Genomic Insights into Enhanced Medium-Chain Fatty Acid Production in Megasphaera elsdenii

Abstract The shift toward a sustainable bioeconomy has increased interest in microbial platforms capable of producing valuable fatty acids. Megasphaera elsdenii is emerging as a promising candidate for fatty acid bioproduction, although its performance varies depending on the strain. This study compares two M. elsdenii strains, JCM 1772 (ATCC 25940) and JCM 35779, revealing that JCM 35779 produces up to 5.8 times more hexanoic acid than JCM 1772. Comparative genomic analysis identified key differences between the strains, including the loss of enzymes involved in the pyruvate-to-butyric acid pathway in JCM 35779, indicating a rerouting of carbon flux that favors chain elongation toward hexanoic acid instead of butyric acid. Overall, this work links genomic variation to metabolic phenotype, establishes JCM 35779 as a superior medium-chain fatty acid producer, and supports the development of M. elsdenii as an effective platform for sustainable production of medium-chain fatty acids. Highlights Pig-feces M. elsdenii shows >5 times higher HA production than its rumen strain. Genomic analysis reveals strain-specific deletions in pathways for MCFA synthesis. This includes etfB2, cat1 and abfD.