Structural and Genetic Basis of Dermacoccus abyssi Persistence in Egg White

Bacterial cell wall peptidoglycan (PG) is a key structural barrier enabling resistance to environmental stresses and natural antimicrobials in food matrices. In this study, phylogenetic, chemical, and ultrastructural analyses were conducted on Dermacoccus abyssi HZAU 226, a persistent spoilage bacterium isolated from spoiled egg white, to elucidate the structural basis of its survival under lysozyme-rich conditions. Phylogenomic analysis identified HZAU 226 as a novel strain of D. abyssi (sharing 97.05% average nucleotide identity and 75.6% digital DNA-DNA hybridization) closely related to the deep-sea type strain MT1.1 T . Chemical and genomic characterization revealed an A4α-type PG chemotype (with a Lys:Glu:Ala:Ser molar ratio of approximately 1:2:1:0.7), with fem family genes supporting extensive interpeptide cross-linking. Transmission electron microscopy and atomic force microscopy demonstrated a uniquely thickened cell wall (25-35 nm) and orthogonally arranged “piecrust” and “rib” nanostructures on the PG surface, consistent with a DivIVA-associated, structure-guided division pattern. The dense and highly cross-linked PG network effectively reduced lysozyme accessibility, conferring enhanced tolerance in egg-based food environments. These findings provide mechanistic insight into the persistence of actinomycetal spoilage bacteria and highlight cell wall structural robustness as a critical factor influencing microbial survival in protein-rich foods. • A food-derived strain Dermacoccus abyssi HZAU 226 was isolated from spoiled egg white. • Highly cross-linked A4α peptidoglycan confers resistance to egg lysozyme. • AFM reveals nanoscale piecrust and rib structures for mechanical reinforcement. • DivIVA-associated structure-guided division supports antimicrobial tolerance. • Cell wall structural robustness underpins persistence in food environments.