Tuning microbial protein quality and composition by using acidic or salted cheese whey permeate

The growing demand for sustainable protein sources is driving the food industry to explore alternative production systems. To this end, we explored microbial protein (MP) production from synthetic cheese whey permeate (CWP) using kefir, a synergistic culture of yeasts and bacteria, under nearly-extreme conditions relevant to the food industry (acidic pH, high salinity, upper mesophilic temperatures), and different operational modes (continuous, fed-batch). The composition and yield of MP were influenced by the cultivation conditions, with bacteria being substantially more impacted than yeasts. The most promising conditions for continuous aerobic, protein-rich MP production were mildly acidic pH, low salt content and mesophilic temperature, achieving final biomass concentrations up to ∼12 g L−1 with a protein content up to 51%. The community composition was highly dependent on the applied conditions, with higher NaCl concentrations leading to greater bacterial diversity, while the yeast community was more stable with Trichosporon and Meyerozyma dominating in almost all cases. Fed-batch cultivation resulted in higher biomass concentrations compared to continuous mode, but yielded MP with lower protein content and slightly reduced nutritional quality, potentially due to the different culture dynamics as a result of the operational strategy. The MP produced had a high essential amino acid (AA) content, with 100 g of microbial biomass produced with 0% NaCl in continuous and fed-batch mode covering at least 60 and 86% of the human daily requirements in essential AA, respectively. These findings show the potential for tailored MP production from CWP by selectively increasing bacterial or yeast abundance and impacting their biomass properties to achieve the desired macromolecular composition. Since synthetic cheese whey permeate was used, the results should be considered an idealized baseline, as real wastewater matrices may contain complex organics and trace inhibitors that could affect microbial community dynamics and process performance.