Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces

Impact of sampling and DNA extraction methods on skin microbiota assessment

(2020) Yanisse Boulesnane et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces

(2019) Aleksandra Checinska Sielaff et al.   Microbiome

Influence of sampling and DNA extraction on 16S rRNA gene amplicon sequencing - Comparison of the bacterial community between two food processing plants

(2018) Anna Kristina Witte et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing

(2018) Jakob Brandt et al.   Frontiers in Microbiology

Decrease of microbial community diversity, biogenic amines formation, and lipid oxidation by phloretin in Atlantic salmon fillets

(2018) Jing Wang et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

(2017) Conor J. Doyle et al.   ENVIRONMENTAL MICROBIOLOGY

Impact of environmental factors on the culturability and viability of Listeria monocytogenes under conditions encountered in food processing plants

(2017) Anaïs Overney et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Deciphering Diversity Indices for a Better Understanding of Microbial Communities

(2017) Bo-Ra Kim et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing

(2017) Marilena Marino et al.   Frontiers in Microbiology

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

(2017) Anna Vesty et al.   PLoS One

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

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

Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions

(2016) Giuseppina Stellato et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment

(2016) Monika Dzieciol et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Contamination of salmon fillets and processing plants with spoilage bacteria

(2016) Trond Møretrø et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon-processing plants

(2016) S. Langsrud et al.   JOURNAL OF APPLIED MICROBIOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods

(2016) Santosh Keisam et al.   Scientific Reports

Meat Processing Plant Microbiome and Contamination Patterns of Cold-Tolerant Bacteria Causing Food Safety and Spoilage Risks in the Manufacture of Vacuum-Packaged Cooked Sausages

(2015) Jenni Hultman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The microbiology of cold smoked salmon

(2015) Trond Løvdal   FOOD CONTROL

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

(2015) Nicholas A Bokulich et al.   eLife

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing

(2015) Marcia L. Hart et al.   PLoS One

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

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

(2014) Stéphane Chaillou et al.   ISME Journal

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

The importance of the viable but non-culturable state in human bacterial pathogens

(2014) Laam Li et al.   Frontiers in Microbiology

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation

(2013) Danilo Ercolini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density

(2013) S. Wong 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

Exploring the Sources of Bacterial Spoilers in Beefsteaks by Culture-Independent High-Throughput Sequencing

(2013) Francesca De Filippis et al.   PLoS One

Next-generation approaches to the microbial ecology of food fermentations

(2012) Nicholas A. Bokulich et al.   BMB Reports

Bacterial Community Structure in the Drinking Water Microbiome Is Governed by Filtration Processes

(2012) Ameet J. Pinto et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Monitoring of bacterial load in terms of culturable and non-culturable cells on new materials placed in a delicatessen serve over counter

(2012) Olivier Firmesse et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Evaluation of the spoilage potential of bacteria isolated from spoiled raw salmon (Salmo salar) fillets stored under modified atmosphere packaging

(2012) Sabrina Macé et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Molecular approaches for viable bacterial population and transcriptional analyses in a rodent model of dental caries

(2012) M.I. Klein et al.   Molecular Oral Microbiology

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Understanding and modelling bacterial transfer to foods: a review

(2007) F. Pérez-Rodríguez et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY