Metagenomics reveal the specificities of the microbiota of three traditional Lebanese goat milk fermented products
Résumé
Three traditional Lebanese fermented raw goat milk products Ambriss, Serdaleh and Labneh El Darff are in danger of extinction, threatening the loss of their microbial heritage. The first two are produced in amphorae by successive filling of milk and surface salt dressing, followed by whey evacuation, while the last one is made from Laban drained in a goat skin. This study aimed to reveal the characteristics and diversity of these products in order to preserve their biological resources. A questionnaire regarding farming and production practices was conducted among 50 producers, among which 15 samples of Serdaleh, 11 of Ambriss and 4 of Labneh El Darff were collected for microbiological, metagenetic and metagenomic analyses. Labneh El Darff has low bacterial diversity and is dominated by Lactobacillus delbrueckii subsp. bulgaricus. Serdaleh and Ambriss might share a similar dominant microbiota but with different proportions of Lactococcus lactis subsp. lactis, L. kefiranofaciens, L. kefiri and L. diolivorans species. The presence of contaminating species was also detected in several products, which will help improving product safety and quality. Finally, 58 prokaryotic metagenome-assembled genomes (MAGs) were reconstituted, which can be used to highlight specific characteristics of these strains and to select isolates for further metabolic studies.
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