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2023
Direct and indirect pathways of land management effects on wetland plant litter decomposition
Science of The Total Environment
2022
Strain level and comprehensive microbiome analysis in inflammatory bowel disease via multi-technology meta-analysis identifies key bacterial influencers of disease
Frontiers in Microbiology
2022
Pesticide residue exposure provides different responses of the microbiomes of distinct cultures of the stored product pest mite Acarus siro
BMC Microbiology
2022
FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities
International Journal of Food Microbiology
2022
Molecular Genetics and Genomics Tools in Biodiversity Conservation
2022
Exploring the universal healthy human gut microbiota around the World
Computational and Structural Biotechnology Journal
2022
Local Environmental Conditions Promote High Turnover Diversity of Benthic Deep-Sea Fungi in the Ross Sea (Antarctica)
Journal of Fungi
2022
Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb
Molecular Ecology Resources
2022
Physical activity enhances the improvement of body mass index and metabolism by inulin: a multicenter randomized placebo-controlled trial performed in obese individuals
BMC Medicine
2022
The Effect of Residual Pesticide Application on Microbiomes of the Storage Mite Tyrophagus putrescentiae
Microbial Ecology
2022
Analysis and Interpretation of metagenomics data: an approach
Biological Procedures Online
2022
Applying meta-data of soybean grain in origin trace and quarantine inspection
Food Research International
2022
The Negative Effects of Feces-Associated Microorganisms on the Fitness of the Stored Product Mite Tyrophagus putrescentiae
Frontiers in Microbiology
2022
A manager’s guide to using eDNA metabarcoding in marine ecosystems
PeerJ
2022
Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies
Environmental Microbiome
2022
Human Blood Bacteriome: Eubiotic and Dysbiotic States in Health and Diseases
Cells
2022
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties
NAR Genomics and Bioinformatics
2022
Prophylactic Delivery of a Bacteriophage Cocktail in Feed Significantly Reduces Salmonella Colonization in Pigs
Microbiology Spectrum
2022
High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota
BMC Microbiology
2022
Towards Improved Detection and Identification of Rust Fungal Pathogens in Environmental Samples Using a Metabarcoding Approach
Phytopathology®
2022
Composition and Diversity of the Culturable Endophytic Community of Six Stress-Tolerant Dessert Plants Grown in Stressful Soil in a Hot Dry Desert Region
Journal of Fungi
2022
Microbially mediated arsenic mobilization in the clay layer and underlying aquifer in the Hetao Basin, Inner Mongolia, China
Science of The Total Environment
2022
Customization of a DADA2-based pipeline for fungal internal transcribed spacer 1 (ITS1) amplicon data sets
JCI Insight
2022
Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans
Microbial Ecology
2022
Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers
MycoKeys
2022
Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms
PLOS ONE
2022
Two-year systematic investigation reveals alterations induced on chemical and bacteriome profile of PM2.5 by African dust incursions to the Mediterranean atmosphere
Science of The Total Environment
2022
The functional evolution of termite gut microbiota
Microbiome
2022
Similar heterotrophic communities but distinct interactions supported by red and green‐snow algae in the Antarctic Peninsula
New Phytologist
2022
Microbial communities across activated sludge plants show recurring species-level seasonal patterns
ISME Communications
2022
To compare the performance of prokaryotic taxonomy classifiers using curated 16S full-length rRNA sequences
Computers in Biology and Medicine
2022
Local endemism and ecological generalism in the assembly of root‐colonizing fungi
Ecological Monographs
2022
Changes to bacterial communities and soil metabolites in an apple orchard as a legacy effect of different intercropping plants and soil management practices
Frontiers in Microbiology
2022
Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups
Scientific Reports
2022
Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding
Molecular Ecology
2022
16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences
Frontiers in Bioinformatics
2021
Gut Microbiota Parameters Potentially Useful in Clinical Perspective
Microorganisms
2021
Characterization of the Oral and Esophageal Microbiota in Esophageal Precancerous Lesions and Squamous Cell Carcinoma
Frontiers in Cellular and Infection Microbiology
2021
Effects of microbial organic fertilizers on Astragalus membranaceus growth and rhizosphere microbial community
Annals of Microbiology
2021
The RNA-binding protein tristetraprolin regulates RALDH2 expression by intestinal dendritic cells and controls local Treg homeostasis
Mucosal Immunology
2021
Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age
Archives of Microbiology
2021
Gut Microbial Alterations in Diarrheal Baer's Pochards (Aythya baeri)
Frontiers in Veterinary Science
2021
Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content
Microbial Ecology
2021
Microbiome profiles are associated with cognitive functioning in 45-month-old children
Brain, Behavior, and Immunity
2021
Conducting research on diet–microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design
Journal of Human Nutrition and Dietetics
2021
RESCRIPt: Reproducible sequence taxonomy reference database management
PLOS Computational Biology
2021
Accurate annotation of protein coding sequences with IDTAXA
NAR Genomics and Bioinformatics
2021
Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs
Frontiers in Microbiology
2021
Deciphering the succession patterns of bacterial community and their correlations with environmental factors and flavor compounds during the fermentation of Zhejiang rosy vinegar
International Journal of Food Microbiology
2021
Submucosal microbiome of peri‐implant sites: A cross‐sectional study
Journal of Clinical Periodontology
2021
Assessment of littoral algal diversity from the northern Gulf of Mexico using environmental DNA metabarcoding
Journal of Phycology
2021
Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers
Water Research
2021
The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs
Environmental DNA
2021
Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis
Scientific Reports
2021
Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem
Molecular Ecology Resources
2021
A β‐lactamase gene of Fusarium oxysporum alters the rhizosphere microbiota of soybean
The Plant Journal
2021
Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species
Journal of Hazardous Materials
2021
Cardinium inhibits Wolbachia in its mite host, Tyrophagus putrescentiae, and affects host fitness
FEMS Microbiology Ecology
2021
Metabarcoding of Soil Fungi from Different Urban Greenspaces Around Bournemouth in the UK
EcoHealth
2021
Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
Scientific Reports
2021
BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities
mSystems
2021
MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses
Data in Brief
2021
Ectomycorrhizal fungal community assembly on seedlings of a Neotropical monodominant tree
Biotropica
2021
ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
PeerJ
2021
Exogenous enzymes and probiotics alter digestion kinetics, volatile fatty acid content and microbial interactions in the gut of Nile tilapia
Scientific Reports
2021
Methodological Approaches Frame Insights into Endophyte Richness and Community Composition
Microbial Ecology
2021
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding
Molecular Ecology Resources
2021
Toward a reliable assessment of potential ecological impacts of deep‐sea polymetallic nodule mining on abyssal infauna
Limnology and Oceanography: Methods
2021
Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities
Molecular Ecology Resources
2021
Bacterial community structure alterations within the colorectal cancer gut microbiome
BMC Microbiology
2021
Harnessing the plant microbiome to promote the growth of agricultural crops
Microbiological Research
2021
Identifying biases and their potential solutions in human microbiome studies
Microbiome
2021
Association between vaginal microbiota and risk of early pregnancy miscarriage
Comparative Immunology, Microbiology and Infectious Diseases
2020
Species Identification in Plant-Associated Prokaryotes and Fungi Using DNA
Phytobiomes Journal
2020
The Diversity, Composition, and Putative Functions of Gill-Associated Bacteria of Bathymodiolin Mussel and Vesicomyid Clam from Haima Cold Seep, South China Sea
Microorganisms
2020
Molecular characterization of cultivable bacteria associated with adult Schistocerca gregaria, using 16S rRNA
Journal of Taibah University for Science
2020
Study on the Effect of Huanglian Jiedu Decoction on the Composition of Gut Microflora in SD Rats Based on 16S rRNA Sequencing
Evidence-Based Complementary and Alternative Medicine
2020
Construction & assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data
Indian Journal of Medical Research
2020
Associations between Diet, the Gut Microbiome, and Short-Chain Fatty Acid Production among Older Caribbean Latino Adults
Journal of the Academy of Nutrition and Dietetics
2020
Falling bacterial communities from the atmosphere
Environmental Microbiome
2020
Understanding and interpreting community sequencing measurements of the vaginal microbiome
BJOG: An International Journal of Obstetrics & Gynaecology
2020
Method development for cross-study microbiome data mining: Challenges and opportunities
Computational and Structural Biotechnology Journal
2020
MetaCurator: A hidden Markov model‐based toolkit for extracting and curating sequences from taxonomically‐informative genetic markers
Methods in Ecology and Evolution
2020
Benchmarking the MinION: Evaluating long reads for microbial profiling
Scientific Reports
2020
The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community
Genes
2020
The Rhodamine Isothiocyanate Analogue as a Quorum Sensing Inhibitor Has the Potential to Control Microbially-Induced Biofouling
Marine Drugs
2020
Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
Microbiome
2020
Candidatus Amarolinea and Candidatus Microthrix Are Mainly Responsible for Filamentous Bulking in Danish Municipal Wastewater Treatment Plants
Frontiers in Microbiology
2020
Nest microbiota and pathogen abundance in sea turtle hatcheries
Fungal Ecology
2020
Molecular Characterization of Trichoderma spp. Isolates by Internal Transcribed Spacer (ITS) Region Sequencing Technique and its Use as a Biocontrol Agent
The Open Biotechnology Journal
2020
Randomised, double-blind, placebo-controlled trial of oral probiotic Streptococcus salivarius M18 on head and neck cancer patients post-radiotherapy: a pilot study
Scientific Reports
2020
Characterisation of Extracts and Anti-Cancer Activities of Fomitopsis pinicola
Nutrients
2020
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Frontiers in Microbiology
2020
Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits
Scientific Reports
2020
Are you what you eat? A highly transient and prey‐influenced gut microbiome in the grey house spider Badumna longinqua
Molecular Ecology
2020
Sandy soils amended with bentonite induced changes in soil microbiota and fungistasis in maize fields
Applied Soil Ecology
2020
A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome
Reviews in Aquaculture
2020
The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection
Canadian Journal of Infectious Diseases and Medical Microbiology
2020
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
IMA Fungus
2020
Depot Medroxyprogesterone Acetate and the Vaginal Microbiome as Modifiers of Tenofovir Diphosphate and Lamivudine Triphosphate Concentrations in the Female Genital Tract of Ugandan Women: Implications for Tenofovir Disoproxil Fumarate/Lamivudine in Preexposure Prophylaxis
Clinical Infectious Diseases
2020
Full Issue PDF
Phytobiomes Journal
2020
Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers
npj Biofilms and Microbiomes
2020
Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)
mBio
2020
Applied Barcoding: The Practicalities of DNA Testing for Herbals
Plants
2020
Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis
Frontiers in Ecology and Evolution
2020
MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge
Water Research
2020
Joining Illumina paired-end reads for classifying phylogenetic marker sequences
BMC Bioinformatics
2020
Belowground microbial communities respond to water deficit and are shaped by decades of maize hybrid breeding
Environmental Microbiology
2020
Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States
Journal of Agricultural and Food Chemistry
2020
Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes
Frontiers in Bioengineering and Biotechnology
2020
Ericoid mycorrhizal symbiosis: theoretical background and methods for its comprehensive investigation
Mycorrhiza
2019
Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon
Frontiers in Microbiology
2019
Multi-omics and potential applications in wine production
Current Opinion in Biotechnology
2019
Protective effect of Lactobacillus reuteri KUB-AC5 against Salmonella Enteritidis challenge in chickens
Beneficial Microbes
2019
Vaginal Microbiota Composition Correlates Between Pap Smear Microscopy and Next Generation Sequencing and Associates to Socioeconomic Status
Scientific Reports
2019
Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data
Frontiers in Microbiology
2019
Extracellular Enzyme Activity and Its Implications for Organic Matter Cycling in Northern Chinese Marginal Seas
Frontiers in Microbiology
2019
Metagenomics to Assist in the Diagnosis of Bloodstream Infection
The Journal of Applied Laboratory Medicine
2019
Applying biotechnology for drinking water biofiltration: advancing science and practice
Current Opinion in Biotechnology
2019
Plant assemblages in atmospheric deposition
Atmospheric Chemistry and Physics
2019
Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia
mSystems
2019
DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products
BMC Genomics
2019
Species abundance information improves sequence taxonomy classification accuracy
Nature Communications
2019
Anacapa Toolkit : An environmental DNA toolkit for processing multilocus metabarcode datasets
Methods in Ecology and Evolution
2019
Lactobacillus Dominate in the Intestine of Atlantic Salmon Fed Dietary Probiotics
Frontiers in Microbiology
2019
Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica
Frontiers in Microbiology
2019
The Pedological Context Modulates the Response of Soil Microbial Communities to Agroecological Management
Frontiers in Ecology and Evolution
2019
Metagenomic reconstructions of gut microbial metabolism in weanling pigs
Microbiome
2019
Proto-dolomite formation in microbial consortia dominated by Halomonas strains
Extremophiles
2019
Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data
Frontiers in Genetics
2019
Pollen metabarcoding as a tool for tracking long‐distance insect migrations
Molecular Ecology Resources
2019
Quantitative multi‐locus metabarcoding and waggle dance interpretation reveal honey bee spring foraging patterns in Midwest agroecosystems
Molecular Ecology
2019
Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory
European Journal of Clinical Microbiology & Infectious Diseases
2018
IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
Microbiome
2018
A constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria)
BMC Research Notes
2018
Taxonomy annotation and guide tree errors in 16S rRNA databases
PeerJ
2018
A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data
PeerJ
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