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2025
Using Flower eDNA Metabarcoding to Identify the Effects of Forest Structure and Microclimate on Flower‐Visiting Arthropods
Environmental DNA
2025
Metagenomics
2025
Short- and long-term sex-dependent effects of a nutritional supplement after hatching on growth, metabolism and gut microbiota in broiler chickens
British Poultry Science
2025
Mangrove consortium resistant to the emerging contaminant DEHP: Composition, diversity, and ecological function of bacteria
PLOS One
2025
Interest of inulin in obesity: comparison of the prebiotic effect of edible-food sources versus purified inulin from chicory root
European Journal of Nutrition
2025
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020
Molecular Ecology Resources
2025
Plant Genetic Bases Associated With Microbiota Descriptors Shed Light Into a Novel Holobiont Generalist Genes Theory
Environmental Microbiology
2025
Three‐dimensional conservation planning of fish biodiversity metrics to achieve the deep‐sea 30×30 conservation target
Conservation Biology
2025
Using the long-term genetic monitoring network ARMS-MBON to detect marine non-indigenous species along the European coasts
Biological Invasions
2025
Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics
Environmental Microbiology
2025
Gut microbiota dysfunction in Crohn’s disease
Frontiers in Cellular and Infection Microbiology
2025
Contrasting diversity patterns using Autonomous Reef Monitoring Structures deployed in pelagic vs. benthic environments
Continental Shelf Research
2025
A Confidence Scoring Procedure for eDNA Metabarcoding Records and Its Application to a Global Marine Fish Dataset
Environmental DNA
2025
Soil Prokaryotic Diversity Responds to Seasonality in Dehesas, Modulated by Tree Identity and Canopy Effect
Microbiology Research
2025
Low‐Effort eDNA Sampling Reveals Fish Community Patterns in a Neotropical River Basin
Environmental DNA
2025
Short-read next-generation sequencing of 16s rRNA gene amplicons for characterizing amplicon sequence variants (ASVs) and determination of gene copy numbers using ion Torrent platform
Nucleosides, Nucleotides & Nucleic Acids
2025
Multi‐Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats
Molecular Ecology Resources
2025
Manual of Molecular Microbiology
2025
Contrasting Dynamics and Biotic Association Networks in Estuarine Microbenthic Communities Along an Environmental Disturbance Gradient
Environmental DNA
2025
Freshwater Foraminifera Biodiversity in New England (USA): Evaluation of Field Sites and a Botanical Garden
Ecology and Evolution
2025
Prevalence of pelagic diatoms and harmful algae in tellinid bivalve diets during record low sea ice in the Pacific Arctic determined by DNA metabarcoding
Frontiers in Marine Science
2025
Pioneering DNA metabarcoding analysis of the African wolf (Canis lupaster) diet
Mammalian Biology
2025
Detecting Threatened Ichthyofauna in a Mediterranean Intensive Agricultural Landscape: From DNA Traces to Electrofishing
Aquatic Conservation: Marine and Freshwater Ecosystems
2025
High‐frequency sampling unveils biotic and abiotic drivers of rapid phytoplankton morphological changes
New Phytologist
2025
Metabarcoding identifies macroalgal composition as a driver of benthic invertebrate assemblages in restored habitats
Scientific Reports
2025
DNA Divers: Volunteer‐based eDNA capture for local and global marine biodiversity monitoring
Methods in Ecology and Evolution
2025
Sulfamethazine biodegradation in sediments is driven by chronic exposure concentrations
Ecotoxicology and Environmental Safety
2025
Diet of European hake (Merluccius merluccius) preflexion larvae in the Atlantic through DNA metabarcoding: eating fish from the very beginning
Marine Biodiversity
2024
DNA metabarcoding as a tool for characterising the spatio-temporal distribution of planktonic larvae in the phylum Echinodermata
Coral Reefs
2024
DNA metabarcoding reveals a diverse, omnivorous diet of Arctic amphipods during the polar night, with jellyfish and fish as major prey
Frontiers in Marine Science
2024
Functional and compositional responses of stream microphytobenthic communities to multiple stressors increase and release in a mesocosm experiment
Science of The Total Environment
2024
Swarm and UNOISE outperform DADA2 and Deblur for denoising high-diversity marine seafloor samples
ISME Communications
2024
Spatial and temporal diversity of Simulium damnosum s.l. gut microbiota and association with Onchocerca volvulus infection in Cameroon
Infection, Genetics and Evolution
2024
Spatio-temporal variation of the endangered Dupont’s Lark diet across Iberia and Morocco
PLOS ONE
2024
SimpleMetaPipeline: Breaking the bioinformatics bottleneck in metabarcoding
Methods in Ecology and Evolution
2024
Fish Gut Metabarcoding Detects Diets and Parasites Simultaneously
Environmental DNA
2024
Effects of livestock on arthropod biodiversity in Iberian holm oak savannas revealed by metabarcoding
Journal of Environmental Management
2024
Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches
Environmental DNA
2024
Towards eDNA informed biodiversity studies – Comparing water derived molecular taxa with traditional survey methods
Progress in Oceanography
2024
The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves
Molecular Ecology
2024
A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species
iScience
2024
Detecting Fish Diversity in Urban‐Impacted Ecosystems: A Comparative Approach of eDNA Metabarcoding and UVC
Environmental DNA
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
Unveiling the impact of human urine fertilization on soil bacterial communities: A path toward sustainable fertilization
Applied Soil Ecology
2024
Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data
FEMS Microbiology Letters
2024
Multiple nutrient limitation of the soil micro-food web in a tropical grassland revealed by nutrient-omission fertilization
Applied Soil Ecology
2024
Net gain: Low‐cost, trawl‐associated eDNA samplers upscale ecological assessment of marine demersal communities
Environmental DNA
2024
DNA-based marine benthic assessment methods can perform as morphological ones, but an intercalibration is needed
Ecological Indicators
2024
Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment
Ecology and Evolution
2024
Comparative identification of phytoplankton taxonomic and functional group approach in karst lakes using classical microscopy and eDNA metabarcoding for ecological status assessment
Hydrobiologia
2024
Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing
European Journal of Protistology
2024
Investigating pelagic biodiversity and gelatinous zooplankton communities in the rapidly changing European Arctic: An eDNA metabarcoding survey
Environmental DNA
2024
Assessment of microphytobenthos communities in the Kinzig catchment using photosynthesis-related traits, digital light microscopy and 18S-V9 amplicon sequencing
Frontiers in Ecology and Evolution
2024
Common birds combine pest control and seed dispersal in apple orchards through a hybrid interaction network
Agriculture, Ecosystems & Environment
2024
Simple approaches for evaluation of OTU quality based on dissimilarity arrays
Metabarcoding and Metagenomics
2024
Naegleria fowleri Detected in Grand Teton National Park Hot Springs
ACS ES&T Water
2024
Biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring
Science of The Total Environment
2024
Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands
Ecology and Evolution
2024
Fishing in the gene-pool: implementing trawl-associated eDNA metaprobe for large scale monitoring of fish assemblages
Reviews in Fish Biology and Fisheries
2024
A belly full of jelly? DNA metabarcoding shows evidence for gelatinous zooplankton predation by several fish species in Greenland waters
Royal Society Open Science
2024
Serial cultures in invert emulsion and monophase systems for microbial community shaping and propagation
Microbial Cell Factories
2024
Epigallocatechin Gallate Enzymatic Alpha Glucosylation Potentiates Its Skin-Lightening Activity—Involvement of Skin Microbiota
Molecules
2024
Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota
Journal of Hazardous Materials
2024
Methods in Molecular Biology
2024
Plant roots affect free-living diazotroph communities in temperate grassland soils despite decades of fertilization
Communications Biology
2024
Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates
Science of The Total Environment
2024
Seasonality of primary production explains the richness of pioneering benthic communities
Nature Communications
2024
Effects of small-scale outplanting fertilization on conifer seedling growth and fungal community establishment
Trees, Forests and People
2024
Non‐extractive fish diversity assessment in Mediterranean rhodolith beds
Aquatic Conservation: Marine and Freshwater Ecosystems
2024
Metabarcoding and microscopy characterization of phytoplankton from frontal areas of the Argentine Sea
Frontiers in Marine Science
2024
Gazing into the abyss: A glimpse into the diversity, distribution, and behaviour of heterotrophic protists from the deep‐sea floor
Environmental Microbiology
2023
Dietary niche overlap and resource partitioning among six steppe passerines of Central Spain using DNA metabarcoding
Ibis
2023
Metabarcoding the eukaryotic community of a threatened, iconic Mediterranean habitat: Posidonia oceanica seagrass meadows
Frontiers in Marine Science
2023
Homogeneity in terrestrial land cover is reflected in fish diversity patterns in a Chinese river system
Environmental DNA
2023
Impact of local iron enrichment on the small benthic biota in the deep Arctic Ocean
Frontiers in Marine Science
2023
Evaluation of 96‐well high‐throughput DNA extraction methods for 16S rRNA gene metabarcoding
Molecular Ecology Resources
2023
Environmental drivers of eukaryotic plankton and fish biodiversity in an Arctic fjord
Polar Biology
2023
Soundscapes and deep learning enable tracking biodiversity recovery in tropical forests
Nature Communications
2023
Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem
Environmental DNA
2023
Environmental DNA reveals spatial patterns of fish and plankton diversity at a floating offshore wind farm
Environmental DNA
2023
Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding
iScience
2023
Water masses shape pico-nano eukaryotic communities of the Weddell Sea
Communications Biology
2023
Comparing different computational approaches for detecting long‐term vertical transmission in host‐associated microbiota
Molecular Ecology
2023
Invert emulsions alleviate biotic interactions in bacterial mixed culture
Microbial Cell Factories
2023
Microbiability of milk composition and genetic control of microbiota effects in sheep
Journal of Dairy Science
2023
State-of-the-art of data analyses in environmental DNA approaches towards its applicability to sustainable fisheries management
Frontiers in Marine Science
2023
Exploration of fMRI brain responses to oral sucrose after Roux-en-Y gastric bypass in obese yucatan minipigs in relationship with microbiota and metabolomics profiles
Clinical Nutrition
2023
Feeding ecology of a highly aerial bird during its long breeding season
Avian Research
2023
Diversity of protist genera in periphyton of tufa-depositing karstic river
Annals of Microbiology
2023
Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts
Biology
2023
Metagenomics reveals the structure of Mastrevirus–host interaction network within an agro-ecosystem
Virus Evolution
2023
Occurrence of biogenic amines and their correlation with bacterial communities in the Ivorian traditional fermented fish adjuevan during the storage
Folia Microbiologica
2023
Integrative taxonomy approach to detect spatial and temporal variability of the Mediterranean benthic communities through artificial substrate units (ASUs)
Frontiers in Marine Science
2023
Impact of phosphorus limitation on medium-chain-length polyhydroxyalkanoate production by activated sludge
Applied Microbiology and Biotechnology
2023
Prey choice in insectivorous steppe passerines: New insights from DNA metabarcoding
Global Ecology and Conservation
2023
Contaminants reach everywhere: Fish dietary samples should be surface decontaminated prior to molecular diet analysis
Ecology and Evolution
2023
Exploring the diversity of microeukaryotic communities in New England tide pools
Aquatic Microbial Ecology
2023
Trapped DNA fragments in marine sponge specimens unveil North Atlantic deep-sea fish diversity
Proceedings of the Royal Society B: Biological Sciences
2023
The distribution of coastal fish eDNA sequences in the Anthropocene
Global Ecology and Biogeography
2023
Bioinformatic and Statistical Analysis of Microbiome Data
2023
Selecting the best: Interspecific and age-related diet differences among sympatric steppe passerines
Avian Research
2023
Assessing arthropod diversity metrics derived from stream environmental DNA: spatiotemporal variation and paired comparisons with manual sampling
PeerJ
2023
Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania
Nature Communications
2023
Habitat partitioning of soil microbial communities along an elevation gradient: from plant root to landscape scale
Oikos
2023
A large database linking the rumen bacterial composition and milk traits in Lacaune sheep
Scientific Data
2023
Polar lake microbiomes have distinct evolutionary histories
Science Advances
2023
Coastal rocky reef fish monitoring in the context of the Marine Strategy Framework Directive: Environmental DNA metabarcoding complements underwater visual census
Ocean & Coastal Management
2023
Mechanisms shaping dissolved organic matter and microbial community in lake ecosystems
Water Research
2023
DNA metabarcoding of mock communities highlights potential biases when assessing Neotropical fish diversity
Environmental DNA
2023
Vertical organization of microbial communities in Salineta hypersaline wetland, Spain
Frontiers in Microbiology
2023
Machine learning in marine ecology: an overview of techniques and applications
ICES Journal of Marine Science
2023
Covariation between microeukaryotes and bacteria associated with Planorbidae snails
PeerJ
2023
High taxonomic diversity and miniaturization in benthic communities under persistent natural CO 2 disturbances
Proceedings of the Royal Society B: Biological Sciences
2022
Niche separation between two dominant crustacean predators in European estuarine soft-bottom habitats
Ecological Indicators
2022
Origin of marine invertebrate larvae on an Arctic inflow shelf
Marine Ecology Progress Series
2022
Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding
Frontiers in Genetics
2022
PM 7/151 (1) Considerations for the use of high throughput sequencing in plant health diagnostics1
EPPO Bulletin
2022
Adaptations of microbial communities and dissolved organics to seasonal pressures in a mesotrophic coastal Mediterranean lake
Environmental Microbiology
2022
Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum
Journal of Hazardous Materials
2022
Metagenetic characterization of bacterial communities associated with ready-to-eat leafy vegetables and study of temperature effect on their composition during storage
Food Research International
2022
Benthic foraminifera as proxies for the environmental quality assessment of the Kuwait Bay (Kuwait, Arabian Gulf): Morphological and metabarcoding approaches
Science of The Total Environment
2022
Cecinothofagus Nieves-Aldrey & Liljeblad (Hymenoptera, Cynipidae) is likely an endoparasitoid of the gall-maker genus Aditrochus Rübsaamen (Hymenoptera, Pteromalidae)
Journal of Hymenoptera Research
2022
DNA metabarcoding reveals the importance of gelatinous zooplankton in the diet ofPandalus borealis, a keystone species in the Arctic
Molecular Ecology
2022
Dietary wheat and reduced methane yield are linked to rumen microbiome changes in dairy cows
PLOS ONE
2022
Comparison of Fecal Sample Collection Methods for Microbial Analysis Embedded within Colorectal Cancer Screening Programs
Cancer Epidemiology, Biomarkers & Prevention
2022
Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River
Microorganisms
2022
Measuring protected-area effectiveness using vertebrate distributions from leech iDNA
Nature Communications
2022
Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better
Metabarcoding and Metagenomics
2022
Facilitating the adoption of high‐throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step‐by‐step description
EPPO Bulletin
2022
Effect of freeze-dried kombucha culture on microbial composition and assessment of metabolic dynamics during fermentation
Food Microbiology
2022
Intra‐genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing
Environmental Microbiology
2022
Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant–Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient
Microbial Ecology
2022
For all audiences: Incorporating immature stages into standardised spider inventories has a major impact on the assessment of biodiversity patterns
Molecular Ecology Resources
2022
Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale
Frontiers in Marine Science
2022
Inoculation of arbuscular mycorrhizal fungi increases lettuce yield without altering natural soil communities
Archives of Agronomy and Soil Science
2022
ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently
BMC Bioinformatics
2022
Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities
Communications Biology
2022
The Yucatan minipig model: A new preclinical model of malnutrition induced by a low-calorie/low-protein diet
Clinical Nutrition
2022
Environmental DNA persistence and fish detection in captive sponges
Molecular Ecology Resources
2022
Using DNA Metabarcoding to Characterize the Prey Spectrum of Two Co-Occurring Themisto Amphipods in the Rapidly Changing Atlantic-Arctic Gateway Fram Strait
Genes
2022
Capture by hybridization for full‐length barcode‐based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems
Molecular Ecology Resources
2022
Do pseudogenes pose a problem for metabarcoding marine animal communities?
Molecular Ecology Resources
2022
Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding
Proceedings of the Royal Society B: Biological Sciences
2022
Benthic invertebrates in Svalbard fjords—when metabarcoding does not outperform traditional biodiversity assessment
PeerJ
2022
Seasonal dynamics of marine protist communities in tidally mixed coastal waters
Molecular Ecology
2022
Evolution of the spontaneous sourdoughs microbiota prepared with organic or conventional whole wheat flours from South Brazil
Anais da Academia Brasileira de Ciências
2022
Planktonic microbial communities from microbialite‐bearing lakes sampled along a salinity‐alkalinity gradient
Limnology and Oceanography
2022
Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands
Microbial Ecology
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
Evaluating bioinformatics pipelines for population‐level inference using environmental DNA
Environmental DNA
2022
Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota
mSystems
2022
Diversity of Microbial Eukaryotes Along the West Antarctic Peninsula in Austral Spring
Frontiers in Microbiology
2022
Illuminating protist diversity in pitcher plants and bromeliad tanks
PLOS ONE
2022
ExTaxsI: an exploration tool of biodiversity molecular data
GigaScience
2022
DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets
PeerJ
2022
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation
Molecular Ecology Resources
2022
Vectors as Sentinels: Rising Temperatures Increase the Risk of Xylella fastidiosa Outbreaks
Biology
2022
Action of Mangifera indica Leaf Extract on Acne-Prone Skin through Sebum Harmonization and Targeting C. acnes
Molecules
2021
Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities
mSystems
2021
A Comparison of the Colonic Microbiome and Volatile Organic Compound Metabolome of Anoplocephala perfoliata Infected and Non-Infected Horses: A Pilot Study
Animals
2021
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification
Molecular Ecology Resources
2021
DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions
Microorganisms
2021
On the use of sequence-quality information in OTU clustering
PeerJ
2021
Multiple Selection Criteria for Probiotic Strains with High Potential for Obesity Management
Nutrients
2021
The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils
Journal of Eukaryotic Microbiology
2021
Assessing ecological status in karstic lakes through the integration of phytoplankton functional groups, morphological approach and environmental DNA metabarcoding
Ecological Indicators
2021
Swarm v3: towards tera-scale amplicon clustering
Bioinformatics
2021
The impact of DNA extract homogenization and replication on marine sediment metabarcoding diversity and heterogeneity
Environmental DNA
2021
Lecture Notes in Computer Science
2021
Horizontal and vertical small-scale patterns of protist communities at the Atlantic deep-sea floor
Deep Sea Research Part I: Oceanographic Research Papers
2021
Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization
Environmental Pollution
2021
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce
mSystems
2021
Linking Pélardon artisanal goat cheese microbial communities to aroma compounds during cheese-making and ripening
International Journal of Food Microbiology
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
Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity
The ISME Journal
2021
Boreal soil microbial diversity and seed onion mycorrhizal colonization is unaffected by preceding one season crop cultivation
European Journal of Soil Biology
2021
An accurate and exact clustering algorithm for next generation sequencing metagenomic sequences
Mathematical Methods in the Applied Sciences
2021
Identifying Potential Hosts of Short-Branch Microsporidia
Microbial Ecology
2021
Cropping systems impact changes in soil fungal, but not prokaryote, alpha-diversity and community composition stability over a growing season in a long-term field trial
FEMS Microbiology Ecology
2021
Metabarcoding as a quantitative tool for estimating biodiversity and relative biomass of marine zooplankton
ICES Journal of Marine Science
2021
Diversity, Functions and Antibiotic Resistance of Sediment Microbial Communities From Lake Geneva Are Driven by the Spatial Distribution of Anthropogenic Contamination
Frontiers in Microbiology
2021
Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems
Environment International
2021
Population Dynamics and Yeast Diversity in Early Winemaking Stages without Sulfites Revealed by Three Complementary Approaches
Applied Sciences
2021
Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces
Food Microbiology
2021
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts
Microbial Genomics
2021
Evolution of fungal community associated with ready-to-eat pineapple during storage under different temperature conditions
Food Microbiology
2021
Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Scientific Reports
2021
Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat
Applied and Environmental Microbiology
2021
Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network
Microorganisms
2021
Yeast and Filamentous Fungi Microbial Communities in Organic Red Grape Juice: Effect of Vintage, Maturity Stage, SO2, and Bioprotection
Frontiers in Microbiology
2021
Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey
PeerJ
2021
High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally
Ecology and Evolution
2021
Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments
Frontiers in Microbiology
2021
Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot
Molecular Ecology Resources
2021
A Parasite’s Paradise: Biotrophic Species Prevail Oomycete Community Composition in Tree Canopies
Frontiers in Forests and Global Change
2021
Trophic niche overlap between round sardinella (Sardinella aurita) and sympatric pelagic fish species in the Western Mediterranean
Ecology and Evolution
2021
Mycorrhizal inoculation increases fruit production without disturbance of native arbuscular mycorrhizal community in jujube tree orchards (Senegal)
Symbiosis
2021
Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding
Frontiers in Marine Science
2021
Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake
Environmental Microbiology
2021
SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements
Molecular Ecology Resources
2021
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding
Molecular Ecology Resources
2021
Diversity and predicted inter- and intra-domain interactions in the Mediterranean Plastisphere
Environmental Pollution
2021
OTU picking on large datasets: comparing methods on a diversity of situations
ARPHA Conference Abstracts
2021
Ciliates (Alveolata, Ciliophora) as bioindicators of environmental pressure: A karstic river case
Ecological Indicators
2021
DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review
Frontiers in Marine Science
2021
Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae
Frontiers in Ecology and Evolution
2021
Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility
Molecular Ecology
2021
MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences
Bioinformatics
2021
Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient
Environmental Microbiology
2021
FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers
Briefings in Bioinformatics
2021
The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
Metabarcoding and Metagenomics
2021
Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction
Frontiers in Microbiology
2021
Succession of Microbial Community in a Small Water Body within the Alluvial Aquifer of a Large River
Water
2021
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
BMC Bioinformatics
2021
Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage
Foods
2021
Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a High Arctic Fjord (Isfjorden, Svalbard)
Frontiers in Microbiology
2021
High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans
Communications Biology
2021
Partial overlap of fungal communities associated with nettle and poplar roots when co-occurring at a trace metal contaminated site
Science of The Total Environment
2021
Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding
Molecular Ecology
2021
Use of environmental DNA in assessment of fish functional and phylogenetic diversity
Conservation Biology
2021
Genetic Diversity in Marine Planktonic Ciliates (Alveolata, Ciliophora) Suggests Distinct Geographical Patterns – Data From Chinese and European Coastal Waters
Frontiers in Marine Science
2021
Seasonal Variability in the Zooplankton Community Structure in a Sub-Arctic Fjord as Revealed by Morphological and Molecular Approaches
Frontiers in Marine Science
2021
A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes
Diversity
2021
Microbial community diversity and composition in river sediments contaminated with tetrabromobisphenol A and copper
Chemosphere
2021
To the canopy and beyond: Air dispersal as a mechanism of ubiquitous protistan pathogen assembly in tree canopies
European Journal of Protistology
2021
Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae
Frontiers in Plant Science
2021
The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network
Frontiers in Allergy
2021
Mapping differences in mammalian distributions and diversity using environmental DNA from rivers
Science of The Total Environment
2021
Phylogenetic relatedness drives protist assembly in marine and terrestrial environments
Global Ecology and Biogeography
2021
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species
Molecular Ecology Resources
2021
Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding
PeerJ
2021
An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea)
Scientific Reports
2021
Meroplankton Diversity, Seasonality and Life-History Traits Across the Barents Sea Polar Front Revealed by High-Throughput DNA Barcoding
Frontiers in Marine Science
2021
A fine‐scale spatial analysis of fungal communities on tropical tree bark unveils the epiphytic rhizosphere in orchids
New Phytologist
2021
Shark and ray diversity, abundance and temporal variation around an Indian Ocean Island, inferred by eDNA metabarcoding
Conservation Science and Practice
2021
Benthic eDNA metabarcoding provides accurate assessments of impact from oil extraction, and ecological insights
Ecological Indicators
2021
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community
mSystems
2021
The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding
Ecological Indicators
2021
Assessment of littoral algal diversity from the northern Gulf of Mexico using environmental DNA metabarcoding
Journal of Phycology
2021
Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them?
PLOS ONE
2021
Use of metabarcoding and source tracking to identify desirable or spoilage autochthonous microorganism sources during black olive fermentations
Food Research International
2021
Diversity and ecology of protists revealed by metabarcoding
Current Biology
2021
A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay
Molecular Ecology
2021
Modulation of trypanosome establishment in Glossina palpalis palpalis by its microbiome in the Campo sleeping sickness focus, Cameroon
Infection, Genetics and Evolution
2020
Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink
The ISME Journal
2020
A trophic latitudinal gradient revealed in anchovy and sardine from the Western Mediterranean Sea using a multi-proxy approach
Scientific Reports
2020
Assessing the quality of fresh Whitemouth croaker ( Micropogonias furnieri ) meat based on micro‐organism and histamine analysis using NGS, qPCR and HPLC‐DAD
Journal of Applied Microbiology
2020
Post‐natal co‐development of the microbiota and gut barrier function follows different paths in the small and large intestine in piglets
The FASEB Journal
2020
Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea
Journal of Plankton Research
2020
Changes in sediment microbial diversity following chronic copper-exposure induce community copper-tolerance without increasing sensitivity to arsenic
Journal of Hazardous Materials
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
The belowground bacterial and fungal communities differed in their significance as microbial indicator of Moroccan carob habitats
Ecological Indicators
2020
Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences
Ecography
2020
High-throughput sequencing of litter and moss eDNA reveals a positive correlation between the diversity of Apicomplexa and their invertebrate hosts across alpine habitats
Soil Biology and Biochemistry
2020
Deciphering Microbial Community Dynamics and Biochemical Changes During Nyons Black Olive Natural Fermentations
Frontiers in Microbiology
2020
Global comparison of bicosoecid Cafeteria-like flagellates from the deep ocean and surface waters, with reorganization of the family Cafeteriaceae
European Journal of Protistology
2020
Elucidating Biodiversity Shifts in Ballast Water Tanks during a Cross-Latitudinal Transfer: Complementary Insights from Molecular Analyses
Environmental Science & Technology
2020
Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects
Biodiversity and Conservation
2020
Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans
Environmental Microbiology
2020
Heterogeneity of the rice microbial community of the Chinese centuries‐old Honghe Hani rice terraces system
Environmental Microbiology
2020
Centers of endemism of freshwater protists deviate from pattern of taxon richness on a continental scale
Scientific Reports
2020
Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control
Frontiers in Microbiology
2020
Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika
Environmental DNA
2020
The interaction of physical and biological factors drives phytoplankton spatial distribution in the northern California Current
Limnology and Oceanography
2020
Bacterial communities’ taxonomic and functional turnovers both accurately predict marine benthic ecological quality status
Environmental DNA
2020
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads
BMC Bioinformatics
2020
Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere
The ISME Journal
2020
More Than Expected From Old Sponge Samples: A Natural Sampler DNA Metabarcoding Assessment of Marine Fish Diversity in Nha Trang Bay (Vietnam)
Frontiers in Marine Science
2020
Composition and distribution patterns of eukaryotic microbial plankton in the ultra-oligotrophic Eastern Mediterranean Sea
Aquatic Microbial Ecology
2020
Maternal Linoleic Acid Overconsumption Alters Offspring Gut and Adipose Tissue Homeostasis in Young but Not Older Adult Rats
Nutrients
2020
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
GigaScience
2020
Microeukaryote communities exhibit phyla-specific distance-decay patterns and an intimate link between seawater and sediment habitats in the Western Pacific Ocean
Deep Sea Research Part I: Oceanographic Research Papers
2020
Phylogenetic signature of fungal response to long-term chemical pollution
Soil Biology and Biochemistry
2020
BOLDigger – a Python package to identify and organise sequences with the Barcode of Life Data systems
Metabarcoding and Metagenomics
2020
Taxon Appearance From Extraction and Amplification Steps Demonstrates the Value of Multiple Controls in Tick Microbiota Analysis
Frontiers in Microbiology
2020
An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities
Frontiers in Marine Science
2020
Fungal communities in groundwater springs along the volcanic zone of Iceland
Inland Waters
2020
From metabarcoding to metaphylogeography: separating the wheat from the chaff
Ecological Applications
2020
Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
PLOS ONE
2020
Soil protist diversity in the Swiss western Alps is better predicted by topo‐climatic than by edaphic variables
Journal of Biogeography
2020
Reintroducing mothur: 10 Years Later
Applied and Environmental Microbiology
2020
Long-term phytomanagement with compost and a sunflower – Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil
Science of The Total Environment
2020
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Frontiers in Microbiology
2020
Taxonomic differences shape the responses of freshwater aerobic anoxygenic phototrophic bacterial communities to light and predation
Molecular Ecology
2020
Benthic foraminiferal metabarcoding and morphology-based assessment around three offshore gas platforms: Congruence and complementarity
Environment International
2020
DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA
Diversity
2020
Digestive tract microbiota of beef cattle that differed in feed efficiency
Journal of Animal Science
2020
Phenotype Prediction from Metagenomic Data Using Clustering and Assembly with Multiple Instance Learning (CAMIL)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2020
Top-Down and Bottom-Up Controls on Microeukaryotic Diversity (i.e., Amplicon Analyses of SAR Lineages) and Function (i.e., Metatranscriptome Analyses) Assessed in Microcosm Experiments
Frontiers in Marine Science
2020
Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome
Frontiers in Microbiology
2020
Bdellovibrio and Like Organisms in Lake Geneva: An Unseen Elephant in the Room?
Frontiers in Microbiology
2020
From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies
Frontiers in Microbiology
2020
Storm and Ips typographus disturbance effects on carbon stocks, humus layer carbon fractions and microbial community composition in boreal Picea abies stands
Soil Biology and Biochemistry
2020
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
IMA Fungus
2020
A Primer for Microbiome Time-Series Analysis
Frontiers in Genetics
2020
Sequence data describing the fungal community in a tropical quartzite soil
Data in Brief
2020
Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results
Frontiers in Genetics
2020
Protist diversity and function in the dark ocean – Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists
European Journal of Protistology
2020
Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany)
Freshwater Biology
2020
Biodiversity of protists and nematodes in the wild nonhuman primate gut
The ISME Journal
2020
A Probiotic Mixture Induces Anxiolytic- and Antidepressive-Like Effects in Fischer and Maternally Deprived Long Evans Rats
Frontiers in Behavioral Neuroscience
2020
A barotolerant ciliate isolated from the abyssal deep sea of the North Atlantic: Euplotes dominicanus sp. n. (Ciliophora, Euplotia)
European Journal of Protistology
2020
Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence
Journal of Fungi
2020
Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding
Journal of Eukaryotic Microbiology
2019
Silicon limitation facilitates virus infection and mortality of marine diatoms
Nature Microbiology
2019
SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data
BMC Bioinformatics
2019
Diversity and Distribution of Meroplanktonic Larvae in the Pacific Arctic and Connectivity With Adult Benthic Invertebrate Communities
Frontiers in Marine Science
2019
Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater
Frontiers in Microbiology
2019
Non‐specific amplification compromises environmental DNA metabarcoding with COI
Methods in Ecology and Evolution
2019
Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders
Briefings in Bioinformatics
2019
Mamiellophyceae shift in seasonal predominance in the Baltic Sea
Aquatic Microbial Ecology
2019
A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture
Journal of Eukaryotic Microbiology
2019
DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist
Molecular Ecology
2019
Microbial metal‐sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses
Environmental Microbiology
2019
A Bioinformatics Guide to Plant Microbiome Analysis
Frontiers in Plant Science
2019
Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts?
Frontiers in Microbiology
2019
Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches
Molecular Ecology Resources
2019
Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach
Scientific Reports
2019
Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy)
Marine Environmental Research
2019
The biodiversity benefit of native forests and mixed‐species plantations over monoculture plantations
Diversity and Distributions
2019
Gut bacteria are critical for optimal muscle function: a potential link with glucose homeostasis
American Journal of Physiology-Endocrinology and Metabolism
2019
Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring
Molecular Ecology Resources
2019
Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities
Frontiers in Ecology and Evolution
2019
Marine Vertebrate Biodiversity and Distribution Within the Central California Current Using Environmental DNA (eDNA) Metabarcoding and Ecosystem Surveys
Frontiers in Marine Science
2019
Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs
Scientific Reports
2019
Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river
Environmental DNA
2019
Influence of dissolved oxygen content on the bacteria‐induced ennoblement of stainless steels in seawater and its consequence on the localized corrosion risk
Materials and Corrosion
2019
A fundamental difference between macrobiota and microbial eukaryotes: protistan plankton has a species maximum in the freshwater‐marine transition zone of the Baltic Sea
Environmental Microbiology
2019
Microbial amendments alter protist communities within the soil microbiome
Soil Biology and Biochemistry
2019
Dialogue on the nomenclature and classification of prokaryotes
Systematic and Applied Microbiology
2019
Bacterial community activity and dynamics in the biofilm of an experimental hybrid wetland system treating greywater
Environmental Science and Pollution Research
2019
Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding
Ecology and Evolution
2019
Faecalibacterium diversity in dairy cow milk
PLOS ONE
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
Reference Module in Biomedical Sciences
2019
Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
Ecology and Evolution
2019
Incubation and grazing effects on spirotrich ciliate diversity inferred from molecular analyses of microcosm experiments
PLOS ONE
2019
DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies
Scientific Reports
2019
The microbiota of technosols resembles that of a nearby forest soil three years after their establishment
Chemosphere
2019
Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants
Environmental Microbiology
2019
Combining the 5.8S and ITS2 to improve classification of fungi
Methods in Ecology and Evolution
2019
Toward accurate species‐level metabarcoding of arthropod communities from the tropical forest canopy
Ecology and Evolution
2019
Bats as potential suppressors of multiple agricultural pests: A case study from Madagascar
Agriculture, Ecosystems & Environment
2019
Bone Marrow-Derived Cells Restore Functional Integrity of the Gut Epithelial and Vascular Barriers in a Model of Diabetes and ACE2 Deficiency
Circulation Research
2019
Protist Biodiversity and Biogeography in Lakes From Four Brazilian River–Floodplain Systems
Journal of Eukaryotic Microbiology
2019
Benthic foraminiferal DNA metabarcodes significantly vary along a gradient from abyssal to hadal depths and between each side of the Kuril-Kamchatka trench
Progress in Oceanography
2018
Metagenomics
2018
Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture
Marine Pollution Bulletin
2018
Facultative methanotrophs are abundant at terrestrial natural gas seeps
Microbiome
2018
Effects of corn stover management on soil quality
European Journal of Soil Biology
2018
Clarifying the Relationships between Microsporidia and Cryptomycota
Journal of Eukaryotic Microbiology
2018
Diversity of foliar endophytic ascomycetes in the endemic Corsican pine forests
Fungal Ecology
2018
In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different
Pediatric Pulmonology
2018
Consistent patterns of high alpha and low beta diversity in tropical parasitic and free‐living protists
Molecular Ecology
2018
Characterization of protistan plankton diversity in ancient salt evaporation ponds located in a volcanic crater on the island Sal, Cape Verde
Extremophiles
2018
Fungal communities in organic and mineral soil horizons in an industrially polluted boreal forest
Biodiversity
2018
Supervised machine learning outperforms taxonomy‐based environmental DNA metabarcoding applied to biomonitoring
Molecular Ecology Resources
2018
Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada
Frontiers in Microbiology
2018
Long‐read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments
Molecular Ecology Resources
2018
Incomplete Co-cladogenesis Between Zootermopsis Termites and Their Associated Protists
Environmental Entomology
2018
Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean
Frontiers in Microbiology
2018
Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring in salmon aquaculture
Ecological Indicators
2018
The effect of tides on nearshore environmental DNA
PeerJ
2018
Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens
Scientific Reports
2018
Bacterial Communities in Tissues and Surficial Mucus of the Cold-Water Coral Paragorgia arborea
Frontiers in Marine Science
2018
Environment and host identity structure communities of green algal symbionts in lichens
New Phytologist
2018
In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana
The ISME Journal
2018
GeFaST: An improved method for OTU assignment by generalising Swarm’s fastidious clustering approach
BMC Bioinformatics
2018
Treated and untreated wastewater effluents alter river sediment bacterial communities involved in nitrogen and sulphur cycling
Science of The Total Environment
2018
A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy
Metabarcoding and Metagenomics
2018
Carbon and nitrogen turnover in the Arctic deep sea: in situ benthic community response to diatom and coccolithophorid phytodetritus
Biogeosciences
2018
Seed bank and seasonal patterns of the eukaryotic SAR (Stramenopila, Alveolata and Rhizaria) clade in a New England vernal pool
Journal of Plankton Research
2018
Ubiquitous abundance distribution of non-dominant plankton across the global ocean
Nature Ecology & Evolution
2018
The Hidden Diversity of Flagellated Protists in Soil
Protist
2018
Neobodonids are dominant kinetoplastids in the global ocean
Environmental Microbiology
2018
Protists Within Corals: The Hidden Diversity
Frontiers in Microbiology
2018
The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
Science of The Total Environment
2018
Microbial Communities in the East and West Fram Strait During Sea Ice Melting Season
Frontiers in Marine Science
2018
Temporal Bacterial Surveillance of Salmon Aquaculture Sites Indicates a Long Lasting Benthic Impact With Minimal Recovery
Frontiers in Microbiology
2018
Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants
Water Research
2018
eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity
Ecology and Evolution
2018
Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus Pseudo-nitzschia: Genetic, Morphological, and Ecological Characterisation
Frontiers in Microbiology
2018
Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding
FEMS Microbiology Ecology
2017
High-resolution characterization of the human microbiome
Translational Research
2017
A clinician's guide to microbiome analysis
Nature Reviews Gastroenterology & Hepatology
2017
Metagenome sequence clustering with hash-based canopies
Journal of Bioinformatics and Computational Biology
2017
A from‐benchtop‐to‐desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies
Molecular Ecology Resources
2017
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
The ISME Journal
2017
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept
Frontiers in Microbiology
2017
Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning
Environmental Science & Technology
2017
Exploring the Ecological Coherence between the Spatial and Temporal Patterns of Bacterioplankton in Boreal Lakes
Frontiers in Microbiology
2017
Microbiome sharing between children, livestock and household surfaces in western Kenya
PLOS ONE
2017
The Protistan Microbiome of Grassland Soil: Diversity in the Mesoscale
Protist
2017
The parabasalid symbiont community of Heterotermes aureus: Molecular and morphological characterization of four new species and reestablishment of the genus Cononympha
European Journal of Protistology
2017
Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem
Frontiers in Marine Science
2017
Marine Animal Forests
2017
Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections
BMC Genomics
2017
Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions
Environmental Microbiology
2017
Yeasts dominate soil fungal communities in three lowland Neotropical rainforests
Environmental Microbiology Reports
2017
UniEuk: Time to Speak a Common Language in Protistology!
Journal of Eukaryotic Microbiology
2017
High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy
Scientific Reports
2017
Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests
Nature Ecology & Evolution
2017
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents
The ISME Journal
2017
Host specificity, pathogen exposure, and superinfections impact the distribution of Anaplasma phagocytophilum genotypes in ticks, roe deer, and livestock in a fragmented agricultural landscape
Infection, Genetics and Evolution
2017
PipeCraft: Flexible open‐source toolkit for bioinformatics analysis of custom high‐throughput amplicon sequencing data
Molecular Ecology Resources
2017
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates
Nature Communications
2017
Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species
Nature Communications
2017
OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
mSphere
2016
Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation
Frontiers in Microbiology
2016
Marine Animal Forests
2016
Comparison of three clustering approaches for detecting novel environmental microbial diversity
PeerJ
2016
Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods
mSystems
2016
Unexpected biodiversity of ciliates in marine samples from below the photic zone
Molecular Ecology
2016
Open-Source Sequence Clustering Methods Improve the State Of the Art
mSystems
2016
Landscape‐scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton
Ecology Letters
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
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