Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description

(2017) Lucas Auer et al.   Molecular Ecology Resources

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity

(2016) Lysiane Fougy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Insight into the Genome of Brochothrix thermosphacta, a Problematic Meat Spoilage Bacterium

(2016) Tamsyn Stanborough et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages

(2016) Margarita Andreevskaya et al.   Standards in Genomic Sciences

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Multilocus Sequence Typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic Lactic Acid Bacterium Causing Spoilage of Packaged Perishable Foods

(2015) Riitta Rahkila et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Bacterial populations and the volatilome associated to meat spoilage

(2015) Annalisa Casaburi et al.   FOOD MICROBIOLOGY

Bacterial spoilers of food: Behavior, fitness and functional properties

(2015) Benoît Remenant et al.   FOOD MICROBIOLOGY

Genetic discrimination of foodborne pathogenic and spoilage Bacillus spp. based on three housekeeping genes

(2015) S. Caamaño-Antelo et al.   FOOD MICROBIOLOGY

Emerging DNA-based technologies to characterize food ecosystems

(2015) Andrea Galimberti et al.   FOOD RESEARCH INTERNATIONAL

Assessing the Unseen Bacterial Diversity in Microbial Communities

(2015) Alejandro Caro-Quintero et al.   Genome Biology and Evolution

Metagenomic insights into the dynamics of microbial communities in food

(2015) Gilles Kergourlay et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Lactic acid bacteria and their controversial role in fresh meat spoilage

(2015) Vasileios Pothakos et al.   MEAT SCIENCE

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

(2015) Zhihong Sun et al.   Nature Communications

Emergence Shapes the Structure of the Seed Microbiota

(2014) Matthieu Barret et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

(2014) Mathieu Almeida et al.   BMC GENOMICS

Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum

(2014) R. Rahkila et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

(2014) Stéphane Chaillou et al.   ISME Journal

A phylogenomics approach for selecting robust sets of phylogenetic markers

(2014) Salvador Capella-Gutierrez et al.   NUCLEIC ACIDS RESEARCH

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

(2013) Dong-Lei Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

(2013) Danilo Ercolini   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

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

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

Population Genetics of Lactobacillus sakei Reveals Three Lineages with Distinct Evolutionary Histories

(2013) Stéphane Chaillou et al.   PLoS One

Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics

(2012) T.T. Nieminen et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Spoilage microbiota associated to the storage of raw meat in different conditions

(2012) Agapi I. Doulgeraki et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Genome Sequences of Pseudomonas fragi Strains A22 and B25

(2012) Y. Mei et al.   JOURNAL OF BACTERIOLOGY

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

A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

(2012) Michiel Vos et al.   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Exploiting bacterial DNA gyrase as a drug target: current state and perspectives

(2011) Frédéric Collin et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems

(2011) Simon Roux et al.   FEMS MICROBIOLOGY ECOLOGY

Fingerprint of lactic acid bacteria population in beef carpaccio is influenced by storage process and seasonal changes

(2011) Isabelle Lucquin et al.   FOOD MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Diversity of Leuconostoc gasicomitatum associated with meat spoilage

(2009) Elina J. Vihavainen et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

(2009) P. Forterre et al.   NUCLEIC ACIDS RESEARCH

Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei

(2008) S. Chaillou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences

(2008) B. Ghebremedhin et al.   JOURNAL OF CLINICAL MICROBIOLOGY