IMPROVING THE PRECISION OF ALICYCLOBACILLUS SPOILAGE PREDICTIONS AT THE INTERSECTION OF GENOTYPE AND ENVIRONMENT

The goal of this project is to determine the kinetics and dynamics of spoilage and the associated expression of spoilage-specific genes among Alicyclobacillus spp. in industrially relevant beverage matrices and storage conditions.By assessing the impact of environment and genotype on spoilage, precise prediction models can be developed. I will achieve this goal using the following objectives:1. Model guaiacol spoilage kinetics and dynamics among guaiacol-producing strains in industrially relevant beverage matrices and storage conditions. Hypothesis: Spoilage by Alicyclobacillus spp. is conditional on the strain, beverage matrix attributes, 3 and storage conditions of the product. The guaiacol production-ability of 75 different strains will be screened under optimal laboratory conditions using a peroxidase colorimetric assay (PECA). Based on these findings, the 75 strains will be grouped into high, medium, and low-risk spoilage categories. Spoilage kinetics and dynamics under industry-relevant spoilage conditions (matrix compositions, storage conditions) will be determined for 3 representative isolates within each high, medium, and low risk spoilage category.2. Identify genes involved in spoilage using comparative genomics and transcriptomics. Hypothesis: Genes beyond the guaiacol biosynthesis gene vdcC determine spoilage rate and are variably expressed among strains in different environments. The genes required for guaiacol production will be investigated using whole genome sequencing and a genome wide association study (GWAS). Subsequently, transcriptomics will be used to determine patterns in gene expression in high-risk Alicyclobacillus spp. within beverages over the course of their shelf-life and in incubation conditions studied in objective 1.By studying the intersection of environment and genotype, I will address the need for high precision Alicyclobacillus spoilage prediction. This approach to microbial quality will advance the field by identifying genes for spoilage and diverse matrix-specific factors which are absent from current culture-dependent methods. This approach to addressing spoilage will facilitate more sustainable approaches to quality management for the food industry.