Analysis of the bacterial composition of fermented milk products using high-throughput sequencing

Contamination by microorganisms of food products leads to a change in their texture, taste and aroma, significantly reduces the shelf life. The development of high-throughput DNA analysis methods has made it possible to improve the screening of microorganisms, allowing simultaneous analysis of all bacterial taxa at once. It has previously been demonstrated that high-throughput sequencing is able to identify potentially dangerous microorganisms in various substrates. The bacterial composition of fermented dairy products and cheeses was analyzed using high-throughput sequencing. In yoghurts, bacteria from the genera Streptococcus and Lactococcus are most abundantly represented. Genera of bacteria were found that should not be contained in yoghurts normally: Enterococcus sp., Bacillus sp. and Staphylococcus sp. In addition, opportunistic bacteria of the genera Enterobacter and Escherichia were found. The processed cheese had the most diverse microbial community. Genera of bacteria that normally should not be contained in processed cheese were also found: Bacillus sp., Staphylococcus sp. and Enterococcus sp. Opportunistic bacteria of the genera Proteus (7.31%), Klebsiella (3.94%) and Escherichia (2.56%) were also found. Bacteria from the genera Lactococcus, Lactobacillus and Streptococcus were the most abundant in cottage cheese. Genera of bacteria were found that normally should not be contained in cottage cheese: Acetobacter sp., Acinetobacter sp. and Lysinibacillus sp. Despite the fact that lactic acid bacteria were detected in the studied products in the largest relative abundance, the data obtained indicate that a stricter approach to quality control of fermented milk products is needed. Opportunistic bacteria were present in almost all the products that were analyzed.