Exploring Genome-Wide Mutation Dynamics and Bacterial Cellulose Impairment in Komagataeibacter intermedius Cultivated...

Background: Bacterial cellulose (BC), natively synthesized by Komagataeibacter spp., is a biodegradable biomaterial with superior mechanical properties. However, under agitated cultivation, cellulose-producing strains (Cel⁺) often transition to nonproducing mutants (Cel^-), restricting scalability and hindering widespread use. Agitation-associated shear stress, elevated oxygen levels, and genetic mutations have been linked to the emergence of the Cel^- phenotype. A genome-wide investigation that considers population heterogeneity and dynamics is essential to reveal the mutational landscape and evolutionary processes driving this phenotypic shift. Results: Over successive rounds of agitated cultivation, K. intermedius ENS15 transitioned to a planktonic state, losing BC production. Whole-genome sequencing revealed both structural variations (SVs) and nonstructural variations (NSVs). Contrary to the previous reports, SVs, including insertion sequence-mediated junction events, did not affect the genes related to BC synthesis. Instead, the accumulation and positive selection of NSVs, such as frameshift and replication slippage events in key BC-related genes, strongly correlated with the loss of cellulose synthesis. Conclusions: This study provides the first genome-wide population-level analysis revealing mutational dynamics underlying the BC phenotypic switch in Komagataeibacter spp. cultivated under agitated conditions. We show that the BC-related gene mutations are not solely driven by SVs, with NSVs emerging as equally critical contributors. Furthermore, genomic evidence suggests possible involvement of regulatory mechanisms, such as quorum sensing and cyclic dimeric guanosine monophosphate signaling, prompting future studies on regulatory processes under agitated cultivation conditions. These findings highlight the importance of examining genetic heterogeneity to understand phenotypic adaptation for strain improvement strategies.