Assessment of Bacterial Composition of Locally Processed Back-Slopped Yogurt Through Next-Generation Sequencing

Yogurt is a healthy food consumed all over the world by people of all groups. It contains bacterial microbiota, which has positive effects on the health of its consumers. For decades yogurt has been prepared traditionally by the method of back-slopping. Recently, it is also prepared commercially by using bacteria in different combinations. In this study, we aimed to detect and identify bacteria present in locally processed yogurt using the advanced next-generation sequencing (NGS) method. Yogurt samples were collected from open-air shops located in different areas of Pakistan. All yogurt samples were mixed to make one composite sample. DNA was extracted from yogurt using the phenol-chloroform (organic) method. Extracted DNA was used to perform NGS/Illumina high-throughput sequencing of hypervariable regions (V3 and V4) of the 16S rRNA gene. In the composite yogurt sample, 100% bacteria were detected with a total count of 40423. The number of phyla was 3, of which proteobacteria showed the highest abundance (89.9%). Four classes of bacterial microbiota were detected in which the proportion of class Gamma proteobacteria was the highest (84.8%). The numbers of orders, families, and genera to which bacteria belonged were 9, 10, and 15, respectively. Genus Stenotrophomonas had the highest relative abundance (48.8%), which was followed by Citrobacter with a relative abundance of 11.2%. The lowest relative abundance (0.1%) was exhibited by 2 genera Tepidimonas and Enterobacter. The relative abundance of 4 detected bacterial species was less than 1%. Three species (Mycobacterium tuberculosis, Pantoea agglomerans, and Raoultella ornithinolytica) belonged to culturable bacteria and one species (Tepidimonas spp.) belonged to nonculturable bacteria. Our data demonstrate the presence of wide diversity of bacterial microbiota in locally processed back-slopped yogurt.