Microbial communities of a variety of cheeses and comparison between core and rind region of cheeses

摘要

Understanding the microbial community of cheeseis important in the dairy industry, as the microbiotacontributes to the safety, quality, and physicochemicaland sensory properties of cheese. In this study, themicrobial compositions of different cheeses (Cheddar,provolone, and Swiss cheese) and cheese locations (core,rind, and mixed) collected from the Arbuthnot DairyCenter at Oregon State University were analyzed using16S rRNA gene amplicon sequencing with the IlluminaMiSeq platform (Illumina, San Diego, CA). A total of225 operational taxonomic units were identified fromthe 4,675,187 sequencing reads generated. Streptococcuswas observed to be the most abundant organism inprovolone (72 to 85%) and Swiss (60 to 67%), whereasLactococcus spp. were found to dominate Cheddarcheese (27 to 76%). Species richness varied significantlyby cheese. According to alpha diversity analysis,porter-soaked Cheddar cheese exhibited the highestmicrobial richness, whereas smoked provolone cheeseshowed the lowest. Rind regions of each cheese changedcolor through smoking and soaking for the beverageprocess. In addition, the microbial diversity of the rindregion was higher than the core region because smokingand soaking processes directly contacted the rindregion of each cheese. The microbial communities of thesamples clustered by cheese, indicated that, within agiven type of cheese, microbial compositions were verysimilar. Moreover, 34 operational taxonomic units wereidentified as biomarkers for different types of cheesethrough the linear discriminant analysis effect sizemethod. Last, both carbohydrate and AA metabolitescomprised more than 40% of the total functional annotatedgenes from 9 varieties of cheese samples. Thisstudy provides insight into the microbial compositionof different types of cheese, as well as various locationswithin a cheese, which is applicable to its safety andsensory quality.