16S rRNA metagenomic analysis reveals significant changes of microbial compositions during fermentation from ewe milk to doogh with antimicrobial activity

ABSTRACT The consumption of locally produced organic foods has become a popular trend in those seeking better health through diet. Despite their proposed health benefits, there are concerns regarding the safety of these foods, as they may contain pathogens due to poor hygienic conditions during production. This study aimed to explore the microbial inhibitory effects of ewe milk, yogurt, and doogh prepared by nomads from Ghasr-e-Shirin region in Iran, and to identify the bacterial community of these products using next-generation sequencing of 16S rRNA gene. The antimicrobial activity of cell-free supernatants (CFSs) of samples were evaluated against 3 fungi and 5 bacteria by agar disc diffusion and broth microdilution assays. The findings of this research showed that there is great diversity of bacteria in milk collected by nomads. The most dominant bacteria were Enterobacteriaceae (49.16%) in milk. However, non-lactic acid bacteria were overtaken by Lactobacillus delbrueckii (99.9%) in doogh and yogurt. The CFSs of yogurt and doogh showed growth inhibitory activity against the microorganisms used in this study.