Comparative Analysis of Plant-Based and Animal-Based Protein Fermentation Relays

Thesis Abstract

The study investigates comparative dynamics in fermentation relays for plant-based and animal-based protein production to address sustainability, efficiency, and sensory quality differentials across bioprocesses. The problem centers on whether plant-derived substrates can match or exceed the performance of conventional animal-based proteins in fermentation-enabled relay systems, considering microbial kinetics, product yield, and environmental footprints under scalable conditions. The aim is to elucidate differential drivers of fermentation performance and to establish evidence-based guidelines for optimizing relay strategies across protein sources. Specific objectives include (1) quantify growth kinetics and substrate utilization of representative microbial consortia on plant-based versus animal-based protein feeds; (2) compare product yields, purification efficiency, and process economics in continuous fermentation relays; (3) assess sensory attributes and nutritional profiles of produced proteins; (4) evaluate environmental impacts through life cycle assessment (LCA) and identify trade-offs between feedstock type and energy intensity; and (5) develop a predictive model linking substrate type, reactor configuration, and product quality. The methodology adopts a comparative, mixed-methods design integrating quantitative process data with qualitative insights from process engineers. The population comprises industrially relevant fermentation strains (Corynebacterium glutamicum and Escherichia coli-based production platforms) deployed in two parallel relay configurations operating at 0.5–1.0 L pilot scales. A total of 12 experimental runs per feedstock type (plant-based and animal-based) across three relay stages (primary growth, intermediate conversion, and final polishing) will be conducted, with triplicate biological repeats to ensure statistical robustness. Data collection employs high-frequency online sensors for pH, dissolved oxygen, optical density, and off-gas analysis, complemented by offline measurements of substrate concentrations (HPLC), amino acid composition (LC-MS/MS), and protein yields (gravimetric and Kjeldahl methods). Economic performance will be assessed through mass and energy balances, capital and operating costs, and a mini-LCA following ISO 14040/14044 standards. Sensory and nutritional assessments of final protein concentrates will utilize rheological profiling, differential scanning calorimetry (DSC), and in vitro protein digestibility assays, paired with amino acid score calculations. Analytical techniques include regression analysis to model growth kinetics and yield relationships, ANOVA to compare means across feedstocks and relay stages, and multivariate analysis (PCA and PLS-DA) to explore correlations among process variables and product quality attributes. A systems- dynamics-inspired modeling framework will be employed to simulate relay stage transitions and to forecast performance under varying substrate compositions. The study will test the hypotheses that plant-based substrates enable comparable protein yields with lower energy input per unit of product and that sensory profiles of plant-derived proteins can be tuned to approach those of animal-derived proteins through relay optimization and downstream processing. Theoretical grounding will draw on the Theory of Constraints for process optimization and the Resource-Based View to interpret capabilities derived from substrate versatility. The analysis will also incorporate risk assessment for contamination and process resilience under feedstock variability. Expected findings include that plant-based feeds can achieve protein yields within 85–95% of animal-based relays under optimized relay sequencing, with significantly reduced energy footprints (15–25% lower) due to milder fermentation temperatures and improved downstream clarification. Sensory and nutritional profiling is anticipated to reveal comparable essential amino acid content when co-cultures or post-fermentation treatments are applied, with specific aroma and texture enhancements achievable through controlled cooling and filtration strategies. The study contributes to knowledge by clarifying the feasibility and boundaries of plant-based fermentation relays for high-value proteins, offering a transferable methodology for cross-feedstock optimization and a decision-support framework for industry adoption. It also extends the literature on sustainable bioprocessing, providing empirical benchmarks for process economics and environmental performance. Key recommendations include (1) adoption of plant-based relay configurations in environments with high feedstock variability; (2) investment in sensor-driven control strategies and adaptive feed strategies to sustain product quality; (3) integration of targeted downstream processing to enhance sensory properties of plant-derived proteins; and (4) further research into strain engineering and co-culture approaches to maximize efficiency and resilience under plant-based substrates.