Graduate Thesis Or Dissertation
 

An Investigation of Seasonal Microbiome Changes in Raw Milk from Organic and Conventional Dairy Farms in Oregon

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https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/3484zq262

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  • Raw milk microbiome is important to food safety and security. However, understanding the complexities of how the dairy farm environment may affect the microbiome is difficult. Since there are a variety of operating parameters for dairy farmers to use on their farms, each farming environment is unique. What makes the milk producers more unique is the differences between organic and conventional farming practices. Organic farms must meet the National Organic Program requirement, which include 120 or more days on pasture with 30% of the dry matter intake from pasture, and no treatment with antibiotics. This study aims to look at the microbiome of raw milk produced on organic and conventional farms in Oregon. Samples were gathered from organic (n=4), and conventional (n=3) dairy farms on a quarterly basis in 2020. 16S rRNA gene-based amplicon sequencing was performed to assess the microbiome of raw milk and farm environmental samples. There was a change in alpha diversity between the organic and conventional milk samples in the spring (P-value: 0.012), and a slight difference in the summer (P-value: 0.07). The core microbiome (all seasons) of organic milk consisted of four bacteria (Escherichia-Shigella, Romboutsia, Streptococcus, and UCG-005). There were 11 core microbiome bacteria identified in conventional milk (Bifidobacterium, Clostridium sensu stricto 1, Corynebacterium, Escherichia-Shigella, Jeotgalibaca, Klebsiella, Phascolarctobacterium, Pseudomonas, Streptococcus, and UCG-005). There was one taxon (Acetobacter) present only in organic raw milk for all seasons, and four unique taxa (Aerococcus, Facklamia, Lactobacillus, and Sphingomonas) found in conventional raw milk across all seasons. There was a significant impact on APC and CC plate counts by farming type (ANOVA; P value <0.05). Overall organic and conventional milk exhibit similar microbiome profiles across their respective farming types. Escherichia-Shigella was the most abundant bacteria and found in all seasons and farming types. Overall, there is little evidence to support that there is a difference between the microbiomes of organic and conventional raw milk.
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  • Pending Publication
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  • 2021-06-08 to 2022-01-09

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