Assessment of overall microbial community shift during Cheddar cheese production from raw milk to aging

Cheese is a fermented dairy product that is made from animal milk and is considered to be a healthy food due to its available nutrients and potential probiotic characteristics. Since the microbes in the cheese matrix directly contribute to the quality and physicochemical properties of cheese, it is important to understand the microbial properties of cheese. In this study, Cheddar cheeses produced on three different dates at the Arbuthnot Dairy Center at Oregon State University were collected to determine the microbial community structure. A total of 773,821 sequencing reads and 271 amplicon sequence variants (ASVs) were acquired from 108 samples. Streptococcus and Lactococcus were observed as the most abundant ASVs in the cheese, which were used as the starter lactic acid bacteria (SLAB). Escherichia coli was detected in the raw milk; however, it was not detected after inoculating with SLAB. According to an alpha diversity analysis, SLAB inoculation decreased the microbial richness by inhibiting the growth of other bacteria present in the milk. A beta diversity analysis showed that microbial communities before the addition of SLAB clustered together, as did the samples from cheese making and aging. Non-starter lactic acid bacteria (NSLAB) were detected 15 weeks into aging for the June 6th and June 26th produced cheeses, and 17 weeks into aging for the cheese produced on April 26th. These NSLAB were identified as an unidentified group of Lactobacillaceae. This study characterizes the changes in the Cheddar cheese microbiome over the course of production from raw milk to a 6-month-aged final product.