Investigating the bacterial microbiota of traditional fermented dairy products using propidium monoazide with single-molecule real-time sequencing

摘要

Traditional fermented dairy foods have been the majorcomponents of the Mongolian diet for millennia. Inthis study, we used propidium monoazide (PMA; bindsto DNA of nonviable cells so that only viable cells areenumerated) and single-molecule real-time sequencing(SMRT) technology to investigate the total and viablebacterial compositions of 19 traditional fermented dairyfoods, including koumiss from Inner Mongolia (KIM),koumiss from Mongolia (KM), and fermented cow milkfrom Mongolia (CM); sample groups treated with PMAwere designated PKIM, PKM, and PCM. Full-length16S rRNA sequencing identified 195 bacterial species in121 genera and 13 phyla in PMA-treated and untreatedsamples. The PMA-treated and untreated samples differedsignificantly in their bacterial community compositionand α-diversity values. The predominant speciesin KM, KIM, and CM were Lactobacillus helveticus,Streptococcus parauberis, and Lactobacillus delbrueckii,whereas the predominant species in PKM, PKIM, andPCM were Enterobacter xiangfangensis, Lactobacillushelveticus, and E. xiangfangensis, respectively. Weightedand unweighted principal coordinate analyses showed aclear clustering pattern with good separation and onlyminor overlapping. In addition, a pure culture methodwas performed to obtain lactic acid bacteria resourcesin dairy samples according to the results of SMRT sequencing.A total of 102 LAB strains were identifiedand Lb. helveticus (68.63%) was the most abundant, inagreement with SMRT sequencing results. Our resultsrevealed that the bacterial communities of traditionaldairy foods are complex and vary by type of fermenteddairy product. The PMA treatment induced significantchanges in bacterial community structure.