Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure

Biodiversity, dynamics and ecology of bacterial community during grape marc storage for the production of grappa

(2013) Petros A. Maragkoudakis et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Catabolic flexibility of mammalian-associated lactobacilli

(2013) Michelle M O’Donnell et al.   Microbial Cell Factories

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity

(2013) Tamara Smokvina et al.   PLoS One

Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344T during Growth in Beer

(2013) Vanessa Pittet et al.   PLoS One

Grape marcs as unexplored source of new yeasts for future biotechnological applications

(2013) Favaro Lorenzo et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG

(2013) François P. Douillard et al.   PLoS Genetics

Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways

(2012) Anthony R Borneman et al.   BMC GENOMICS

The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain

(2012) Stefano Campanaro et al.   BMC GENOMICS

Complete Genome Sequence of the Beer Spoilage Organism Pediococcus claussenii ATCC BAA-344T

(2012) V. Pittet et al.   JOURNAL OF BACTERIOLOGY

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

(2012) Nicholas A. Bokulich et al.   PLoS One

Spontaneous organic cocoa bean box fermentations in Brazil are characterized by a restricted species diversity of lactic acid bacteria and acetic acid bacteria

(2011) Zoi Papalexandratou et al.   FOOD MICROBIOLOGY

Diversity of acetic acid bacteria present in healthy grapes from the Canary Islands

(2011) Maria José Valera et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Acidification of grape marc for alcoholic beverage production: Effects on indigenous microflora and aroma profile after distillation

(2011) Barbara Bovo et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Structure-function relationships of the antibacterial activity of phenolic acids and their metabolism by lactic acid bacteria

(2011) A.F. Sánchez-Maldonado et al.   JOURNAL OF APPLIED MICROBIOLOGY

Complete Resequencing and Reannotation of the Lactobacillus plantarum WCFS1 Genome

(2011) R. J. Siezen et al.   JOURNAL OF BACTERIOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Effects of yeast inoculation on volatile compound production by grape marcs

(2010) Barbara Bovo et al.   ANNALS OF MICROBIOLOGY

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data

(2010) Fengfeng Zhou et al.   BIOINFORMATICS

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Efficient production of l-lactic acid from cassava powder by Lactobacillus rhamnosus

(2010) Limin Wang et al.   BIORESOURCE TECHNOLOGY

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Gene duplications in prokaryotes can be associated with environmental adaptation

(2010) Marit S Bratlie et al.   BMC GENOMICS

The RNA polymerase subunits E/F from the Antarctic archaeon Methanococcoides burtonii bind to specific species of mRNA

(2010) Davide De Francisci et al.   ENVIRONMENTAL MICROBIOLOGY

Alterations in d-amino acid concentrations and microbial community structures during the fermentation of red and white wines

(2010) Shiro Kato et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter

(2010) V. Galeote et al.   MICROBIOLOGY-SGM

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

(2010) HÉLÈNE AGOGUÉ et al.   MOLECULAR ECOLOGY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Adaptation factors of the probiotic Lactobacillus rhamnosus GG

(2010) S. Lebeer et al.   Beneficial Microbes

Phenotypic and genomic diversity ofLactobacillus plantarumstrains isolated from various environmental niches

(2009) Roland J. Siezen et al.   ENVIRONMENTAL MICROBIOLOGY

Stress resistance of biofilm and planktonic Lactobacillus plantarum subsp. plantarum JCM 1149

(2009) Hiromi Kubota et al.   FOOD MICROBIOLOGY

Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution

(2009) Hui Cai et al.   Genome Biology and Evolution

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Survival of Lactobacillus casei (LC-1) adhered to prebiotic vegetal fibers

(2009) Karla Bigetti Guergoletto et al.   Innovative Food Science & Emerging Technologies

Lactobacillus fabifermentans sp. nov. and Lactobacillus cacaonum sp. nov., isolated from Ghanaian cocoa fermentations

(2009) K. De Bruyne et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

An overview of the mosaic bacteriocin pln loci from Lactobacillus plantarum

(2009) Dzung B. Diep et al.   PEPTIDES

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

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

Polyphasic taxonomy of acetic acid bacteria: An overview of the currently applied methodology

(2008) Ilse Cleenwerck et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

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

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

SSF production of lactic acid from cellulosic biosludges

(2007) Aloia Romaní et al.   BIORESOURCE TECHNOLOGY

Genera and species in acetic acid bacteria

(2007) Yuzo Yamada et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY