Bacterial diversity analysis in Kazakh fermented milks Shubat and Ayran by combining culture-dependent and culture-independent methods

Abstract

Shubat (fermented camel milk beverage) and Ayran (yogurt) are popular traditional fermented milk products in Kazakhstan. However, the natural microbial diversity in these fermented dairy products is not well studied. In this study, we paired high-throughput sequencing with the traditional culture-dependent method to evaluate the bacterial diversity in these two fermented milk products. A total of 137 operational taxonomic units were obtained from Shubat and Ayran samples, by using 16S rRNA gene sequencing. The three most abundant operational taxonomic units were of the Lactobacillus and Streptococcus genera. In the 55 bacterial strains isolated through the culture-dependent method, the dominant species belonged to Leuconostoc and Enterococcusgenera. Moreover, probiotic properties, such as acid tolerance, bile salt tolerance, and antibiotic resistance of 26 selected lactic acid bacteria were also tested. Eight strains showed excellent survival rates under acidic pH or bile salt stress and were susceptible to the antibiotics used in the experiment. This is the first systematic study to identify the indigenous strains and natural bacterial diversity in Shubat and Ayran. We expect our results to facilitate the commercial production and quality control of these milk products.