Theses and Dissertations

ORCID

https://orcid.org/0009-0004-8223-0826

Advisor

Bailey, R. Hart

Committee Member

Schilling, M. Wes

Committee Member

Silva, Juan L.

Committee Member

White, Shecoya

Date of Degree

8-13-2024

Original embargo terms

Visible MSU Only 1 year

Document Type

Dissertation - Open Access

Major

Food Science, Nutrition & Health Promotion (Food Science & Technology)

Degree Name

Doctor of Philosophy (Ph.D.)

College

College of Agriculture and Life Sciences

Department

Department of Food Science, Nutrition and Health Promotion

Abstract

A complex multi-vector processed beef value stream was biomapped and work-in-process (WIP) was sampled at various processing points that affected the product microbiome. Coliform Petrifilm™ was used to analyze samples qualitatively and quantitatively across the meat and glaze vectors. There was an impact (p≤0.05) of the glaze distribution system on coliforms. The pumps of the glaze system were fully disassembled and additional microbial data were obtained through swabbing. WIP and sponge samples were subjected to 16S V1/V2 gene amplification with primers designed for taxonomic identification. Sequencing was conducted on the Illumina MiSeq platform and bioinformatics were developed in QIIME 2 workflows. Bespoke sample groupings were created to compare process steps, with alpha and beta diversity measures analyzed using multivariate statistical models to assess microbial community dynamics. The pumps were found to harbor a diverse and distinct microbiota, acting as reservoirs for fermentative bacteria due to biofilm formation facilitated by carbohydrates in the glaze. The distinct microbial communities found in these pumps, especially one of the three systems, revealed the need for specialized sanitation. A novel weekly deep-clean process was developed and deployed to the glaze pumps utilizing guided disassembly and manual scrubbing, gaseous chlorine dioxide, and a quaternary ammonium hydrogen peroxide biofilm stripper. The implementation of this protocol led to a reduction in coliform presence (p≤0.05), with detection rates dropping from 1.14% to 0.08% in the product and from 32.82% to 0.63% in the glaze. To provide ongoing assessment of the value stream, a unique Environmental Monitoring Program (EMP) was developed to monitor WIP samples collected routinely. After enumeration on EC Petrifilm™, colonies were isolated and subjected to automated biochemical and MALDI-TOF identification. Results showed wide agreement (85.2%) between the two systems with discrepancies resolved by nanopore WGS. The EMP revealed a coliform microbiome with few similarities to the meat and glaze samples analyzed by 16S prior to the sanitation intervention. Isolates confirmed frequent identification of non-lactose fermenting organisms on EC Petrifilm™, illustrating the vulnerability of the method to break-through growth earlier than previously documented.

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