The sources and transmission routes of microbial populations throughout a meat processing facility

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon

(2019) Joran Martijn et al.   ENVIRONMENTAL MICROBIOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

(2019) Benjamin J Callahan et al.   NUCLEIC ACIDS RESEARCH

Culture-Independent Evaluation of Bacterial Contamination Patterns on Pig Carcasses at a Commercial Slaughter Facility

(2019) BENJAMIN ZWIRZITZ et al.   JOURNAL OF FOOD PROTECTION

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

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

Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse

(2019) Arnaud Bridier et al.   Scientific Reports

Anoxybacillus sediminis sp. nov., a novel moderately thermophilic bacterium isolated from a hot spring

(2018) Inam Ullah Khan et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints

(2018) Gang Liu et al.   WATER RESEARCH

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

The use of next generation sequencing for improving food safety: Translation into practice

(2018) Balamurugan Jagadeesan et al.   FOOD MICROBIOLOGY

Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept

(2017) Ivan Nastasijevic et al.   INTERNATIONAL JOURNAL OF FOOD 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

A new perspective on microbial landscapes within food production

(2016) Nicholas A Bokulich et al.   CURRENT OPINION IN BIOTECHNOLOGY

Defining the food microbiome for authentication, safety, and process management

(2016) B. C. Weimer et al.   IBM JOURNAL OF RESEARCH AND DEVELOPMENT

Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs

(2016) Evelyne Mann et al.   MEAT SCIENCE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Food safety trends: From globalization of whole genome sequencing to application of new tools to prevent foodborne diseases

(2016) Siyun Wang et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters

(2016) Rebekah Henry et al.   WATER RESEARCH

Application of Metagenomic Sequencing to Food Safety: Detection of Shiga Toxin-Producing Escherichia coli on Fresh Bagged Spinach

(2015) Susan R. Leonard et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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 use of PCR-DGGE to determine bacterial fingerprints for poultry and red meat abattoir effluent

(2015) O. de Smidt   LETTERS IN APPLIED MICROBIOLOGY

World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010

(2015) Arie H. Havelaar et al.   PLOS MEDICINE

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

(2015) Nicholas A Bokulich et al.   eLife

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

(2014) Stéphane Chaillou et al.   ISME Journal

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Omics approaches in food safety: fulfilling the promise?

(2014) Teresa M. Bergholz et al.   TRENDS IN MICROBIOLOGY

BAT - Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

(2014) Pedro Cardoso et al.   Methods in Ecology and Evolution

Recent discoveries and applications of Anoxybacillus

(2013) Kian Mau Goh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Attachment and biofilm formation by foodborne bacteria in meat processing environments: Causes, implications, role of bacterial interactions and control by alternative novel methods

(2013) Efstathios Giaouris et al.   MEAT SCIENCE

Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)

(2013) Krissi M. Hewitt et al.   PLoS One

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

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

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

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

Changes in microbial contamination levels of porcine carcasses and fresh pork in slaughterhouses, processing lines, retail outlets, and local markets by commercial distribution

(2012) Y.M. Choi et al.   RESEARCH IN VETERINARY SCIENCE

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Thermophilic bacilli and their importance in dairy processing

(2010) Sara A. Burgess et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The formation of spores in biofilms ofAnoxybacillus flavithermus

(2009) S.A. Burgess et al.   JOURNAL OF APPLIED MICROBIOLOGY