Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment

(2022) Songzhe Fu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Prokaryotic diversity in marine and freshwater recirculating aquaculture systems

(2022) Stefanos Moschos et al.   Reviews in Aquaculture

Microbial community dynamics in a hatchery recirculating aquaculture system (RAS) of sole (Solea senegalensis)

(2021) Diana Bastos Almeida et al.   AQUACULTURE

The first sequenced Sphaerotilus natans bacteriophage– Characterization and potential to control its filamentous bacterium host

(2021) Rute Ferreira et al.   FEMS MICROBIOLOGY ECOLOGY

High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon

(2021) J. Graf et al.   mBio

Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes

(2021) Connor L. Brown et al.   Scientific Reports

Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities

(2021) Eduard Fadeev et al.   Frontiers in Microbiology

Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus

(2021) Gábor Torma et al.   Viruses-Basel

Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology

(2021) Leho Tedersoo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca

(2021) Nadia Darwish et al.   Scientific Reports

Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures

(2021) Teresa Nogueira et al.   Antibiotics-Basel

Isolation and characterization of Bacillus spp. from aquaculture cage water and its inhibitory effect against selected Vibrio spp.

(2021) E. Uzun Yaylacı   ARCHIVES OF MICROBIOLOGY

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

A continuously changing selective context on microbial communities associated to fish, from egg to fork

(2020) Marie Filteau et al.   Evolutionary Applications

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus

(2020) Bas Berbers et al.   Scientific Reports

Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework

(2020) Wasim. Uddin et al.   Molecular Ecology Resources

Microbiome Profiling Reveals a Microbial Dysbiosis During a Natural Outbreak of Tenacibaculosis (Yellow Mouth) in Atlantic Salmon

(2020) James W. Wynne et al.   Frontiers in Microbiology

Characterization of the bacterial communities associated with biofilters in two full-scale recirculating aquaculture systems

(2020) Yuexin Ma et al.   Journal of Oceanology and Limnology

Bacterial surface colonization, preferential attachment and fitness under periodic stress

(2019) Maor Grinberg et al.   PLoS Computational Biology

Emerging viruses in aquaculture

(2019) Frederick SB Kibenge   Current Opinion in Virology

Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques

(2019) Margaret E. Hunter et al.   Scientific Reports

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate

(2019) Gottfried J. Palm et al.   Nature Communications

Microbial Communities in a Flow-Through Fish Farm for Lumpfish (Cyclopterus lumpus L.) During Healthy Rearing Conditions

(2019) Irene Roalkvam et al.   Frontiers in Microbiology

Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis

(2019) Terje Klemetsen et al.   MicrobiologyOpen

Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

(2019) Ryan P. Bartelme et al.   mSphere

Generating amplicon reads for microbial community assessment with next‐generation sequencing

(2019) M. Gołębiewski et al.   JOURNAL OF APPLIED MICROBIOLOGY

The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

(2019) Julien Alban Nguinkal et al.   Genes

Identification of Chryseobacterium spp. isolated from clinically affected fish in California, USA

(2019) FdA Sebastião et al.   DISEASES OF AQUATIC ORGANISMS

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

(2018) Garold Fuks et al.   Microbiome

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial community analysis of marine recirculating aquaculture system bioreactors for complete nitrogen removal established from a commercial inoculum

(2018) Marina Brailo et al.   AQUACULTURE

Bacterial and microeukaryotic plankton communities in a semi-intensive aquaculture system of sea bass (Dicentrarchus labrax): A seasonal survey

(2018) Letícia N. Duarte et al.   AQUACULTURE

Characterization of the skin and gill microbiomes of the farmed seabass (Dicentrarchus labrax) and seabream (Sparus aurata)

(2018) Daniela Rosado et al.   AQUACULTURE

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

(2017) Ryan P. Bartelme et al.   Frontiers in Microbiology

High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

(2017) Wirulda Pootakham et al.   Scientific Reports

Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH

(2016) Jennifer Hüpeden et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic analysis shows diverse, distinct bacterial communities in biofilters among different marine recirculating aquaculture systems

(2016) Zhitao Huang et al.   AQUACULTURE INTERNATIONAL

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Biofilms: an emergent form of bacterial life

(2016) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria

(2016) Olga V. Tsoy et al.   Frontiers in Microbiology

Antimicrobial resistance of Aeromonas hydrophila isolated from different food sources: A mini-review

(2016) Deyan Stratev et al.   Journal of Infection and Public Health

First Detection of Bat White-Nose Syndrome in Western North America

(2016) Jeffrey M. Lorch et al.   mSphere

Monitoring and managing microbes in aquaculture - Towards a sustainable industry

(2016) Mikkel Bentzon-Tilia et al.   Microbial Biotechnology

Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

(2015) Kristy Deiner et al.   BIOLOGICAL CONSERVATION

Analysis of environmental variables on population dynamic change ofHaliscomenobacter hydrossis, the bulking causative filament in Macau wastewater treatment plant

(2015) Congyuan Cao et al.   Desalination and Water Treatment

Investigation of Intertidal Wetland Sediment as a Novel Inoculation Source for Anaerobic Saline Wastewater Treatment

(2015) Xueqing Shi et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Alkalinity regulation in calcium carbonate-buffered lakes

(2015) Beat Müller et al.   LIMNOLOGY AND OCEANOGRAPHY

Distribution and Evolution of Nitrogen Fixation Genes in the Phylum Bacteroidetes

(2015) Jun-ichi Inoue et al.   MICROBES AND ENVIRONMENTS

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

(2015) Mads Albertsen et al.   PLoS One

Emerging flavobacterial infections in fish: A review

(2015) Thomas P. Loch et al.   Journal of Advanced Research

ggplot2:Elegant Graphics for Data Analysis

(2015) Pedro M. Valero-Mora   Journal of Statistical Software

RAS and microbial maturation as tools for K-selection of microbial communities improve survival in cod larvae

(2014) Kari J.K. Attramadal et al.   AQUACULTURE

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters

(2014) Samik Bagchi et al.   PLoS One

Microorganisms in recirculating aquaculture systems and their management

(2014) Eugene Rurangwa et al.   Reviews in Aquaculture

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Biofilm Formation by the Fish Pathogen Flavobacterium columnare: Development and Parameters Affecting Surface Attachment

(2013) Wenlong Cai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

(2013) Jonas Ghyselinck et al.   PLoS One

Network Analysis Highlights Complex Interactions between Pathogen, Host and Commensal Microbiota

(2013) Sébastien Boutin et al.   PLoS One

Farming different species in RAS in Nordic countries: Current status and future perspectives

(2012) Johanne Dalsgaard et al.   AQUACULTURAL ENGINEERING

Describing microbial communities and performing global comparisons in the ‘omic era

(2012) Tom O Delmont et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

New developments in recirculating aquaculture systems in Europe: A perspective on environmental sustainability

(2010) C.I.M. Martins et al.   AQUACULTURAL ENGINEERING

Microbial diversity of biological filters in recirculating aquaculture systems

(2010) Harold J Schreier et al.   CURRENT OPINION IN BIOTECHNOLOGY