Fungi are known to produce many chemically diversified metabolites, yet their ecological roles ar... more Fungi are known to produce many chemically diversified metabolites, yet their ecological roles are not always fully understood. The blue cheese making fungus Penicillium roqueforti thrives in different ecological niches and is known to produce a wide range of metabolites, including mycotoxins. Three P. roqueforti populations have been domesticated for cheese production and two populations thrive in other anthropized environments, i.e., spoiled food, lumber and silage. Here, we looked for differences in targeted and untargeted metabolite production profiles between populations using HPLC-HR-Q-TOF and UHPLC-Q-TOF-HR-MS/MS. The noncheese populations produced several fatty acids and different terpenoids, lacking in cheese strains. The Termignon cheese population displayed intermediate metabolite profiles between cheese and non-cheese populations, as previously shown for other traits. The non-Roquefort population, the cheese population with the strongest domestication syndrome, produced the lowest quantities of measured metabolites, including known mycotoxins such as mycophenolic acid (MPA), andrastin A and PR toxin. Its inability to produce MPA was due to a deletion in the mpaC gene, while a premature stop codon in ORF 11 of the PR toxin gene cluster explained its absence and the accumulation of its eremofortin A & B intermediates. In the Roquefort population, we detected no PR toxin nor eremofortins A or B, but found no indel or frameshift mutation, suggesting downregulation. Our results suggest that domesticated cheese populations were selected for lower toxin production while populations from other anthropized environments maintained high metabolite diversity, the bioactivities of these compounds being likely important in these ecological niches.
Additional file 7: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Figure S7. Fortified Neighbor Joining phylogram. Calculated from core SNP data with Kimura 2-para... more Figure S7. Fortified Neighbor Joining phylogram. Calculated from core SNP data with Kimura 2-parameter distances, bootstrap nâ =â 100 (PDF 717 kb)
Additional file 1: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Figure S1. Whole Genome Synteny Dotplot. Sequences of CRBO_1381 and UBOCC-A-315001 were compared ... more Figure S1. Whole Genome Synteny Dotplot. Sequences of CRBO_1381 and UBOCC-A-315001 were compared against PSU-1 using SyMap. The algorithm finds pairwise genome alignment â anchorsâ - represented by dots - and computes blocks of synteny (PDF 11 kb)
Interactions de bactéries à gram négatif dans un écosystème microbien complexe de fromage à pâte pressée non cuite
ANR-07-PNRA-010.Le projet GRAMME vise a developper une methodologie contribuant a evaluer les ben... more ANR-07-PNRA-010.Le projet GRAMME vise a developper une methodologie contribuant a evaluer les benefices et risques, sur les plans sensoriel et sanitaire, associes aux bacteries a Gram negatif au sein des communautes microbiennes des fromages. Dans un premier volet, parmi 173 souches de bacteries a Gram negatif isolees de lait et divers fromages, 20 souches ont ete selectionnees sur la base de leur biodiversite (18 especes differentes dont 8 Enterobacteriaceae) et de facteurs de risques (antibioresistance, production d’amines biogenes in vitro). Un deuxieme volet vise a caracteriser le comportement de ces souches dans la pâte d’un fromage modele au sein d’un consortium modele (10 especes de bacteries Gram+ et levures). Certaines Enterobacteriaceae (Hafnia alvei, Citrobacter freundii…) ont atteint des niveaux eleves dans la pâte du fromage (106-107 UFC/g). H. alvei n’a pas modifie sensiblement la dynamique du consortium microbien au cours de l’affinage, tandis que C. freundii a limite...
Abstract Smear-ripened cheeses develop a viscous, red-orange smear on their surfaces during ripen... more Abstract Smear-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.
Abstract Smear-ripened cheeses develop a viscous, red-orange smear on their surfaces during ripen... more Abstract Smear-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.
Etude de l'altération "framboisé" dans les cidres français : implication de Zymomonas mobilis, aspects physiologiques, taxonomiques et impacts sur l'industrie cidricole
Le " framboise ", principale alteration du cidre, est caracterise en premier lieu par u... more Le " framboise ", principale alteration du cidre, est caracterise en premier lieu par une accumulation d'acetaldehyde (impact organoleptique negatif). Nous avons demontre que l'origine de la maladie correspond a la presence de l'espece Zymomonas mobilis. Il s'agit de la premiere detection de cette bacterie dans des cidres francais. Des tests phenotypiques et genetiques ont ete realises sur differentes souches correspondant d'une part, aux isolats francais et d'autre part, aux sous-especes Z. Mobilis subsp. Mobilis et Z. Mobilis subsp. Pomaceae. D'un point de vue phenotypique et genetique, les tests realises ont montre la presence de trois groupes distincts demontrant clairement que les isolats francais appartiennent a une nouvelle sous-espece : Z. Mobilis subsp. Francensis. D'autre part, afin de mieux comprendre les facteurs ayant une incidence sur le developpement de l'alteration, une caracterisation de la souche type a ete realisee. Cette souche est capable de croitre dans des conditions typiquement rencontrees lors de la fabrication du cidre. Dans un deuxieme temps, la croissance et la production d'acetaldehyde ont ete evaluees a l'aide d'un plan d'experience. Un modele de risque de la production d'acetaldehyde a ete cree et des mesures preventives ont ainsi ete proposees. Enfin, une methode de detection et d'identification de Z. Mobilis par PCR en duplex a ete mise au point permettant la detection precoce de la bacterie directement dans le cidre.
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) compri... more Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging to sect. Restricti from various isolation sources and four continents were characterized by DNA sequencing, and 193 isolates were selected for phylogenetic analyses and phenotypic studies. Species delimitation methods based on multispecies coalescent model were employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS + 28S), CaM, benA and RPB2, and supported recognition of 21 species, including 14 new. All these species were also strongly supported in ML and BI analyses. All recognised species can be reliably identified by all four examined genetic loci. Phenotype analysis was performed to support the delimitation of new species and includes colony characteristics on seven cultivation media incubated at several temperatures, growth on an osmotic gradient (six media with NaCl concentration from 0 to 25 %) and analysis of morphology including scanning electron microscopy. The micromorphology of conidial heads, vesicle dimensions, temperature profiles and growth parameters in osmotic gradient were useful criteria for species identification. The vast majority of species in sect. Restricti produce asperglaucide, asperphenamate or both in contrast to species in sect. Aspergillus. Mycophenolic acid was detected for the first time in at least six members of the section. The ascomata of A. halophilicus do not contain auroglaucin, epiheveadride or flavoglaucin which are common in sect. Aspergillus, but shares the echinulins with sect. Aspergillus.
Bacterial genes of tyrosine decarboxylases were recently identified. Here we continued the sequen... more Bacterial genes of tyrosine decarboxylases were recently identified. Here we continued the sequencing of the tyrosine decarboxylase locus of Lactobacillus brevis IOEB 9809 and determined a total of 7979 bp. The sequence contained four complete genes encoding a tyrosyl-tRNA synthetase, the tyrosine decarboxylase, a probable tyrosine permease and a Na+/H+ antiporter. Rapid amplification of cDNA ends (RACE) was employed to determine the 5P-end of mRNAs containing the tyrosine decarboxylase gene. It was located only 34^35 nucleotides upstream of the start codon, suggesting that the preceding tyrosyl-tRNA synthetase gene was transcribed separately. In contrast, reverse transcription-polymerase chain reactions (RT-PCRs) carried out with primers designed to amplify regions spanning gene junctions showed that some mRNAs contained the four genes. Homology searches revealed similar clusters of four genes in the genome sequences of Enterococcus faecalis and Enterococcus faecium. Phylogenetic analyses supported the hypothesis that these genes evolved all together. These data suggest that bacterial tyrosine decarboxylases are encoded in an operon containing four genes.
bioRxiv (Cold Spring Harbor Laboratory), Mar 27, 2022
Many fungi have been domesticated for food production, with genetic differentiation between popul... more Many fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers. We studied the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, with no differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild-type conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed evidence of multiple horizontal gene transfers, particularly between P. nalgiovense and P. salamii. Some horizontal gene transfers involving P. biforme, also found in dry-cured meat products, were also detected. We also detected positive and purifying selection based on amino-acid changes. Our genetic and phenotypic findings suggest that human selection has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense, and P. biforme, providing an interesting case of convergent adaptation to the same human-made environment. .
bioRxiv (Cold Spring Harbor Laboratory), Jan 23, 2023
Domestication is an excellent case study for understanding adaptation and multiple fungal lineage... more Domestication is an excellent case study for understanding adaptation and multiple fungal lineages have been domesticated for fermenting food products. Studying domestication in fungi has thus both fundamental and applied interest. Genomic studies have revealed the existence of four populations within the blue-cheese-making fungus Penicillium roqueforti. The two cheese populations show footprints of domestication, but the adaptation of the two non-cheese populations to their ecological niches (i.e. silage/spoiled food and lumber/spoiled food) has not been investigated yet. Here, we reveal the existence of a new P. roqueforti population, specific to French Termignon cheeses, produced using small-scale traditional practices, with spontaneous blue mould colonisation. This Termignon population is genetically differentiated from the four previously identified populations, providing a novel source of genetic diversity for cheese making. Phenotypically, the non-Roquefort cheese population was the most differentiated, with specific traits beneficial for cheese making, in particular higher tolerance to salt, to acidic pH and to lactic acid. Our results support the view that this clonal population, used for many cheese types in multiple countries, is a domesticated lineage on which humans exerted strong selection. The Termignon population displayed substantial genetic diversity, both mating types, horizontally transferred regions previously detected in the non-Roquefort population, and intermediate phenotypes between cheese and non-cheese populations. The lumber/spoiled food and silage/spoiled food populations were not more tolerant to crop fungicides but showed faster growth in various carbon sources (e.g. dextrose, pectin, sucrose, xylose and/or lactose), which can be beneficial in their ecological niches. Such contrasted phenotypes between P. roqueforti populations, with beneficial traits .
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
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