To ferment or not to ferment? Evaluating the impact of pre-fermentation of cheese whey permeate on microbial protein production with designed synthetic communities

Abstract

Cheese whey permeate (CWP) is an abundant yet underutilized side stream of the dairy industry, commonly directed towards low-value applications. Being rich in carbon and nutrients, it offers a promising substrate for microbial protein (MP) production, enabling resource recovery and reducing its environmental impact. However, its composition is highly variable due to production and storage conditions—especially in lactose (40–60 g/L) and lactic acid (0–15 g/L) levels—compromising process stability, biomass yields, and nutritional quality during MP production. To address these challenges, this study explored (1) the design of two- to four-member synthetic microbial communities capable of co-utilizing lactose and lactic acid, and (2) the impact of partial or full CWP pre-fermentation on MP yields, nutrient uptake, and protein quality. High-throughput screening identified consortia’s that outperformed pure cultures, achieving up to 108 % higher protein concentrations and 152 % higher optical densities. The four-member community emerged as the most robust across both lactose-rich and lactic acid-rich substrates. Validation in stirred tank reactors confirmed that CWP pre-fermentation improved biomass yields by 21.7–59.0 % and protein contents by 23.3–58.7 %. Consumption efficiencies for chemical oxygen demand, nitrogen, and phosphorus reached 97.0 %, 41.1 %, and 86.6 %, respectively. Nevertheless, MP from unfermented CWP exhibited a higher amino acid score (0.92) compared to that of fermented CWP (0.79). This study highlights the importance of substrate standardization and tailored microbial community selection for optimizing MP production from dairy side streams.