Chloé Gapp

Les microorganismes ont des rôles technologiques essentiels en fabrication fromagère, notamment pour l'acidification du lait. Afin de maitriser au mieux la production, les fromagers utilisent des ferments sélectionnés. Cependant, ces ferments sont pour la plupart génériques car utilisés par un grand nombre de fromagers dans de nombreux pays et continents, et donc déconnectés du terroir. L'objectif de cette thèse était de concevoir des ferments autochtones multifonctionnels, provenant de la zone AOP Brie de Meaux, par ingénierie de communautés. Deux approches d'ingénierie ont été combinées dans ce projet : l'approche descendante basée sur l'application de pressions environnementales pour sélectionner des communautés adaptées, et l'approche ascendante qui elle consiste en l'assemblage de microorganismes isolés sur la base de la connaissance de leur écologie afin d'obtenir un microbiome présentant des fonctions désirées. Dans un premier temps, des laits crus de la zone AOP ont été récoltés et des fermentations séquentielles ont été effectuées. Ces fermentations séquentielles ont permis de sélectionner majoritairement des bactéries lactiques. L'étude de ces communautés a montré un lien fort entre l'évolution de la structure des communautés et la fonction d'acidification. Dans un deuxième temps, les laits crus et fermentés ont été utilisés pour construire une collection de microorganismes isolés constituée de 1167 bactéries. Des cribles d'acidification, de production de gaz, et d'inhibition du pathogène Listeria monocytogenes, ont été appliqués pour sélectionner les candidats présentant les fonctions d'intérêt. Puis des tests de compatibilité ainsi qu'une analyse de génomes ont permis d'exclure les bactéries posant des problèmes de compatibilité, celles portant des gènes résistances à des antibiotiques et/ou porteuses de prophages. Ces travaux ont montré qu'il était possible de mobiliser la diversité des microorganismes du lait cru pour concevoir des ferments autochtones en combinant des approches d'ingénierie descendante et ascendante. Cette double approche pourrait être utilisée à plus large échelle pour la sélection d'autres microorganismes et microbiomes d'intérêt.

Mosquitoes rely on their microbiota for B vitamin synthesis. We previously found that Aedes aegypti third-instar larvae cleared of their microbiota were impaired in their development, notably due to a lack of folic acid (vitamin B9). In this study, we found that diet supplementation using a cocktail of seven B vitamins did not improve mosquito developmental success, but rather had a significant impact on the sex-ratio of the resulting adults, with an enrichment of female mosquitoes emerging from B vitamin-treated larvae. A transcriptomic analysis of male and female larvae identified some sex-specific regulated genes upon vitamin treatment. When treating germ-free larvae with individual B vitamins, we detected a specific toxic effect related to biotin (vitamin B7) exposure at high concentrations. We then provided germ-free larvae with varying biotin doses and showed that males are sensitive to biotin toxicity at a lower concentration than females. Gnotobiotic larvae exposed to controlled low bacterial counts or with bacteria characterised by slower growth, show a male-enriched adult population, suggesting that males require less bacteria-derived nutrients than females. These findings indicate that during larval development, mosquitoes have sex-specific nutritional requirements and toxicity thresholds, which impact the sex ratio of adults.

Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping, which consists of using part of the previous production to inoculate a new one, can be used as a model engineering approach to investigate community dynamics during serial propagations. In this study, 26 raw milk samples were serially propagated 6 times each, giving rise to 26 community lineages. Bacterial community structures were analyzed by metabarcoding, and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high variability of structure and diverse acidification properties between community lineages. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure. IMPORTANCE: Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy backslopping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.

Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping can be used as a model engineering approach to investigate the dynamics of communities during serial propagations. In this study, 26 raw milk samples were used to generate lineages of 6 communities obtained by serial propagation. Bacterial community structures were analyzed by metabarcoding and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high inter-lineage variability of community structures as well as diverse acidification properties. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure. Importance Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy blacksloping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.

Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide–streptogramin A–pleuromutilin resistance among Firmicutes.