Les résultats présentés dans ce mémoire ont démontré que la diversité au sein des souches de Geotrichum spp. et Galactomyces spp. isolées de produits laitiers ou de l’environnement est bien présente, autant au niveau phénotypique que génomique. Cette diversité a de fait mené à l’identification de sous-groupes variables selon le caractère étudié, qui pourraient éventuellement être identifiés à titre de sous-espèces. Malheureusement, étant donné un manque de données génomiques complètes, aucun gène-clé explicitement impliqué dans l’affinage des fromages et unique aux différents groupes de souches n’a pu être identifié.
D’un point de vue industriel, le regroupement des souches de Geotrichum spp. démontre un fort potentiel pour le développement de différents types de ferments d’affinage. Tel qu’illustré dans ce travail, la caractérisation phénotypique des souches de Geotrichum spp. implique de nombreuses analyses afin de dresser un portrait complet de leurs capacités et caractéristiques plutôt variables. Afin de faciliter leur classification, l’idéal aurait été d’être en mesure d’associer des gènes clés aux caractéristiques phénotypiques des souches étudiées, par exemple leur capacité à développer des pseudo-hyphes, leur capacité alcalinisante ou protéolytique, ou encore leur capacité à consommer certaines substances carbonées. De la sorte, pour une caractérisation et classification ultérieure de nouvelles souches de G. candidum, il aurait été nécessaire d’évaluer la présence ou l’absence de ces gènes clés afin de déterminer pour quel type de fromage les souches devraient être utilisées : des fromages à croute fleurie ou à croute lavée, à pâte molle ou à pâte ferme, à saveurs douces ou prononcées, aux arômes soufrés ou davantage fruités, etc. Or, en raison de l’assemblage incomplet des génomes des souches de Geotrichum spp., il n’a pas été possible, hors de tout doute, d’associer des gènes spécifiques aux caractéristiques phénotypiques. Ainsi, le re-séquençage des génomes des souches de Geotrichum spp. avec une technologie complémentaire (ex : PacBio) sera essentiel afin d’obtenir les représentations génomiques les plus complètes possible, et de fait établir un portrait plus représentatif des gènes définissant chacune des souches.
La réalisation de ce travail a mené à de nouveaux questionnements et de nouvelles avenues de recherche. En rapport aux analyses phénotypiques réalisées sur les souches, il a été observé que certaines souches de G. candidum avaient le potentiel de libérer des composés aromatiques non seulement associés aux arômes soufrés (ail, chou, ferme), ces derniers découlant souvent de l’activité protéolytique, mais également associés à des arômes fruités, ceux-ci découlant davantage de l’activité lipolytique. De fait, il serait intéressant de caractériser l’activité lipolytique des souches ainsi que de
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doser les composés aromatiques libérés lors de l’affinage de caillés modèles pour avoir un meilleur portrait de l’activité des souches en contexte de fabrication fromagère. Par ailleurs, une autre façon d’obtenir un portrait plus détaillé et complet des activités métaboliques des souches de G. candidum en cours d’affinage de caillé modèle serait de mesurer l’activité des souches par transcriptomique. En rapport aux analyses de biologie moléculaire, il serait idéal de pouvoir comparer les gènes identifiés par génomique par rapport à ceux obtenus par trancriptomique afin d’évaluer si seulement à partir des génomes des souches, et donc de gènes clés, il est réellement possible de les classer selon le type de fromage à fabriquer, ou bien si des analyses complémentaires sont nécessaires.
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