Coupling Stickland fermentation with reverse β-oxidation represents a new mode of medium-chain carboxylate production

Abstract

Biotechnologies for producing medium-chain carboxylic acids (MCCAs) by chain elongating bacteria (CEB) promise to shift the oleochemical industry away from existing land use practices, vulnerable supply chains, and significant environmental costs. Realizing this potential requires a broader understanding of CEB physiology, which is currently based on lactate and ethanol utilization, despite these bacteria thriving in protein-rich digestive tracts and organic waste bioreactors. Through comparative genomic analysis of known MCCA producers and physiological examination of the recently isolated species Peptonella octanoica as a model system, we show that amino acid utilization is a broadly distributed yet largely overlooked trait of many CEB. Among several amino acid-fermenting lineages, a conserved metabolic architecture couples Stickland fermentation with reverse {beta}-oxidation (R{beta}O), enabling MCCA production when acetate or electron-accepting amino acids are limiting. We show how this coupling manages thermodynamic constraints on lactate and amino acid oxidation by driving longer-chain product formation as hydrogen partial pressure increases. We further reveal that amino acid-fermenting CEB are abundant not only in gut microbiomes but also engineered bioreactors, where their novel physiology provides a mechanistic basis for high titer n-octanoate production from proteinaceous organic wastes. Beyond biomanufacturing, these findings broaden our understanding of CEB across anaerobic microbiomes in which amino acid fermentation and chain elongation are intersecting ecological strategies.