Detection of the lactic acid bacterial community in small scale white cheese processing facility using shotgun metagenomics and culturomics

Abstract

This study aims to characterize lactic acid bacteria (LAB) community in small-scale white cheese processing facility highly favored by consumers. Shotgun metagenomics and culturomics based on MALDI-TOF MS approaches were employed. Samples from various production stages and equipment surfaces were collected. Dominant phyla in dairy and equipment samples were Firmicutes (63–70%) and Proteobacteria (84–89%), respectively. Lactococcus was the most abundant LAB genus across all samples, with Lactococcus lactis as dominant species followed by Streptococcus, Enterococcus, and Lactobacillus, indicating LAB community diversity contributing to product characteristics. Culturomics identified 12 LAB species, including Enterococcus faecalis and Lactobacillus delbrueckii. Metagenomics provided insights into microbial composition and dynamics in dairy environment, while culturomics identified specific LAB species. The combined approach offers a comprehensive view of dairy microbial communities, aiding industrial development by informing starter culture combinations for improved dairy products and processes.