Zheng Zhao | ALES Graduate Seminar

Event details: A graduate exam seminar is a presentation of the student’s final research project for their degree. This is an ALES PhD Final Exam Seminar by Zheng Zhao. This seminar is open to the general public to attend.

Zoom Link: https://ualberta-ca.zoom.us/j/92669959219

PhD with Dr. Michael Gaenzle.

Thesis Topic: Selection of Fermentation Cultures for Dairy Products and Plant-Based Alternatives

Abstract:

Fermentation serves as a sustainable approach to enhancing product quality while meeting clean-label expectations. The selection and application of appropriate fermentation cultures significantly affects the quality and shelf life of fermented dairy and plant-based alternatives. This thesis investigates the metabolic diversity of lactic acid bacteria (LAB) in the fermentation of both dairy and plant-based substrates. By integrating advanced sequencing technologies with culture-based methods, this work improves microbial detection and identification, informs the selection of robust strains, and advances the functional understanding of fermentation cultures. The findings contribute to the development of targeted fermentation strategies that enhance product quality, safety, and sustainability in both traditional and emerging food systems.

Sequence-based methods were critically assessed, revealing key challenges: the limited taxonomic resolution of gene amplicon sequencing, PCR biases that distort quantitative relationships, the inability to distinguish viable from dead cells, and concerns about the completeness and contamination of metagenome-assembled genomes. Advances in sequencing technologies, applied through culturomics, live basecalling, high-accuracy whole-genome sequencing, and hybrid assembly, are proposed as smart microbial detection strategies to improve the accuracy, resolution, and sensitivity of microbial analysis in food systems.

To address fungal spoilage in dairy products, 113 LAB strains were screened, identifying Lactiplantibacillus plantarum, Furfurilactobacillus milii, and Lentilactobacillus parabuchneri as potent antifungal adjuncts. The antifungal effects were strain-specific and metabolite-dependent, with hydroxy fatty acids and acetate identified as key inhibitory compounds. When applied in cheese models, selected LAB strains extended the mold-free shelf life of both Crescenza and Gouda cheeses, though their efficacy varied with cheese type and ripening time. Yeast growth was not inhibited in Crescenza cheese, whereas in Gouda cheese, inhibition occurred but diminished with longer ripening.

Finally, the fermentative properties of Lactococcus lactis from different phylogenetic lineages were compared in dairy and plant-based matrices. Plant-associated strains exhibited superior performance in plant substrates, linked to their genomic traits, while dairy strains performed best in milk. One ancestral strain demonstrated high adaptability to both environments. Collectively, this work advances our understanding of strain selection, antifungal protection, and microbial ecology, contributing to the development of high-quality, bioprotective fermenting cultures for dairy and plant-based systems.