Comparative Genomics Reveals the Molecular Mechanisms of a Newly Isolated Pediococcus cellicola zy165 Strain and Its Adaptation in Corn Silage.

Authors

Samaila Usman, Dongmei Xu, Jing Ma, Neha Sheoran, Charles Obinwanne Okoye, Xusheng Guo

Published in

Biochemical genetics. May 06, 2025. Epub May 06, 2025.

Abstract

Understanding how lactic acid bacteria (LAB) adapt to the silage environment is crucial for optimizing fermentation processes and developing efficient inoculants. In this study, Pediococcus cellicola zy165, isolated from fermented whole-crop corn, was subjected to whole-genome sequencing and comparative genomic analysis with two reference strains from NCBI (P. cellicola DSM 17757, and P. cellicola NBRC 106103, isolated from distilled-spirit-fermenting cellars), to elucidate its adaptation mechanisms in silage. The genome of P. cellicola zy165, which includes a circular plasmid and a CRISPR element, revealed enrichment in genes linked to carbohydrate metabolism, transport, and regulatory functions. Key adaptations for silage fermentation were evidenced by the presence of diverse phosphotransferase system (PTS) components, facilitating efficient sugar uptake and metabolism, alongside enzymes like phosphoglycerate mutase and L-lactate dehydrogenase, which are pivotal for glycolysis and lactic acid production, respectively. Additionally, the strain's genome encodes for acetate kinase, suggesting a strategic approach to pH management and energy conservation. Unique to P. cellicola zy165, genes encoding alpha-galactosidase and fructoselysine 6-phosphate deglycase were identified, indicating specialized capabilities for carbohydrate degradation in the silage niche. Structural variations and mutation analyses further highlighted adaptive genetic changes, including those in DNA metabolic processes, which could enhance survival under silage conditions. These genomic insights highlight the potential of P. cellicola zy165 as an effective silage inoculant, showcasing its evolutionary adaptations to the anaerobic, nutrient-rich corn silage environment.

PMID:
40327195
Bibliographic data and abstract were imported from PubMed on 06 May 2025.

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