Natural fermented milk is an abundant source of microbial resources, some of which possess probiotic properties that can help prevent and treat human diseases. However, many potential probiotics have not yet been isolated using traditional pure-culture methods. Culturomics, a relatively novel approach, can be primarily employed to cultivate and identify previously unknown and uncultured bacteria. Nevertheless, their application in natural fermented milk remains limited. Therefore, the primary objective of this study was to evaluate the bacterial diversity in natural fermented milk and explore its microbial potential. For this purpose, we collected three natural fermented milk samples from Inner Mongolia and subjected them to enrichment culture in blood culture bottles for 14 d. Bacterial isolates were obtained from the samples at 0, 3, 7, and 14 days using two culture temperatures and four media, and full-length 16S rRNA gene sequencing was performed for each sample at each time point. The results revealed that 488 strains were isolated from three samples belonging to 3 phyla, 11 genera, and 27 species. The method using two culture temperatures (20 °C and 30 °C) and two media (MRS and RCM + Vb) yielded most of the isolates after 3, 7, and 14 days of enrichment culture. Furthermore, full-length 16S rRNA gene sequencing confirmed that this method significantly increased bacterial diversity in natural fermented milk. In conclusion, the culturomics method demonstrates great potential for the isolation of a greater number of bacterial species and is advantageous for further exploration of the diversity of culturable microorganisms in natural fermented milk.
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