Temporal Shotgun Metagenomics Revealed the Potential Metabolic Capabilities of Specific Microorganisms During Lambic Beer Production

Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species

(2019) Marko Verce et al.   Frontiers in Microbiology

Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies

(2019) Cecilia Noecker et al.   mSystems

Acetic acid bacteria in fermented foods and beverages

(2018) Jonas De Roos et al.   CURRENT OPINION IN BIOTECHNOLOGY

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese

(2018) A. S. Bertuzzi et al.   mSystems

Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process

(2018) Louise Vermote et al.   INTERNATIONAL DAIRY JOURNAL

Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species

(2018) Jonas De Roos et al.   Frontiers in Microbiology

Metagenomics reveals flavour metabolic network of cereal vinegar microbiota

(2017) Lin-Huan Wu et al.   FOOD MICROBIOLOGY

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C

(2017) Caiti Smukowski Heil et al.   YEAST

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation

(2017) Peter R. Sternes et al.   GigaScience

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota

(2016) Alejandra Escobar-Zepeda et al.   FOOD MICROBIOLOGY

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Metagenomics insights into food fermentations

(2016) Francesca De Filippis et al.   Microbial Biotechnology

Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains

(2015) S. Crauwels et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

The microbial diversity of an industrially produced lambic beer shares members of a traditionally produced one and reveals a core microbiota for lambic beer fermentation

(2015) Freek Spitaels et al.   FOOD MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Brettanomyces yeasts — From spoilage organisms to valuable contributors to industrial fermentations

(2015) Jan Steensels et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

New insights on the features of the vinyl phenol reductase from the wine-spoilage yeast Dekkera/Brettanomyces bruxellensis

(2014) Tiziana Mariarita Granato et al.   ANNALS OF MICROBIOLOGY

Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

(2014) Sam Crauwels et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Key to Acetate: Metabolic Fluxes of Acetic Acid Bacteria under Cocoa Pulp Fermentation-Simulating Conditions

(2014) Philipp Adler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Oxidation of Metabolites Highlights the Microbial Interactions and Role ofAcetobacter pasteurianusduring Cocoa Bean Fermentation

(2014) Frédéric Moens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The Microbial Diversity of Traditional Spontaneously Fermented Lambic Beer

(2014) Freek Spitaels et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

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

(2013) Danilo Ercolini   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Acetobacter lambici sp. nov., isolated from fermenting lambic beer

(2013) F. Spitaels et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Tomáš Větrovský et al.   PLoS One

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

(2012) Juan M. Gonzalez et al.   PLoS One

Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity

(2012) Koen Illeghems et al.   PLoS One

Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

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

Integrative analysis of environmental sequences using MEGAN4

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

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

Dekkera and Brettanomyces growth and utilisation of hydroxycinnamic acids in synthetic media

(2008) Victoria Harris et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Growth and volatile compound production by Brettanomyces/Dekkera bruxellensis in red wine

(2008) A. Romano et al.   JOURNAL OF APPLIED MICROBIOLOGY

Formation of 4-vinyl and 4-ethyl derivatives from hydroxycinnamic acids: Occurrence of volatile phenolic flavour compounds in beer and distribution of Pad1-activity among brewing yeasts

(2007) Nele Vanbeneden et al.   FOOD CHEMISTRY