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Tracking microbiome shifts throughout cheddar cheese production.

B. Rackerby


Tracking microbiome shifts throughout cheddar cheese production.
J. Choi1, B. Rackerby*1, S. Lee1, R. Frojen1, L. Goddik1, S. Ha2, S. Park1. 1Department of Food Science and Technology, Oregon State University Corvallis, OR, 2Department of Food Science and Technology, Chung-Ang University Ansung, Geonggi-Do, South Korea.

It is essential for the dairy industry to understand the microbial community structure of cheese as manufacturing practices influence the microbiome which in turn drives safety and sensory characteristics, thereby affecting the quality of the cheese. While some organisms impart desirable characteristics, others are associated with a reduction in quality. To characterize the shifts in microbial community structure throughout the cheddar cheese making process, 3 batches of cheddar cheese were produced at the Oregon State University Creamery on April 26, June 6, and June 26, 2018. Samples were collected from 36 time points throughout processing and separated into 3 stages: pre-inoculation, production, and aging (6 mo). Environmental samples were collected from the facility to identify a source of non-starter lactic acid bacteria (NSLAB), contaminants of cheese which often impart negative characteristics. DNA was isolated from all samples and sequenced at the 16S rRNA V4 region using an Illumina MiSeq to analyze differences in microbial populations. All cheese samples were predominated by Streptococcus and Lactococcus, both of which were present in the starter lactic acid bacteria (SLAB). Raw and pasteurized milks showed high levels of α diversity before the addition of SLAB. Upon SLAB inoculation, microbial richness decreased significantly and microbial compositions shifted. NSLAB appeared 15 weeks after aging and were determined to be an unidentified group of Lactobacillaceae. Beta diversity analysis revealed that community structure changed sequentially throughout production, and that the April cheese differed from the 2 June produced cheeses, indicating that microbiota differ across both production stage and batch. Functionally, post-inoculation samples from production and ripening clustered together, sharing similar functional properties that differed significantly from pre-inoculation samples. Addition of SLAB reduced the microbial richness and shifted the microbial communities to be more similar both compositionally and functionally. A source of NSLAB was not determined, however growth was present in 39 of 72 samples.

Keywords: cheese, microbiome, high-throughput sequencing.

Biography: I received my BS in Microbiology at Oregon State University where I am currently a masters student in the department of Food Science and technology studying how prebiotic dairy components impact the human gut microbiome, and the influence this has on human gut health. In the past I have worked in quality assurance in the wine industry, as well as in biomedical research and development working on immunotherapeutic devices. I am excited to learn how microbiology and food quality impact human health.