Characterization of microbiota isolated from white cheese and milk processing facility

In this study, it was aimed to determine the microbiota of industrially produced white cheese, dairy products that occur during production and equipment using in production by culturomics based on Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and shotgun metagenomic sequencing methods and evaluate the results in terms of lactic acid bacteria. In this line, dairy samples from raw milk to final product (raw milk, starter culture added milk, clot, curd, white cheese) and equipment surface samples using in production (raw milk truck, cheese vessel, stirrer, cutting wire, cheesecloth) are collected from a small-scale dairy plant. 109 isolates identified at species level belonging to Lactococcus lactis, Lactobacillus delbrueckii, Lactobacillus crispatus, Lactobacillus fermentum, Lactobacillus paracasei, Lactobacillus brevis, Streptococcus thermophilus, Enterococcus faecalis, Enterococcus faecium, Enterococcus durans and Pediococcus pentosaceus and 9 isolates identified as Enterococcus at genus level by MALDI-TOF MS. 4 of the isolates couldn't be identified by MALDI-TOF MS and resulted Enterococcus faecium, Lactococcus lactis, Enterococcus gallinarum ve Enterococcus gallinarum/Enterococcus casseliflavus as "The closest strain found by database if there is no identification". These isolates have the potential to be new species. Microbial profile of dairy samples and equipment surface samples determined by shotgun metagenomic sequencing differed. Firmicutes was found as the dominant phylum (ranging from 63% to 70%) in the dairy samples while Proteobacteria was found as the dominant phylum (ranging from 84% to 89%) in the equipment surface samples. Firmicutes was found in the equipment surface samples by 5-14%. Lactococcus was the most abundant lactic acid bacteria genus for all samples. Among all bacterial species, the dominant species in dairy samples was Stapylococcus aureus (ranging from 21% to 37%). This followed by Streptococcus, Enterococcus, Leuconostoc, Weisella, Lactobacillus and Pediococcus genera respectively. Lactococcus lactis was the dominant species. The biodiversity obtained by metagenomics was much higher than the biodiversity obtained by culturomics. 11 species of Lactococcus genus, 46 species of Enterococcus genus, 54 species of Lactobacillus genus, 64 species of Streptococcus genus and 2 species of Pediococcus genus were determined by metagenomics while 1 species of Lactococcus genus, 3 species of Enterococcus genus, 6 species of Lactobacillus genus, 1 species of Streptococcus genus and 1 species of Pediococcus genus were determined by MALDI-TOF MS. In the continuation of this study, it is planned to examine the potential of bacteria isolated from samples to be starter culture and obtain a white cheese starter culture. In addition, the potential of being a new lactic acid bacteria species will be examined with whole genome sequencing analyzes of 4 isolates that couldn't be identified by MALDI-TOF MS.