Indigenous microbiome as a key strategy for producing green chemicals

Introduction Reactors used for conventional anaerobic fermentation (C-AF) devoted to metabolite production are typically seeded with sludge collected from anaerobic digesters. This inoculum contains methanogens, which are the principal consumers of metabolites involved in biogas production. The use of the indigenous microbial community naturally present in the agroindustrial waste (AGW) was evaluated as an alternative inoculum to take advantage of its naturally scarce methanogenic abundance. Methods Self-AF (lacking external inoculum) and C-AF were compared in terms of bioconversion yields and metabolite profiles. The effect of pH on community specialization and product distribution was assessed across the pH range naturally occurring during self-acidification. Results Self-AF showed high bioconversion yields to metabolites (65.7 %) when compared to C-AF (58.7 %). Nevertheless, the inherent pH changes that the process suffered from self-acidification also resulted in metabolite profile oscillation. Whereas a pH of 4.5 maximized the lactic acid and ethanol production (13.9 and 11.7 g·L −1 , respectively) due to the lactic acid bacteria prevalence, when a pH of 6 was reached, the microbiome specialized in carboxylates production, leading to a concentration of 29.8 g·L −1 in the steady state, with Clostridiales (51.8%) and Bifidobacteriaceae (21.4 %) as key bacteria. Conclusion This study demonstrated the feasibility of conducting AF in the absence of external inoculum. Moreover, the wide bacterial metabolisms present in the indigenous microbiome revealed its capability of maximizing product portfolio using self-AF.