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2025
The role of microbial diversity and moss preference in shaping ecosystem multifunctionality during biological soil crusts succession in nutrient-limited sandy soils
Plant and Soil
2025
From air to insight: the evolution of airborne DNA sequencing technologies
Microbiology
2025
Gut Microbiota and Advances in Microbiome Sequencing-Based Technologies: Opportunities for Potential Biologics Discovery in Meat Animals
Meat and Muscle Biology
2025
A species-level identification pipeline for human gut microbiota based on the V3-V4 regions of 16S rRNA
Frontiers in Microbiology
2025
Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing
Microbiology Spectrum
2025
Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?
Poultry Science
2025
Deciphering Bacterial Community Succession and Pathogen Dynamics in ICU Ventilator Circuits Through Full-Length 16S rRNA Sequencing for Mitigating the Risk of Nosocomial Infections
Microorganisms
2025
Species‐level exploration of the gut microbiome in the leaf‐eating Presbytis monkeys reflected the effects of anthropogenic activity and specialized dietary niches: Conservation on the fourth biodiversity level
iMetaOmics
2025
Changes in gut microbiome associated with parity in sows using full-length 16S rRNA amplicon sequencing
Korean Journal of Veterinary Service
2025
Effects of species and sex on the gut microbiome of four laboratory-reared fruit fly lines (Diptera: Tephritidae) using full-length 16S rRNA PacBio Kinnex sequencing
BMC Microbiology
2025
Sampling techniques and genomic analysis of biological material from artworks
Journal of Forensic Sciences
2025
Urban Watershed Microbiology, Volume 1
2025
Comparison of the microbiome of sputum from HIV/AIDS patients using PacBio 16S rRNA sequencing and ddPCR
BMC Infectious Diseases
2025
Unlocking the enhanced trichloroethylene bioremediation potential of mud volcano by targeting synergistic microbial stimulation and electron transfer using microbial fuel cells (MFCs)
Chemical Engineering Journal
2024
Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing
Urolithiasis
2024
Approaches for Potato Crop Improvement and Stress Management
2024
Characterization and Phylogenetic Analysis of the Chloroplast Genomes of Stephania japonica var. timoriensis and Stephania japonica var. discolor
Genes
2024
Soil depth and physicochemical properties influence microbial dynamics in the rhizosphere of two Peruvian superfood trees, cherimoya and lucuma, as shown by PacBio-HiFi sequencing
Scientific Reports
2024
Einführung in die Bioinformatik in der Mikrobiologie
2024
Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation
International Journal of Molecular Sciences
2024
A novel method to assess the integrity of frozen archival DNA samples: Alpha‐diversity ratios of short‐ and long‐read 16S rRNA gene sequences
Methods in Ecology and Evolution
2024
High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform
PNAS Nexus
2023
Alternations of ensiling performance and bacterial community in response to different native grassland in Mongolian Plateau
Journal of Applied Microbiology
2023
Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses
Frontiers in Physiology
2023
The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling
Applied and Environmental Microbiology
2023
Einführung in die Bioinformatik in der Mikrobiologie
2023
Analysis of the bacterial and fungal populations in South African sorghum beer (umqombothi) using full-length 16S rRNA amplicon sequencing
World Journal of Microbiology and Biotechnology
2023
Advances in the oral microbiota and rapid detection of oral infectious diseases
Frontiers in Microbiology
2023
Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations
Frontiers in Microbiology
2023
Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq
Frontiers in Microbiology
2023
Current approaches on the roles of lactic acid bacteria in crop silage
Microbial Biotechnology
2023
Learning Materials in Biosciences
2022
Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing
Clinical Epigenetics
2022
Species identification of bacterial communities in the small brown planthopper, Laodelphax striatellus (Hemiptera: Delphacidae)
Journal of Applied Entomology
2022
Primary studies on the effect of coal bio-gasification in situ in the Qinshui basin
Journal of Petroleum Exploration and Production Technology
2022
Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome
Frontiers in Genetics
2022
Compositional stability of sediment microbial communities during a seagrass meadow decline
Frontiers in Marine Science
2022
Urinary Microbiome of Reproductive-Age Asymptomatic European Women
Microbiology Spectrum
2022
Temporal variation in the prokaryotic community of a nearshore marine environment
Scientific Reports
2022
Research Progress on Forage Production, Processing and Utilization in China
2022
The response regularity of biohydrogen production by anthracite H2-producing bacteria consortium to six conventional veterinary antibiotics
Journal of Environmental Management
2022
Dataset of response characteristics of H2-producing bacteria consortium to β-lactams, aminoglycosides, macrolides, quinolones antibiotics
Data in Brief
2022
Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns
FEMS Microbiology Ecology
2022
Applying meta-data of soybean grain in origin trace and quarantine inspection
Food Research International
2022
Effects of different harvest frequencies on microbial community and metabolomic properties of annual ryegrass silage
Frontiers in Microbiology
2022
Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts
PeerJ
2022
Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production
Frontiers in Microbiology
2022
Dental Implants and Oral Microbiome Dysbiosis
2022
16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences
Frontiers in Bioinformatics
2022
Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan
Frontiers in Microbiology
2022
Dataset of coal bio-gasification and coalbed methane stimulation by single well nutrition injection in Qinshui anthracite coalbed methane wells
Data in Brief
2022
To compare the performance of prokaryotic taxonomy classifiers using curated 16S full-length rRNA sequences
Computers in Biology and Medicine
2022
Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes
mSystems
2022
Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions
Forensic Science International: Genetics
2021
The Destruction of the Anaerobic Environment Caused by Rumen Fistula Surgery Leads to Differences in the Rumen Microbial Diversity and Function of Sheep
Frontiers in Veterinary Science
2021
Comprehensive Foodomics
2021
Selective DNA and Protein Isolation From Marine Macrophyte Surfaces
Frontiers in Microbiology
2021
Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology
Applied and Environmental Microbiology
2021
Microbial Community-Driven Etiopathogenesis of Peri-Implantitis
Journal of Dental Research
2021
Plant Microbiota Beyond Farming Practices: A Review
Frontiers in Sustainable Food Systems
2021
Intestinal inflammation alters mucosal carbohydrate foraging and monosaccharide incorporation into microbial glycans
Cellular Microbiology
2021
Microbiological Aspects of Root Canal Infections and Disinfection Strategies: An Update Review on the Current Knowledge and Challenges
Frontiers in Oral Health
2021
Diversity of microbial communities and soil nutrients in sugarcane rhizosphere soil under water soluble fertilizer
PLOS ONE
2021
Avenanthramide Metabotype from Whole-Grain Oat Intake is Influenced by Faecalibacterium prausnitzii in Healthy Adults
The Journal of Nutrition
2021
Full-length transcriptome assembly of andrias davidianus (amphibia: caudata) skin via hybrid sequencing
Bioscience Reports
2021
Seasonal Dynamics of Epiphytic Microbial Communities on Marine Macrophyte Surfaces
Frontiers in Microbiology
2021
Coleofasciculaceae, a Monophyletic Home for the Microcoleus steenstrupii Complex and Other Desiccation‐tolerant Filamentous Cyanobacteria
Journal of Phycology
2021
User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences
Molecular Ecology Resources
2021
Identifying biases and their potential solutions in human microbiome studies
Microbiome
2021
Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome
BMC Microbiology
2021
Dynamics of Bacterial and Fungal Communities and Metabolites During Aerobic Exposure in Whole-Plant Corn Silages With Two Different Moisture Levels
Frontiers in Microbiology
2021
Rhizosphere microbiome assembly involves seed-borne bacteria in compensatory phosphate solubilization
Soil Biology and Biochemistry
2021
Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities
BMC Bioinformatics
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
Combination of mass spectrometry and DNA sequencing for detection of antibiotic resistance in diagnostic laboratories
Folia Microbiologica
2020
Next-generation DNA sequencing of oral microbes at the Sir John Walsh Research Institute: technologies, tools and achievements
Journal of the Royal Society of New Zealand
2020
High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater–Sediment Interface of a Deep-Sea Cold Seep in South China Sea
Microorganisms
2020
Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi‐year isolation
Environmental Microbiology
2020
Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country
Diagnostics
2020
Selective Enrichment of Clostridium Spp. by Nutrition Control from Sihe Coal Geological Microbial Communities
Applied Biochemistry and Biotechnology
2020
Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
Molecular Ecology Resources
2020
Status and Potential of Single‐Cell Transcriptomics for Understanding Plant Development and Functional Biology
Cytometry Part A
2020
PacBio sequencing reveals bacterial community diversity in cheeses collected from different regions
Journal of Dairy Science
2020
Dynamics of Fecal Microbiota with and without Invasive Cervical Cancer and Its Application in Early Diagnosis
Cancers
2020
Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation
PLOS Pathogens
2020
Reintroducing mothur: 10 Years Later
Applied and Environmental Microbiology
2020
Comparative and comprehensive analysis on bacterial communities of two full-scale wastewater treatment plants by second and third-generation sequencing
Bioresource Technology Reports
2020
Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing
Water Research
2020
Soil Microbiology
2020
Panel 3: Genomics, precision medicine and targeted therapies
International Journal of Pediatric Otorhinolaryngology
2020
Anaerobic Utilization of Hydrocarbons, Oils, and Lipids
2020
Vaginal Microbiome-Based Bacterial Signatures for Predicting the Severity of Cervical Intraepithelial Neoplasia
Diagnostics
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
2019
High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution
Nucleic Acids Research
2019
PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens
MycoKeys
2019
Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens
Applied and Environmental Microbiology
2019
Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System
Microorganisms
2019
Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon
Environmental Microbiology
2019
Modulation of Metabolome and Bacterial Community in Whole Crop Corn Silage by Inoculating Homofermentative Lactobacillus plantarum and Heterofermentative Lactobacillus buchneri
Frontiers in Microbiology
2019
Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences
Environmental Microbiology Reports
2019
Combining the 5.8S and ITS2 to improve classification of fungi
Methods in Ecology and Evolution
2019
Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs
BMC Microbiology
2019
Long-read amplicon denoising
Nucleic Acids Research
2019
A novel metabarcoding approach to investigate Fusarium species composition in soil and plant samples
FEMS Microbiology Ecology
2019
Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
Environmental Microbiology Reports
2019
Synergetic alginate conversion by a microbial consortium of hydrolytic bacteria and methanogens
Water Research
2019
“Delineating bacterial community structure of rhizosphere metagenome from Kansal Forest”
Ecological Genetics and Genomics
2019
Host and Non-host ‘Whistle Stops’ for Psyllids: Molecular Gut Content Analysis by High-Throughput Sequencing Reveals Landscape-Level Movements of Psylloidea (Hemiptera)
Environmental Entomology
2019
Microbial community and fermentation characteristic of Italian ryegrass silage prepared with corn stover and lactic acid bacteria
Bioresource Technology
2019
Xylitol and sorbitol effects on the microbiome of saliva and plaque
Journal of Oral Microbiology
2019
Dysbiosis and Variation in Predicted Functions of the Granulation Tissue Microbiome in HPV Positive and Negative Severe Chronic Periodontitis
BioMed Research International
2019
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
International Journal of Molecular Sciences
2019
Management of abdominal aortic prosthetic graft and endograft infections. A multidisciplinary update
Journal of Infection and Chemotherapy
2019
Identification of Initial Colonizing Bacteria in Dental Plaques from Young Adults Using Full-Length 16S rRNA Gene Sequencing
mSystems
2019
Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils
Extremophiles
2019
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Nature Communications
2019
Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants
Animal
2018
Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing
Virology Journal
2018
Anaerobic Utilization of Hydrocarbons, Oils, and Lipids
2018
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Scientific Reports
2018
Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi
Ecological Monographs
2018
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
GigaScience
2018
Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake
Science of The Total Environment
2018
Studying microbial functionality within the gut ecosystem by systems biology
Genes & Nutrition
2018
Melanization of mycorrhizal fungal necromass structures microbial decomposer communities
Journal of Ecology
2018
Metagenomics
2018
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
GigaScience
2018
Advances in Plant Ecophysiology Techniques
2018
Learning Materials in Biosciences
2018
Studying the human oral microbiome: challenges and the evolution of solutions
Australian Dental Journal
2018
The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces
Scientific Data
2018
A Sequel to Sanger: amplicon sequencing that scales
BMC Genomics
2018
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
Microbiome
2018
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
Applied and Environmental Microbiology
2018
Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing
Scientific Reports
2018
Forensic Ecogenomics
2018
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
New Phytologist
2018
Probing promise versus performance in longer read fungal metabarcoding
New Phytologist
2018
Precision Medicine
2018
TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
mSphere
2018
Long‐read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments
Molecular Ecology Resources
2018
Deciphering Endodontic Microbial Communities by Next-generation Sequencing
Journal of Endodontics
2018
Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau
Frontiers in Microbiology
2018
Dynamics of acute Montipora white syndrome: bacterial communities of healthy and diseased M. capitata colonies during and after a disease outbreak
Microbiology
2018
Progress of analytical tools and techniques for human gut microbiome research
Journal of Microbiology
2017
Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community
Scientific Reports
2017
Preprinting Microbiology
mBio
2017
Optimizing methods and dodging pitfalls in microbiome research
Microbiome
2017
Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants
Scientific Reports
2017
Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA
Methods in Ecology and Evolution
2017
Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from theChaetoceros neogracilisspecies complex
Journal of Phycology
2017
Metataxonomics reveal vultures as a reservoir for Clostridium perfringens
Emerging Microbes & Infections
2017
An Introductory “How-to” Guide for Incorporating Microbiome Research into Integrative and Comparative Biology
Integrative and Comparative Biology
2017
Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing
Frontiers in Plant Science
2017
microclass: an R-package for 16S taxonomy classification
BMC Bioinformatics
2017
Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments
Frontiers in Microbiology
2017
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept
Frontiers in Microbiology
2017
Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis
Gut Pathogens
2017
A Robust Framework for Microbial Archaeology
Annual Review of Genomics and Human Genetics
2017
Disease Suppressive Soils: New Insights from the Soil Microbiome
Phytopathology®
2017
NIAID, NIEHS, NHLBI, and MCAN Workshop Report: The indoor environment and childhood asthma—implications for home environmental intervention in asthma prevention and management
Journal of Allergy and Clinical Immunology
2017
Soil DNA metabarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations
FEMS Microbiology Ecology
2017
Rumen Microbiome, Probiotics, and Fermentation Additives
Veterinary Clinics of North America: Food Animal Practice
2017
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
Frontiers in Microbiology
2017
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
Nature Biotechnology
2017
Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer
GigaScience
2017
A quantitative SMRT cell sequencing method for ribosomal amplicons
Journal of Microbiological Methods
2016
Multiplex amplicon sequencing for microbe identification in community-based culture collections
Scientific Reports
2016
Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate‐dependent
Molecular Ecology
2016
Considerations For Optimizing Microbiome Analysis Using a Marker Gene
Frontiers in Nutrition
2016
A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
PeerJ
2016
Using PacBio Long-Read High-Throughput Microbial Gene Amplicon Sequencing To Evaluate Infant Formula Safety
Journal of Agricultural and Food Chemistry
2016
High‐resolution community profiling of arbuscular mycorrhizal fungi
New Phytologist
2016
Intricacies of assessing the human microbiome in epidemiologic studies
Annals of Epidemiology
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