Extensive horizontal gene transfer in cheese-associated bacteria

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

British Dietetic Association systematic review of systematic reviews and evidence-based practice guidelines for the use of probiotics in the management of irritable bowel syndrome in adults (2016 update)

(2016) Y. A. McKenzie et al.   JOURNAL OF HUMAN NUTRITION AND DIETETICS

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

(2016) Erik K. Kastman et al.   mBio

Horizontal Gene Flow in Managed Ecosystems

(2015) Cheryl P. Andam et al.   Annual Review of Ecology Evolution and Systematics

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi

(2015) Jeanne Ropars et al.   CURRENT BIOLOGY

The genomics of microbial domestication in the fermented food environment

(2015) John G Gibbons et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Probiotics for the prevention of allergy: A systematic review and meta-analysis of randomized controlled trials

(2015) Carlos A. Cuello-Garcia et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Migration and horizontal gene transfer divide microbial genomes into multiple niches

(2015) Rene Niehus et al.   Nature Communications

Inferring Horizontal Gene Transfer

(2015) Matt Ravenhall et al.   PLoS Computational Biology

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

Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity

(2014) Benjamin E. Wolfe et al.   CELL

Fibronectin-binding proteins are required for biofilm formation by community-associated methicillin-resistantStaphylococcus aureusstrain LAC

(2014) Jennifer McCourt et al.   FEMS MICROBIOLOGY LETTERS

Horizontal gene transfer among microorganisms in food: Current knowledge and future perspectives

(2014) Franca Rossi et al.   FOOD MICROBIOLOGY

Extensive Horizontal Gene Transfer during Staphylococcus aureus Co-colonization In Vivo

(2014) Alex J. McCarthy et al.   Genome Biology and Evolution

Complete genome sequence of Corynebacterium casei LMG S-19264T (=DSM 44701T), isolated from a smear-ripened cheese

(2014) Frederik Walter et al.   JOURNAL OF BIOTECHNOLOGY

Multiple recent horizontal transfers of a large genomic region in cheese making fungi

(2014) Kevin Cheeseman et al.   Nature Communications

The Bacillus subtilis EfeUOB transporter is essential for high-affinity acquisition of ferrous and ferric iron

(2013) Marcus Miethke et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Sequestration and Scavenging of Iron in Infection

(2013) Nermi L. Parrow et al.   INFECTION AND IMMUNITY

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Phylogenetic analysis reveals the coexistence of interfamily and interspecies horizontal gene transfer in Streptococcus thermophilus strains isolated from the same yoghurt

(2013) Xuerui Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

Staphylococcus aureus FepA and FepB Proteins Drive Heme Iron Utilization in Escherichia coli

(2013) Evelyne Turlin et al.   PLoS One

Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease

(2013) C. Gyles et al.   VETERINARY PATHOLOGY

Growth of Aerobic Ripening Bacteria at the Cheese Surface Is Limited by the Availability of Iron

(2012) Christophe Monnet et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

(2012) Jacqueline Z-M Chan et al.   BMC MICROBIOLOGY

Cheese microbes

(2012) Julie E. Button et al.   CURRENT BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations

(2012) O. X. Cordero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria

(2011) Mariana Gabriela Ghinet et al.   PLoS One

Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway

(2011) B. Jochimsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

(2010) L. Tasse et al.   GENOME RESEARCH

Chemistry and biology of siderophores

(2010) Robert C. Hider et al.   NATURAL PRODUCT REPORTS

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

The Arthrobacter arilaitensis Re117 Genome Sequence Reveals Its Genetic Adaptation to the Surface of Cheese

(2010) Christophe Monnet et al.   PLoS One

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

In Silico Prediction of Horizontal Gene Transfer Events in Lactobacillus bulgaricus and Streptococcus thermophilus Reveals Protocooperation in Yogurt Manufacturing

(2009) M. Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi

(2009) T. A. Richards et al.   PLANT CELL

Probiotics in animal nutrition and health

(2009) F. Chaucheyras-Durand et al.   Beneficial Microbes

Actinomycete integrative and conjugative elements

(2008) Evelien M. te Poele et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility

(2008) Hector Osorio et al.   BMC MICROBIOLOGY

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

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

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

Safety assessment of dairy microorganisms: Streptococcus thermophilus☆

(2007) C DELORME   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY