Fish microbiomics: Strengths and limitations of MinION sequencing of gilthead sea bream (Sparus aurata) intestinal microbiota

Diet and Host Genetics Drive the Bacterial and Fungal Intestinal Metatranscriptome of Gilthead Sea Bream

(2022) Fernando Naya-Català et al.   Frontiers in Microbiology

Rice protein concentrate as a fish meal substitute in Oreochromis niloticus: Effects on immune response, intestinal cytokines, Aeromonas veronii resistance, and gut microbiota composition

(2022) Rasha M. Reda et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptomic profiling of Gh/Igf system reveals a prompted tissue-specific differentiation and novel hypoxia responsive genes in gilthead sea bream

(2021) F. Naya-Català et al.   Scientific Reports

Reshaping of Gut Microbiota in Gilthead Sea Bream Fed Microbial and Processed Animal Proteins as the Main Dietary Protein Source

(2021) Paula Solé-Jiménez et al.   Frontiers in Marine Science

New strategies to improve minimap2 alignment accuracy

(2021) Heng Li   BIOINFORMATICS

Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream (Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization

(2021) Fernando Naya-Català et al.   Frontiers in Physiology

Factors Driving Bacterial Microbiota of Eggs from Commercial Hatcheries of European Seabass and Gilthead Seabream

(2021) Babak Najafpour et al.   Microorganisms

yacrd and fpa: upstream tools for long-read genome assembly

(2020) Pierre Marijon et al.   BIOINFORMATICS

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?

(2020) Fabien Magne et al.   Nutrients

Evaluation of PCR conditions for characterizing bacterial communities with full-length 16S rRNA genes using a portable nanopore sequencer

(2020) So Fujiyoshi et al.   Scientific Reports

Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform

(2020) Po-Li Wei et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Bacterial Diversity and Antibiotic Susceptibility of Sparus aurata from Aquaculture

(2020) Vanessa Salgueiro et al.   Microorganisms

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream

(2020) M. Carla Piazzon et al.   Microbiome

Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes

(2019) Mitsuhiko P Sato et al.   DNA RESEARCH

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

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

Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish

(2019) M. Carla Piazzon et al.   Frontiers in Microbiology

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

(2019) Volkan Sevim et al.   Scientific Data

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Metagenome complexity and template length are the main causes of bias in PCR-based bacteria community analysis

(2018) Wentao Peng et al.   JOURNAL OF BASIC MICROBIOLOGY

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos

(2018) Fan Wang et al.   AMB Express

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

(2018) Daniela Rosado et al.   AQUACULTURE

Genomic GC-Content Affects the Accuracy of 16S rRNA Gene Sequencing Based Microbial Profiling due to PCR Bias

(2017) Martin F. Laursen et al.   Frontiers in Microbiology

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene

(2015) G. Estruch et al.   PLoS One

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata)

(2014) Konstantinos A. Kormas et al.   MicrobiologyOpen

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Storage conditions of intestinal microbiota matter in metagenomic analysis

(2012) Silvia Cardona et al.   BMC MICROBIOLOGY

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

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY