Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling.

Cheese taste and flavour properties result from complex metabolic processes occurring in microbial communities. A deeper understanding of such mechanisms makes it possible to improve both industrial production processes and end-product quality through the design of microbial consortia. In this work, we caracterise the metabolism of a three-species community consisting of Lactococcus lactis, Lactobacillus plantarum and Propionibacterium freudenreichii during a seven-week cheese production process.

Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations.

In the last two decades, the extensive genome sequencing of strains belonging to the Saccharomyces genus has revealed the complex reticulated evolution of this group. Among the various evolutionary mechanisms described, the introgression of large chromosomal regions resulting from interspecific hybridization has recently shed light on Saccharomyces uvarum species. In this work we provide the de novo assembled genomes of four S.

Pantograph: A template-based method for genome-scale metabolic model reconstruction.

Genome-scale metabolic models are a powerful tool to study the inner workings of biological systems and to guide applications. The advent of cheap sequencing has brought the opportunity to create metabolic maps of biotechnologically interesting organisms. While this drives the development of new methods and automatic tools, network reconstruction remains a time-consuming process where extensive manual curation is required.

Draft Genome Sequence of Rhodosporidium toruloides CECT1137, an Oleaginous Yeast of Biotechnological Interest.

We report the sequencing of the basidiomycetous yeast Rhodosporidium toruloides CECT1137. The current assembly comprises 62 scaffolds, for a total size of ca. 20.

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum.

In addition to Saccharomyces cerevisiae, the cryotolerant yeast species S. uvarum is also used for wine and cider fermentation but nothing is known about its natural history. Here we use a population genomics approach to investigate its global phylogeography and domestication fingerprints using a collection of isolates obtained from fermented beverages and from natural environments on five continents.

Knowledge-based generalization of metabolic models.

Genome-scale metabolic model reconstruction is a complicated process beginning with (semi-)automatic inference of the reactions participating in the organism's metabolism, followed by many iterations of network analysis and improvement. Despite advances in automatic model inference and analysis tools, reconstruction may still miss some reactions or add erroneous ones. Consequently, a human expert's analysis of the model will continue to play an important role in all the iterations of the reconstruction process.

QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis.

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica.

Background: Yarrowia lipolytica is an oleaginous yeast which has emerged as an important microorganism for several biotechnological processes, such as the production of organic acids, lipases and proteases. It is also considered a good candidate for single-cell oil production. Although some of its metabolic pathways are well studied, its metabolic engineering is hindered by the lack of a genome-scale model that integrates the current knowledge about its metabolism.

Mining the semantics of genome super-blocks to infer ancestral architectures.

The study of evolutionary mechanisms is made more and more accurate by the increase in the number of fully sequenced genomes. One of the main problems is to reconstruct plausible ancestral genome architectures based on the comparison of contemporary genomes. Current methods have largely focused on finding complete architectures for ancestral genomes, and, due to the computational difficulty of the problem, stop after a small number of equivalent minimal solutions have been found.

Unusual composition of a yeast chromosome arm is associated with its delayed replication.

The 11.3-Mb genome of the yeast Lachancea (Saccharomyces) kluyveri displays an intriguing compositional heterogeneity: a region of approximately 1 Mb, covering almost the whole left arm of chromosome C (C-left), has an average GC content of 52.9%, which is significantly higher than the 40.

Exploratory simulation of cell ageing using hierarchical models.

Thorough knowledge of the model organism S. cerevisiae has fueled efforts in developing theories of cell ageing since the 1950s. Models of these theories aim to provide insight into the general biological processes of ageing, as well as to have predictive power for guiding experimental studies such as cell rejuvenation.

A systematic nomenclature of chromosomal elements for hemiascomycete yeasts.

We present a compact, stable, unambiguous and extensible nomenclature for unique chromosomal elements from genomic DNA, developed to meet the increasing need created by the increasing number of yeast sequencing projects. Our proposal, adopted for use in the Génolevures project, is specifically designed to facilitate basic tasks in comparative genomics.