic effect of CPP-ACP sugar-free chewing gum
Journal of Dentistry
2019
Analysis of microbiota in cultures of the green microalga Tetraselmis suecica
European Journal of Phycology
2019
Sustainable Development and Biodiversity
2018
Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis
Molecular Ecology
2018
Over 2.5 million COI sequences in GenBank and growing
PLOS ONE
2018
Neobodonids are dominant kinetoplastids in the global ocean
Environmental Microbiology
2018
Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill
Molecular Ecology
2018
Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species
Evolutionary Applications
2018
Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study
Science of The Total Environment
2018
Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset
Scientific Reports
2018
Illuminating prey selection in an insectivorous bat community exposed to artificial light at night
Journal of Applied Ecology
2018
Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing
PLOS ONE
2018
Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation
Frontiers in Plant Science
2018
(-)-Epicatechin protects the intestinal barrier from high fat diet-induced permeabilization: Implications for steatosis and insulin resistance
Redox Biology
2018
Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro-eukaryotes from a suspected homicide to estimate the post-mortem interval
Scientific Reports
2018
Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size
Environmental Pollution
2018
Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors
Microbiome
2018
Intra-host sequence variability in human papillomavirus
Papillomavirus Research
2018
Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization
PLOS ONE
2018
Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean)
Frontiers in Microbiology
2018
Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato
Microbiome
2018
Geographic distance and mountain ranges structure freshwater protist communities on a European scalе
Metabarcoding and Metagenomics
2018
Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters
Nature Communications
2018
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current
Frontiers in Microbiology
2018
Detection of Coccidioides posadasii from xerophytic environments in Venezuela reveals risk of naturally acquired coccidioidomycosis infections
Emerging Microbes & Infections
2018
Microeukaryote community in a partial nitritation reactor prior to anammox and an insight into the potential of ciliates as performance bioindicators
New Biotechnology
2018
Tick-Bacteria Mutualism Depends on B Vitamin Synthesis Pathways
Current Biology
2018
Shift in skin microbiota of Western European women across aging
Journal of Applied Microbiology
2018
Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus Pseudo-nitzschia: Genetic, Morphological, and Ecological Characterisation
Frontiers in Microbiology
2018
Is Tuber melanosporum colonizing the roots of herbaceous, non-ectomycorrhizal plants?
Fungal Ecology
2018
HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies
Genome Biology
2018
Early-life sickness may predispose Siberian hamsters to behavioral changes following alterations of the gut microbiome in adulthood
Brain, Behavior, and Immunity
2018
Bacterial Abundance and Community Composition in Pond Water From Shrimp Aquaculture Systems With Different Stocking Densities
Frontiers in Microbiology
2018
Effects of triclosan in breast milk on the infant fecal microbiome
Chemosphere
2018
Short-term impacts of anthropogenic stressors on Aedes albopictus mosquito vector microbiota
FEMS Microbiology Ecology
2018
Dynamics of compost microbiota during the cultivation of Agaricus bisporus in the presence of Bacillus velezensis QST713 as biocontrol agent against Trichoderma aggressivum
Biological Control
2018
Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine
Science of The Total Environment
2018
Disparities in second‐generation DNA metabarcoding results exposed with accessible and repeatable workflows
Molecular Ecology Resources
2018
SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing
Nucleic Acids Research
2018
Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions
Molecular Ecology Resources
2018
Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island)
Molecular Ecology
2018
Cryptophyta as major bacterivores in freshwater summer plankton
The ISME Journal
2018
The impact of artificial surfaces on marine bacterial and eukaryotic biofouling assemblages: A high-throughput sequencing analysis
Marine Environmental Research
2018
Composition of Intestinal Microbiota in Two Lines of Rainbow Trout (Oncorhynchus Mykiss) Divergently Selected for Muscle Fat Content
The Open Microbiology Journal
2018
Diversity of bacterial communities in French chicken cuts stored under modified atmosphere packaging
Food Microbiology
2018
Evaluation of marine zooplankton community structure through environmental DNA metabarcoding
Limnology and Oceanography: Methods
2018
Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site
The ISME Journal
2018
Probiotics Strains Modulate Gut Microbiota and Lipid Metabolism in Mule Ducks
The Open Microbiology Journal
2018
Using pseudoalignment and base quality to accurately quantify microbial community composition
PLOS Computational Biology
2018
Understanding bacterial communities for informed biosecurity and improved larval survival in Pacific oysters
Aquaculture
2018
Incorporating molecular-based functional and co-occurrence network properties into benthic marine impact assessments
FEMS Microbiology Ecology
2018
Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System
Frontiers in Microbiology
2018
16S rRNA amplicon sequencing reveals a polymicrobial nature of complicated claw horn disruption lesions and interdigital phlegmon in dairy cattle
Scientific Reports
2018
Tipping point in plant–fungal interactions under severe drought causes abrupt rise in peatland ecosystem respiration
Global Change Biology
2018
Nitrifying and Denitrifying Bacterial Communities in Advanced Nitrogen‐Removal Onsite Wastewater Treatment Systems
Journal of Environmental Quality
2018
Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD
Applied and Environmental Microbiology
2018
Acute intraperitoneal lipopolysaccharide influences the immune system in the absence of gut dysbiosis
Physiological Reports
2018
GeFaST: An improved method for OTU assignment by generalising Swarm’s fastidious clustering approach
BMC Bioinformatics
2018
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
F1000Research
2018
Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon
IMA Fungus
2018
Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates
PeerJ
2018
FROGS: Find, Rapidly, OTUs with Galaxy Solution
Bioinformatics
2018
Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects
Water Research
2018
Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment
Frontiers in Microbiology
2018
Methods in Molecular Biology
2018
Facultative methanotrophs are abundant at terrestrial natural gas seeps
Microbiome
2018
The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis
mSphere
2018
Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems
Scientific Reports
2018
A microorganisms’ journey between plant generations
Microbiome
2018
Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline
Applied and Environmental Microbiology
2018
Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes
Frontiers in Microbiology
2018
Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean
Current Biology
2018
Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave
Microbiome
2018
Sequence clustering in bioinformatics: an empirical study
Briefings in Bioinformatics
2018
In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different
Pediatric Pulmonology
2018
Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding
PeerJ
2018
2018 International Joint Conference on Neural Networks (IJCNN)
2018
Plant host habitat and root exudates shape fungal diversity
Mycorrhiza
2018
Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products
BMC Research Notes
2018
A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship
Frontiers in Microbiology
2018
Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions
PeerJ
2018
Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding
FEMS Microbiology Ecology
2018
A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations
Marine Pollution Bulletin
2017
Sensory profile and volatile aroma composition of reduced alcohol Merlot wines fermented with Metschnikowia pulcherrima and Saccharomyces uvarum
International Journal of Food Microbiology
2017
DACE: a scalable DP-means algorithm for clustering extremely large sequence data
Bioinformatics
2017
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
Molecular Ecology
2017
Bridging the gap between morphological species and molecular barcodes – Exemplified by loricate choanoflagellates
European Journal of Protistology
2017
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept
Frontiers in Microbiology
2017
Effects of short-term flooding on aquatic and terrestrial microeukaryotic communities: a mesocosm approach
Aquatic Microbial Ecology
2017
Bacterial Biofilm Communities and Coral Larvae Settlement at Different Levels of Anthropogenic Impact in the Spermonde Archipelago, Indonesia
Frontiers in Marine Science
2017
Microbiome analysis shows enrichment for specific bacteria in separate anatomical regions of the deep-sea carnivorous spongeChondrocladia grandis
FEMS Microbiology Ecology
2017
Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description
Molecular Ecology Resources
2017
Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections
BMC Genomics
2017
Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle
Journal of Eukaryotic Microbiology
2017
A metabarcoding comparison of windward and leeward airborne algal diversity across the Ko‘olau mountain range on the island of O'ahu, Hawai‘i1
Journal of Phycology
2017
Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding
PLOS ONE
2017
A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater
Viruses
2017
Impact of feed restriction and housing hygiene conditions on specific and inflammatory immune response, the cecal bacterial community and the survival of young rabbits
Animal
2017
From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
GigaScience
2017
ITS1 metabarcoding highlights low specificity of lichen mycobiomes at a local scale
Molecular Ecology
2017
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities
BMC Bioinformatics
2017
A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
GigaScience
2017
Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels
Frontiers in Marine Science
2017
Probiotics in Agroecosystem
2017
Critical Issues in Mycobiota Analysis
Frontiers in Microbiology
2017
Organic amendment practices as possible drivers of biogenic Volatile Organic Compounds emitted by soils in agrosystems
Agriculture, Ecosystems & Environment
2017
OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
mSphere
2017
Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change
Frontiers in Ecology and Evolution
2017
Fine-scale transition to lower bacterial diversity and altered community composition precedes shell disease in laboratory-reared juvenile American lobster
Diseases of Aquatic Organisms
2017
Spatial distribution of environmental DNA in a nearshore marine habitat
PeerJ
2017
Biogeography and diversity of Collodaria (Radiolaria) in the global ocean
The ISME Journal
2017
Characterization of the Culturable Subpopulations of Lactobacillus in the Chicken Intestinal Tract as a Resource for Probiotic Development
Frontiers in Microbiology
2017
High-resolution characterization of the human microbiome
Translational Research
2017
16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome
PLOS ONE
2017
Exploring the Ecological Coherence between the Spatial and Temporal Patterns of Bacterioplankton in Boreal Lakes
Frontiers in Microbiology
2017
Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics
PLOS ONE
2017
Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond
Aquatic Microbial Ecology
2017
Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments
Frontiers in Microbiology
2017
Reconciliation between operational taxonomic units and species boundaries
FEMS Microbiology Ecology
2017
Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene
Harmful Algae
2017
Vector soup: high‐throughput identification of Neotropical phlebotomine sand flies using metabarcoding
Molecular Ecology Resources
2017
Identifying the core seed bank of a complex boreal bacterial metacommunity
The ISME Journal
2017
Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling
Soil Biology and Biochemistry
2017
Invasive Drosophila suzukii facilitates Drosophila melanogaster infestation and sour rot outbreaks in the vineyards
Royal Society Open Science
2017
Habitat- and soil-related drivers of the root-associated fungal community of Quercus suber in the Northern Moroccan forest
PLOS ONE
2017
Integrating “Big Data” into Aquatic Ecology: Challenges and Opportunities
Limnology and Oceanography Bulletin
2017
Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters
The ISME Journal
2017
Microbiome sharing between children, livestock and household surfaces in western Kenya
PLOS ONE
2016
The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates
Scientific Reports
2016
Protist metabarcoding and environmental biomonitoring: Time for change
European Journal of Protistology
2016
Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes
FEMS Microbiology Reviews
2016
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
Journal of Biomedical Semantics
2016
Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods
mSystems
2016
Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms
The ISME Journal
2016
Emerging Technologies for Gut Microbiome Research
Trends in Microbiology
2016
Comparison of three clustering approaches for detecting novel environmental microbial diversity
PeerJ
2016
A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring
Philosophical Transactions of the Royal Society B: Biological Sciences
2016
Landscape‐scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton
Ecology Letters
2016
Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA
PeerJ
2016
Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes
Environmental Microbiology
2016
Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil
Methods in Ecology and Evolution
2016
Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont‐rich aphid genus
Molecular Ecology Resources
2016
Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing
Applied and Environmental Microbiology
2016
Insights into global diatom distribution and diversity in the world’s ocean
Proceedings of the National Academy of Sciences
2016
A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units
PeerJ
2016
Detection of Invertebrate Suppressive Soils, and Identification of a Possible Biological Control Agent for Meloidogyne Nematodes Using High Resolution Rhizosphere Microbial Community Analysis
Frontiers in Plant Science
2016
Inferring neutral biodiversity parameters using environmental DNA data sets
Scientific Reports
2016
CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment
PLOS ONE
2016
A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA
BMC Ecology
2016
Censusing marine eukaryotic diversity in the twenty-first century
Philosophical Transactions of the Royal Society B: Biological Sciences
2016
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
F1000Research
2016
The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data
Genome
2016
Phylogenetic diversity and biogeography of the Mamiellophyceae lineage of eukaryotic phytoplankton across the oceans
Environmental Microbiology Reports
2016
Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches
FEMS Microbiology Ecology
2016
Cover crops prevent the deleterious effect of nitrogen fertilisation on bacterial diversity by maintaining the carbon content of ploughed soil
Geoderma
2016
Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals
Proceedings of the National Academy of Sciences
2016
Cheatgrass invasion alters the abundance and composition of dark septate fungal communities in sagebrush steppe
Botany
2016
Open-Source Sequence Clustering Methods Improve the State Of the Art
mSystems
2016
VSEARCH: a versatile open source tool for metagenomics
PeerJ
2016
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
Environmental Microbiology
2016
Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments
Nature Communications
2016
Bacterial community composition of flocculent matter under a salmonid aquaculture site in Newfoundland, Canada
Aquaculture Environment Interactions
2016
A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity
npj Biofilms and Microbiomes
2016
Microbial eukaryote plankton communities of high‐mountain lakes from three continents exhibit strong biogeographic patterns
Molecular Ecology
2016
The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories
BMC Microbiology
2016
Using environmental (e)DNA sequencing for aquatic biodiversity surveys: a beginner’s guide
Marine and Freshwater Research
2015
Mining environmental high‐throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization
Environmental Microbiology Reports
2015
Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds
Extremophiles
2015
Swarm v2: highly-scalable and high-resolution amplicon clustering
PeerJ
2015
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
PeerJ
2015
Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods
Ecology and Evolution
2015
Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River
Frontiers in Microbiology
2015
Phylogenetic approaches to microbial community classification
Microbiome
2015
Microbial Malaise: How Can We Classify the Microbiome?
Trends in Microbiology
2015
Determinants of community structure in the global plankton interactome
Science
2015
Rarity in aquatic microbes: placing protists on the map
Research in Microbiology
2015
Comparing High‐throughput Platforms for Sequencing the V4 Region of SSU‐rDNA in Environmental Microbial Eukaryotic Diversity Surveys
Journal of Eukaryotic Microbiology
2015
Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?
Ecology and Evolution
2015
Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany)
Environmental Microbiology
2015
Springer Protocols Handbooks
2015
Eukaryotic plankton diversity in the sunlit ocean
Science
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