Predicting metabolic pathways and microbial interactions in dark fermentation systems treating real cheese whey effluents

[Display omitted] •Metabolic pathways and taxonomic contributions in communities were determined.•Lactobacillus dominated carbohydrate consumption and lactate production.•Caproiciproducens and C. sensu stricto 12 competed for the use of lactate.•The hydrogen production was mainly driven by C. sensu stricto 12.•Interactions are influenced by substrate availability and process conditions. Dark fermentation of agro-industrial effluents is a promising way for waste valorization. However, understanding the complex microbial dynamics and metabolic interactions within the microbial communities remains challenging. This study investigates the microbial communities involved in continuous hydrogen production from cheese whey and fermented cheese whey using functional profiling with PICRUSt2. The analysis reveals the primary roles of key microbial genera. Lactobacillus dominates carbohydrate consumption and lactate production, while Clostridium sensu stricto 12 and Caproiciproducens are engaged in a competitive dynamic for lactate utilization. Clostridium sensu stricto 12 drives hydrogen production via electron bifurcation reactions, whereas Caproiciproducens may utilize alternative energy conservation mechanisms. The interaction between these genera is influenced by substrate availability and process conditions. This study highlights the utility of functional profiling in elucidating microbial interactions and metabolic pathways in dark fermentation. The findings emphasize the importance of understanding microbial interactions to optimize biohydrogen production processes.