Reliable estimation of the key variables and of their rates of change in the alcoholic fermentation

International audienceThe paper establishes a rigorous probabilistic framework for the reconciliation of apparently conflicting data from various physical and chemical measurements related to the key biological variables of alcoholic fermentation: the ethanol and the residual sugar concentrations. The analysis is carried out on a database consisting of 15 beer fermentation experiments, for which off-line determinations of ethanol concentration, fermentable sugar concentration, wort density and refractive index are available, as well as on-line records of evolved CO2. The basic reconciliation method uses mass balance and monotonicity constraints derived from the biological knowledge of the fermentation process. In order to provide interpolated values and rate estimates, smoothness requirements are added. The reconciliation procedure gives more reliable estimates than any given measurement, detects outliers, helps fixing problems in the experimental setting and is also applicable on line

Growth and adaptation of microorganisms on the cheese surface

Cet article a été publié une nouvelle fois dans le numéro 362 http://femsle.oxfordjournals.org/content/362/1/1.20#sec-1Microbial communities living on cheese surfaces are composed of various bacteria, yeasts and molds that interact together, thus generating the typical sensory properties of a cheese. Physiological and genomic investigations have revealed important functions involved in the ability of microorganisms to establish themselves at the cheese surface. These functions include the ability to use the cheese's main energy sources, to acquire iron, to tolerate low pH at the beginning of ripening and to adapt to high salt concentrations and moisture levels. Horizontal gene transfer events involved in the adaptation to the cheese habitat have been described, both for bacteria and fungi. In the future, in situ microbial gene expression profiling and identification of genes that contribute to strain fitness by massive sequencing of transposon libraries will help us to better understand how cheese surface communities function

Prediction of Confidence Limits for Diacetyl Concentration During Beer Fermentation

International audienceA dynamic model for diacetyl production and reduction was developed based on experimental data from 14 laboratory-scale (15-L) lager beer fermentations carried out in various conditions of temperature (10–16°C), top pressure (50−850 mbar), initial yeast concentration (5−20 million cells per milliliter) and initial wort gravity (1,036−1,099 g/L). Uncertainties due to measurement errors, model parameters, and batch-to-batch variability were described in a probabilistic framework. The model predicts a probability distribution for the final diacetyl concentration from which a median value and an upper boundary, at a specified confidence level, are derived. It is demonstrated that in-line diacetyl measurements at early stages of fermentation greatly reduce the uncertainty about the final diacetyl level in each specific batch.Predicción de los Límites de Confianza para la Concentración de Diacetilo en Cerveza Durante la Fermentación Se desarrolló un modelo dinámico para la producción y reducción de diacetilo durante la fermentación, basado en datos experimentales de 14 fermentaciones en el laboratorio (15 L) con cerveza lager; estas fermentaciones se realizaron en diferentes condiciones de temperatura (10-16°C), sobrepresión (50–850 mbar), concentración inicial de levadura (5–20 millones de células por mililitro) y densidad inicial del mosto (1,036–1,099 g/L). Las incertidumbres debido a los errores de medición, los parámetros del modelo y la variabilidad de lote a lote, fueron descritas en un marco probabilístico. El modelo pronostica una distribución de probabilidad para la concentración final del diacetilo, de cual se deriva un valor de la mediana y del límite superior de la concentración, a un nivel de confianza especificada. Se demuestra que las mediciones de diacetilo en línea en las fases iniciales de la fermentación reducen de manera significativa la incertidumbre de la concentración final de diacetilo de cada lote

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation

Ecosystème fromager : de l'étude du métabolisme du soufre chez Kluyveromyces lactis et Yarrowia lipolytica à l'interaction entre Kluyveromyces lactis et Brevibacterium aurantiacum

en français : Le métabolisme du soufre, qui occupe une place centrale au sein de la cellule, est aussi important lors de la fabrication des fromages à pâte molle à croûte lavée. L'écosystème fromager assimile les acides aminés soufrés et peut ainsi produire des composés soufrés volatils (CSVs) indispensables à la flaveur de ces produits. Nous avons étudié le métabolisme du soufre chez deux micro-organismes d'affinage, les levures hémiascomycètes Kluyveromyces lactis et Yarrowia lipolytica. L'analyse in silico du phylum des hémiascomycètes nous a donné pour la première fois une vision évolutive de ce métabolisme. Nous avons relevé des différences fondamentales au niveau de la synthèse de la cystéine mais aussi au niveau des enzymes impliquées dans la production de CSVs. Cette analyse constitue une base solide pour l'étude du métabolisme du soufre. Nous avons combiné plusieurs approches exploratoires (transcriptome, métabolome, dosage des CSVs) afin d'avoir une vision globale de ce métabolisme chez K. lactis et Y.lipolytica. Les différences observées se situent notamment au niveau des voies de synthèse de la cystéine et de la taurine. La production de CSVs semble liée à la surexpression de transaminases spécifiques à chaque espèce combinée à l'accumulation de méthionine intracellulaire. L'affinage du fromage dépendant de tout un écosystème, nous avons également étudié l'interaction entre deux micro-organismes d'affinage, K. lactis et Brevibacterium aurantiacum via une approche transcriptomique, en comparant l'expression d'une co-culture à celle des cultures pures. Nous avons observé de profondes modifications métaboliques touchant notamment le métabolisme du carbone et celui de la biotine.en anglais : Sulphur metabolism, which has a central role in the cell, is also important during the manufacturing of smear ripened cheeses. The cheese ecosystem degrades sulphur aminoacids, producing volatile sulphur compounds (VSCs) indispensable for the flavour of these products. We studied sulphur metabolism in two cheese-ripening microorganisms, the hemiascomycetous yeasts Kluyveromyces lactis and Yarrowia lipolytica. The in silico analysis of the phylum of hemiascomycetes gave us for the first time an evolutionary vision of this metabolism. We found fundamental differences at the level of cysteine synthesis, but also at the level of the enzymes involved in the production of VSCs. This analysis constitutes a solid basis for the study of sulphur metabolism. Thus, we combined several exploratory approaches (transcriptome, metabolome, VSCs measurement) to have a global vision of this metabolism in K. lactis and Y. lipolytica. Major differences are observed in particular at the level of cysteine and taurine biosynthesis pathways. VSCs production seems to be connected to the surexpression of species-specific transaminases combined with the accumulation of intracellular methionine. Cheese ripening being dependent on a whole ecosystem, we also studied the interaction between two cheese-ripening microorganisms, K. lactis and Brevibacterium aurantiacum, by a transcriptomic approach comparing the genes expression of a co-culture to that of the pure cultures. We observed profound metabolic modifications especially with respect to carbon and biotin metabolisms.PARIS-AgroParisTech Centre Paris (751052302) / SudocSudocFranceF

Sulfur metabolism in hemiascomycetes yeast

Sulfur metabolism is a central function of the cell. It has been extensively studied in the model yeast Saccharomyces cerevisiae. A comparative genomic study carried out across the hemiascomycetes clade has shown that S. cerevisiae displayed specificities not shared by the other yeast species. For instance, an O-acetylserine pathway was shown to be present in many yeast species. The complex regulatory pathways seem also to be conserved, with the exception of MET28, whose presence seems to be restricted to S. cerevisiae and related species. In order to explore this pathway in two distant yeast species, Kluyveromyces lactis and Yarrowia lipolytica, transcriptomic and metabolomic studies have been carried out in different conditions of sulfur supply. These high-throughput techniques allowed confirmation of the data of the comparative genomics but also the investigation of new components and new functions linked to sulfur metabolism, for instance, the role of the O-acetylserine pathway in cysteine biogenesis and the role of the aminotransferases in the degradation of methionine were confirmed. The screening of the pools of metabolic intermediates affected by the sulfur supply allowed the identification of new components of the pathway in Y. lipolytica such as taurine and hypotaurine, which seemed to play a role of sulfur storage. These methods also allowed the identification of the set of transporters involved in sulfur metabolism. Eventually, the comparison of these results with the data accumulated in the model S. cerevisiae highlighted the large-scale conservation of this pathway but also the large diversity in the regulated steps inside the pathway

Smear-ripened cheeses

Chapter 38International audienceSmear-ripened cheeses develop a viscous, red-orange smear on their surfaces during ripening. For this reason, they are also called red-smear cheeses or bacterial surface-ripened cheeses. During the past decade, tremendous progress has been made in the understanding of the microbiology of the surface microbiota of these cheeses. This progress stems from the knowledge of their microbial diversity gained through the use of culture-dependent and independent methods including high-throughput sequencing, the genomics of the microorganisms composing the smear microbiota with the sequencing of yeast and bacterial species of technological interest, the functions of these microorganisms and their interactions. In this chapter, we will review the current knowledge on the smear cheese microbiota including the factors affecting ripening of smear cheeses, their microbial diversity, the sources of these microorganisms, their genomic features and functions and the pathogens associated with smear cheeses and their control