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bioRxiv · 10.1101/2025.11.13.688382

Kinetic modeling of continuous meta-fermentation quantifies metabolic activity in a complex microbial system

Koga, T.·Kajimoto, K.·Ishizu, M.·Hamada, H.·Miyamoto, H.·Oshiro, M.·Sakai, K.·Tashiro, Y.
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Abstract

One of the serious drawbacks of a complex microbial system is the difficulty in quantifying the metabolic activity of each microorganism. A kinetic model of predominant microbial species was constructed for continuous meta-fermentation in a complex microbial system at several dilution rates (D). The introduction of biomass and lactic acid inhibition terms improved model accuracies at D = 0.05 h-1 and 0.4 h-1, respectively. The coefficient of determination (R2) and root mean square error (RMSE) improved from 0.577 and 5.21 to 0.972 and 0.759, respectively, with the inhibition term at D = 0.05 h-1. The inhibition terms resulted in good R{superscript 2} (0.996) and RMSE (1.27) values at D = 0.4 h-1. By solving the Michaelis-Menten equation in the constructed models, the species flux (SF) was calculated to estimate the metabolic activity (formation and consumption) of each microorganism. At D = 0.05 h-1, Caldibacillus hisashii contributed to lactic acid production at 0.333 g/L/h, whereas Clostridium cochlearium consumed lactic acid at 0.203 g/L/h, suggesting cross-feeding of a metabolite. It is therefore possible to account for consumption that cannot be considered in gene-derived calculations, indicating that this is a promising analytical method for investigating the dynamic behavior of complex microbial systems. Kinetic models for continuous meta-fermentation at several D values were developed. A new metabolic analysis method is proposed to estimate the activity of microbial species in a complex microbial system.

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Koga, T., Kajimoto, K., Ishizu, M., Hamada, H., Miyamoto, H., Oshiro, M., Sakai, K., Tashiro, Y.. 2025-11-14. Kinetic modeling of continuous meta-fermentation quantifies metabolic activity in a complex microbial system. https://doi.org/10.1101/2025.11.13.688382

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