Microbial transfers across a food chain: from grassland to cheese using metagenetic high-throughput sequencing approaches
Résumé
In the context of dramatic changes in food systems (climate, farming practices), a better understanding of microbial community drivers across a food chain is essential to address food quality and global health issues. This major challenge for microbial ecology is fully relevant for farms producing raw milk cheeses, which host a great diversity of interconnected holobionts (grassland, ruminant, human) and environmental microbiomes from soil to dairy product. To address these issues, we set up an experiment to compare agro-ecological (AE) vs intensive (IN) dairy farming systems and to test their response to a forage shortage (outcome of drought). Raw milk cheeses from both systems were fed to rats with humanised microbiota. The bacterial and fungal communities in 736 samples collected across the food chain were characterised by 16S rRNA and ITS genes high-throughput sequencing. Microbial transfers were explored through the analysis of Amplicon Sequence Variants (ASVs) shared between different ecosystems in the food chain. Dissimilarities in microbiota composition assessed using Bray-Curtis distance showed clustering of bacterial and fungal profiles according to their environment of origin. The farming system explained 12-28% of the variance observed in the bacterial community profiles along the food chain from soil to rat faeces. Bedding areas were highlighted as diversity hotspots for downstream microbiomes: above 84% of the teat, air and milk ASVs could originate from bedding. Lysinibacillus stood out as one indicator of the dairy system, showing an increased relative abundance in the faeces of AE cows and cascading effects into the microbiota of cheeses.
HOLOFLUX flagship project TANDEM: https://www6.inrae.fr/holoflux/Nos-Actions/Projets-emblematiques/TANDEM