Comparative Analysis of Fermentation Profiles in Plant-based vs. Dairy Yogurts

Thesis Abstract

Fermentation profiles influence texture, aroma, acidity, and microbial safety in yogurts, yet comparative dynamics between plant-based and dairy matrices remain inadequately characterized, limiting product optimization, nutritional interpretation, and regulatory guidance. This study addresses the gap by examining how substrate type modulates fermentation kinetics, microbial succession, metabolite production, and sensory outcomes under commercial starter cultures. The aim is to compare fermentation profiles between plant-based yogurts (almond and soy bases) and dairy yogurt, and to identify factors shaping microbial ecology and product quality. Specific objectives include (1) quantify fermentation kinetics (pH, titratable acidity, and viscosity) across substrates; (2) profile microbial communities using 16S rRNA gene sequencing and quantify dominant taxa over time; (3) characterize metabolite spectra (lactic acid, acetaldehyde, diacetyl, acetic acid, and aroma precursors) via gas chromatography–mass spectrometry (GC-MS) and targeted HPLC; (4) correlate microbial composition with physicochemical changes and sensory attributes; (5) evaluate consumer acceptability and willingness-to-pay for plant-based versus dairy yogurts; and (6) test the applicability of the Gompertz and logistic growth models for fermentation curves and the Theory of Planned Behavior to predict sensory acceptance. The research adopts a comparative cross-sectional design conducted under controlled pilot-plant conditions. The population comprises commercial starter cultures used for yogurt fermentation and three representative substrate groups dairy milk, almond-based matrix, and soy-based matrix. A stratified random sampling approach will recruit 24 fermentation trials (8 per substrate) using identical starter cultures, incubated at 42°C until peak acidity is reached. Data collection integrates (i) real-time pH and viscosity measurements; (ii) microbial profiling via 16S rRNA sequencing with Illumina MiSeq; (iii) metabolomic analysis through GC-MS for volatile compounds and HPLC for organic acids and sugars; (iv) sensory evaluation with a trained panel for descriptive analysis and a consumer panel (n=150) for acceptability and purchase intent; and (v) economic valuation through contingent valuation surveys. Validity and reliability are ensured through calibration of instruments, triplicate measurements, and cross-validation of sequencing data with quantitative PCR. Data analysis employs mixed-effects models to compare fermentation kinetics across substrates, with substrate as fixed effect and batch as random effect; multivariate analyses (PCA and O2PLS) integrate metabolomic and sensory data to identify key discriminant markers; differential abundance analysis (DESeq2) characterizes microbial succession; regression analyses will link microbial taxa to metabolite profiles and sensory scores. Model specification includes Gompertz growth and logistic models for fermentation curves, and structural equation modeling to test the theoretical framework linking substrate, microbial dynamics, metabolite production, and consumer acceptance. Ethical considerations encompass food safety protocols, disclosure of potential conflicts of interest, and handling of sensory data with informed consent. Expected findings anticipate distinct fermentation trajectories among plant-based matrices, with slower pH decline and differing aromatic profiles relative to dairy yogurt, driven by substrate-specific microbial interactions and substrate-inherent nutrient profiles. Plant-based yogurts are expected to exhibit higher acetaldehyde and diacetyl precursors in the early phases, while dairy yogurts may show more robust lactic acid production and consistent textural development. Microbial communities are anticipated to shift from Lactobacillus-dominated profiles in dairy to substrate-responsive taxa in plant-based matrices, with correlations between specific taxa (e.g., Lactobacillus delbrueckii, Streptococcus thermophilus in dairy; heterotrophic lactic acid bacteria in plant matrices) and volatile compounds enabling discrimination. The study contributes novel, integrative knowledge on how matrix effects shape fermentation ecology, metabolite formation, and sensory perception, informing formulation strategies to optimize texture, aroma, and nutritional quality in plant-based yogurts. The implications extend to regulatory risk assessment, labeling accuracy for probiotic content, and market segmentation strategies. Recommendations include tailoring starter consortia to plant matrices, optimizing fermentation conditions to harmonize acidity and mouthfeel, and incorporating targeted flavor-mortality risk mitigation, as well as extending research to additional plant bases and fat contents to broaden applicability. A core conclusion is that substrate-driven microbial ecology governs fermentation success and consumer acceptability, necessitating matrix-aware process design and quality control.