Graduate Thesis Or Dissertation


High-throughput Sequencing to Characterize the Microbial Diversity and Functional Properties of Cheese Public Deposited

Downloadable Content

Download PDF


Attribute NameValues
  • Cheese is a fermented dairy product that is made from animal milk and is considered to be 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. The purpose of this study understands and compare the microbial compositions of different cheeses (Cheddar, Provolone, and Swiss) and cheese locations (core, rind, and mixed). The second research object was analyzed microbial community shift during Cheddar cheeses making. All the cheese samples produced at the Arbuthnot Dairy Center at Oregon State University were collected to determine the microbial community structure using 16S rRNA gene amplicon sequencing with the Illumina MiSeq platform (Illumina, San Diego, CA). To compare the microbial composition of different types of cheese, a total of 225 operational taxonomic units were identified from the 4,675,187 sequencing reads generated. Streptococcus was observed to be the most abundant organism in Provolone (72 to 85%) and Swiss (60 to 67%), whereas Lactococcus spp. were found to dominate Cheddar cheese (27 to 76%). Species richness varied significantly by cheese. According to alpha diversity analysis, porter-soaked Cheddar cheese exhibited the highest microbial richness, whereas smoked Provolone cheese showed the lowest. Rind regions of each cheese changed color through smoking and soaking for the beverage process. Also, the microbial diversity of the rind region was higher than the core region because smoking and soaking processes directly contacted the rind region of each cheese. The microbial communities of the samples clustered by cheese indicated that, within a given type of cheese, microbial compositions were very similar. Moreover, 34 operational taxonomic units were identified as biomarkers for different types of cheese through the linear discriminant analysis effect size method. Last, both carbohydrate and AA metabolites comprised more than 40% of the total functional annotated genes from 9 varieties of cheese samples. This study provides insight into the microbial composition of different types of cheese, as well as various locations within a cheese, which applies to its safety and sensory quality. As long as the microbial community shift during Cheddar cheese-making, 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 throughout production from raw milk to a six-month-aged final product.
Resource Type
Date Issued
Degree Level
Degree Name
Degree Field
Degree Grantor
Commencement Year
Committee Member
Academic Affiliation
Rights Statement
Peer Reviewed



This work has no parents.

In Collection: