High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk

Naturally fermented yak milk (NFYM) is a traditional Tibetan fermented product that contains a rich microbial community. This study used high-throughput pyrosequencing to investigate the bacterial and fungal community diversity of 16 NFYM samples from the villages Geda and Ningzhong in Tibet. Pyrosequencing produced a total of 112,173 high quality bacterial 16S rRNA gene sequences and 90,980 fungal high quality reads from the NFYM. Sequence analysis grouped the high quality gene sequences into eleven bacterial and five fungal phyla, of which Firmicutes and Ascomycota dominated. At the genus level, Lactobacillus and Saccharomyces were the dominating bacteria and fungi, respectively. Principal coordinate analysis (PCoA) based on weighted and unweighted UniFrac values revealed no significant differences in the structure of bacterial and fungal microbiota. However, multivariate analysis of variance (MANOVA) based on unweighted UniFrac distances showed significant differences (P<0.05) between the bacterial and fungal populations of the two NFYM samples from different villages. After the redundancy analysis (RDA), 49 key responding operational taxonomic units (OTUs) could be identified. Among them, 7 OTUs (Acinetobacter, unidentified Bacteroidetes, Lactobacillus, unidentified Proteobacteria, Streptococcus, Pantoea, and unidentified Firmicutes) were enriched in the Geda village samples, while 42 OTUs (mainly Massilia, Propionibacterium, Lactococcus, Leuconostoc, and Enterococcus) were enriched in the Ningzhong village samples. The present work provided insights into the microbiome of Tibetan NFYM and showed that the microbiota composition may be stratified by their geographic regions.