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

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

(2014) Benjamin E. Wolfe et al.   CELL

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

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

(2013) Danilo Ercolini   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

(2013) Nicholas A. Bokulich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment

(2013) Christoph Jans et al.   BMC GENOMICS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

“Remake” by High-Throughput Sequencing of the Microbiota Involved in the Production of Water Buffalo Mozzarella Cheese

(2012) Danilo Ercolini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses

(2012) Lisa Quigley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of microflora in Latin-style cheeses by next-generation sequencing technology

(2012) Tina S Lusk et al.   BMC MICROBIOLOGY

Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus

(2012) Christoph Jans et al.   FOOD MICROBIOLOGY

Characteristics of microbial biofilm on wooden vats (‘gerles’) in PDO Salers cheese

(2012) Robert Didienne et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Genome Sequence of Leuconostoc pseudomesenteroides Strain 4882, Isolated from a Dairy Starter Culture

(2012) Victoria Meslier et al.   JOURNAL OF BACTERIOLOGY

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production

(2011) Isabelle Verdier-Metz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation

(2011) Jasmin Schröder et al.   BMC GENOMICS

Biodiversity and growth dynamics of lactic acid bacteria in artisanal PDO Ossau-Iraty cheeses made from raw ewe’s milk with different starters

(2011) Fabienne Feutry et al.   FOOD MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Food fermentations: Microorganisms with technological beneficial use

(2011) François Bourdichon et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR

(2011) Wafa Masoud et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

(2010) Emmanuelle Roth et al.   BMC MICROBIOLOGY

Surface microbiota analysis of Taleggio, Gorgonzola, Casera, Scimudin and Formaggio di Fossa Italian cheeses

(2010) Cecilia Fontana et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications

(2010) Hélène Falentin et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Assessment of the microbial diversity at the surface of Livarot cheese using culture-dependent and independent approaches

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

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Commercial Ripening Starter Microorganisms Inoculated into Cheese Milk Do Not Successfully Establish Themselves in the Resident Microbial Ripening Consortia of a South German Red Smear Cheese

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

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Microbial and Sensory Changes Throughout the Ripening of Prato Cheese Made from Milk with Different Levels of Somatic Cells

(2008) P.C.B. Vianna et al.   JOURNAL OF DAIRY SCIENCE

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

(2008) Stephen J. Callister et al.   PLoS One

The rpoB gene as a tool for clinical microbiologists

(2008) Toïdi Adékambi et al.   TRENDS IN MICROBIOLOGY

Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences

(2007) Lineda Ait Tayeb et al.   RESEARCH IN MICROBIOLOGY