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2026
Optimizing rural aquatic remediation: A novel TBEC-IMO composite approach for targeted removal of blackening and odor agents
Bioresource Technology
2026
MEFE: microbiome signature identification based on elastic feature extraction
Frontiers of Computer Science
2026
Genome Analysis
2025
The unresolved struggle of 16S rRNA amplicon sequencing: a benchmarking analysis of clustering and denoising methods
Environmental Microbiome
2025
The role of microbiota in kelp gametophyte development and resilience to thermal stress
Journal of Phycology
2025
From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding
Metabarcoding and Metagenomics
2025
Multitrophic and Multidimensional Insights into Biodiversity and Functional Trait Responses to Precipitation Changes in Alpine Grasslands
Microorganisms
2025
Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga
Proceedings of the Royal Society B: Biological Sciences
2025
Hydrolysate of goat milk casein supplementation alleviates hyperuricemia and modulates gut microbiota in C57BL6/J mice
Food & Function
2025
Effect of dietary zinc supplementation on the gastrointestinal microbiome and host gene expression in the Shank3B−/− mouse model of autism spectrum disorder
Frontiers in Microbiology
2024
The microbiota of Amblyomma americanum reflects known westward expansion
PLOS ONE
2024
Diversity and Endemism of Amphibian Fauna in the Yoko Forest Reserve, Democratic Republic of the Congo
Diversity
2024
PM-profiler: a high-resolution and fast tool for taxonomy annotation of amplicon-based microbiome
Microbiology Spectrum
2024
Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont
npj Biofilms and Microbiomes
2024
ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies
PLOS ONE
2024
A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses
Molecular Ecology Resources
2024
The effects of straw return on soil bacterial diversity and functional profiles: A meta-analysis
Soil Biology and Biochemistry
2024
Differential Effects of Two Common Antiparasitics on Microbiota Resilience
The Journal of Infectious Diseases
2023
Revisiting the intrinsic mycobiome in pancreatic cancer
Nature
2023
Integrating current analyses of the breast cancer microbiome
PLOS ONE
2023
Microbial Community Structure among Honey Samples of Different Pollen Origin
Antibiotics
2023
Changes in Gut Microbiota Associated with Parity in Large White Sows
Animals
2023
The Impact of a Commercial Biostimulant on the Grape Mycobiota of Vitis vinifera cv. Barbera
Microorganisms
2023
Microbiome depiction through user-adapted bioinformatic pipelines and parameters
Journal of Medical Microbiology
2023
Bioinformatic and Statistical Analysis of Microbiome Data
2023
The association between the respiratory tract microbiome and clinical outcomes in patients with COPD
Microbiological Research
2023
Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms
Seminars in Reproductive Medicine
2023
Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil
Scientific Reports
2023
Food & You: A digital cohort on personalized nutrition
PLOS Digital Health
2023
Different and unified responses of soil bacterial and fungal community composition and predicted functional potential to 3 years’ drought stress in a semiarid alpine grassland
Frontiers in Microbiology
2023
The Bacterial DNA Profiling of Chorionic Villi and Amniotic Fluids Reveals Overlaps with Maternal Oral, Vaginal, and Gut Microbiomes
International Journal of Molecular Sciences
2023
Tarhana Microbiota–Metabolome Relationships: An Integrative Analysis of Multi-Omics Data
Food Biotechnology
2023
Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome
Water Research
2023
Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes
Bioinformatics
2023
Exploring the correlation of metabolites changes and microbial succession in solid-state fermentation of Sichuan Sun-dried vinegar
BMC Microbiology
2022
Energy Assessment and Inner Microbial Community Analysis of Internal Circulation (IC) Reactor for Bio-Hydrogen Production Using Brewery Wastewater
BioEnergy Research
2022
Murine Gut Microbiome Meta-analysis Reveals Alterations in Carbohydrate Metabolism in Response to Aging
mSystems
2022
Invariant natural killer T cells minimally influence gut microbiota composition in mice
Gut Microbes
2022
Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies
Environmental DNA
2022
Valorization as a biofertilizer of an agricultural residue leachate: Metagenomic characterization and growth promotion test by PGPB in the forage plant Medicago sativa (alfalfa)
Frontiers in Microbiology
2022
Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation
Frontiers in Cellular and Infection Microbiology
2022
Effects of Nitrate Exposure on Nitrate Reduction Processes in the Wetland Sediments from the Yellow River Estuary
Estuaries and Coasts
2022
The Maternal–Fetal Gut Microbiota Axis: Physiological Changes, Dietary Influence, and Modulation Possibilities
Life
2022
Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes
Water Research
2022
Early Weaning and Milk Substitutes Affect the Gut Microbiome, Metabolomics, and Antibody Profile in Goat Kids Suffering From Diarrhea
Frontiers in Microbiology
2022
Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis
Scientific Reports
2022
The Microbial Quality of Commercial Chopped Romaine Lettuce Before and After the “Use By” Date
Frontiers in Microbiology
2022
Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant
Environmental Microbiome
2022
Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method
mSphere
2021
Diet-ruminal microbiome-host crosstalk contributes to differential effects of calf starter and alfalfa hay on rumen epithelial development and pancreatic α-amylase activity in yak calves
Journal of Dairy Science
2021
Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum
Harmful Algae
2021
Bacterial community structure alterations within the colorectal cancer gut microbiome
BMC Microbiology
2021
Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities
BMC Bioinformatics
2021
Vitamin E alpha- and gamma-tocopherol mitigate colitis, protect intestinal barrier function and modulate the gut microbiota in mice
Free Radical Biology and Medicine
2021
Candida albicans triggers qualitative and temporal responses in gut bacteria
Journal of Medical Mycology
2021
The human milk microbiome: who, what, when, where, why, and how?
Nutrition Reviews
2021
Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database
Frontiers in Microbiology
2021
The Mechanism Underlying of Long-Term Stable Indigo Reduction State in Indigo Fermentation Using Sukumo (Composted Polygonum tinctorium Leaves)
Frontiers in Microbiology
2021
The interplay between Helicobacter pylori and gastrointestinal microbiota
Gut Microbes
2021
Exploration of the microbiome community for saliva, skin, and a mixture of both from a population living in Guangdong
International Journal of Legal Medicine
2021
A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone
Environmental Microbiology
2021
AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data
Bioinformatics
2021
Microbial diversity in tropical marine sediments assessed using culture‐dependent and culture‐independent techniques
Environmental Microbiology
2021
Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data
Journal of Microbiological Methods
2021
Identifying biases and their potential solutions in human microbiome studies
Microbiome
2021
Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies
Frontiers in Microbiology
2021
CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems
Microorganisms
2021
Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting
Periodontology 2000
2021
MUGAN: multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment
Bioinformatics
2021
Methods in Molecular Biology
2021
Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
Ecological Indicators
2021
Identifying optimal bioinformatics protocols for aerosol microbial community data
PeerJ
2020
Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
PLOS ONE
2020
Agricultural land‐use history and restoration impact soil microbial biodiversity
Journal of Applied Ecology
2020
The promise and challenge of cancer microbiome research
Genome Biology
2020
Abrupt dietary changes between grass and hay alter faecal microbiota of ponies
PLOS ONE
2020
Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life
BMC Pediatrics
2020
Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing
PLOS ONE
2020
Bioinformatic strategies to address limitations of 16rRNA short-read amplicons from different sequencing platforms
Journal of Microbiological Methods
2020
Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
BMC Genomics
2020
Nourished, Exposed Beaches Exhibit Altered Sediment Structure and Meiofaunal Communities
Diversity
2020
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes
Computational and Structural Biotechnology Journal
2020
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Frontiers in Microbiology
2020
Generating amplicon reads for microbial community assessment with next‐generation sequencing
Journal of Applied Microbiology
2020
Methods in Lung Microbiome Research
American Journal of Respiratory Cell and Molecular Biology
2020
Comparison of Bacterial DNA Profiles in Mid-Trimester Amniotic Fluid Samples From Preterm and Term Deliveries
Frontiers in Microbiology
2020
Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation
Nature Ecology & Evolution
2020
Spectroradiometric detection of competitor diatoms and the grazer Poteriochromonas in algal cultures
Algal Research
2020
You must choose, but choose wisely: Model-based approaches for microbial community analysis
Soil Biology and Biochemistry
2020
Systematic review: gastric microbiota in health and disease
Alimentary Pharmacology & Therapeutics
2020
Sandy soils amended with bentonite induced changes in soil microbiota and fungistasis in maize fields
Applied Soil Ecology
2020
Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity
PeerJ
2020
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri
Nature Communications
2020
A Uniquely Altered Oral Microbiome Composition Was Observed in Pregnant Rats With Porphyromonas gingivalis Induced Periodontal Disease
Frontiers in Cellular and Infection Microbiology
2019
Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease
Microbiome
2019
A census-based estimate of Earth's bacterial and archaeal diversity
PLOS Biology
2019
Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary
Environmental Microbiology Reports
2019
Are We Overestimating Protistan Diversity in Nature?
Trends in Microbiology
2019
Small-Scale Heterogeneity in Drinking Water Biofilms
Frontiers in Microbiology
2019
Diversity of the oral microbiome between dentate and edentulous individuals
Oral Diseases
2019
The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth
Frontiers in Microbiology
2019
Diet Induces Reproducible Alterations in the Mouse and Human Gut Microbiome
SSRN Electronic Journal
2019
Molecular Heterogeneity in Large-Scale Biological Data: Techniques and Applications
Annual Review of Biomedical Data Science
2019
Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet
Cell Host & Microbe
2019
A comprehensive census of lake microbial diversity on a global scale
Science China Life Sciences
2019
The Lung Microbiome
2019
Stability of temperate coral <em>Astrangia poculata</em> microbiome is reflected across different sequencing methodologies
AIMS Microbiology
2019
Reconstructing functional networks in the human intestinal tract using synthetic microbiomes
Current Opinion in Biotechnology
2018
Anthropogenic N Deposition Alters the Composition of Expressed Class II Fungal Peroxidases
Applied and Environmental Microbiology
2018
Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome
Molecular Ecology
2018
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
F1000Research
2018
Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis
Molecular 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
Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions
Molecular Ecology Resources
2018
Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences
PeerJ
2018
Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment
Scientific Reports
2018
Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets
Frontiers in Microbiology
2018
Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products
mSphere
2018
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
PeerJ
2018
Inferring Variation in Copy Number Using High Throughput Sequencing Data in R
Frontiers in Genetics
2018
Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community
Genomics & Informatics
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