Beyond commensalism: Genomic insights into micrococcin P1-producing Staphylococcus chromogenes

Rahmdel, S.; Türkoglu, T.; Nikjoo, N.; Babaali, E.; Moradi Mirhesari, D.; Nega, M.; Brüggemann, H.; Huang, L.; Witte Paz, M.; Nieselt, K.; Götz, F.

doi:10.1101/2025.08.01.668193

bioRxiv · 10.1101/2025.08.01.668193

Beyond commensalism: Genomic insights into micrococcin P1-producing Staphylococcus chromogenes

Rahmdel, S.·Türkoglu, T.·Nikjoo, N.·Babaali, E.·Moradi Mirhesari, D.·Nega, M.·Brüggemann, H.·Huang, L.·Witte Paz, M.·Nieselt, K.·Götz, F.

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Abstract

Staphylococcus chromogenes (S. chromogenes) is a predominant non-aureus staphylococcal species colonizing the teat skin and mammary gland of dairy ruminants. Although often linked to mild or subclinical mastitis, specific strains may also play protective roles against major udder pathogens. In this study, we characterized two S. chromogenes isolates (4S77 and 4S90) that displayed antimicrobial activity against Gram-positive bacteria. Complete genome sequencing revealed a conserved, plasmid-encoded biosynthetic gene cluster for the thiopeptide bacteriocin micrococcin P1 (MP1). All genes necessary for MP1 biosynthesis, modification, export, and immunity were identified, and compound production was confirmed by HPLC and LC-MS. Comparative analysis with publicly available S. chromogenes genomes revealed that the MP1 cluster appears unique to these isolates. Both strains showed full phenotypic susceptibility to tested antibiotics, despite 4S90 carrying the lnuA gene, which did not confer detectable resistance under standard conditions. Classical staphylococcal toxin genes were also absent. Virulence gene profiling revealed a conserved repertoire of colonization- and persistence-associated genes, including factors involved in adhesion, capsule formation, and iron acquisition, but no markers of aggressive pathogenicity. Mobile genetic elements, including prophages and genomic islands, were common but did not carry antimicrobial resistance or virulence genes, suggesting a low risk of transmission of new pathogenic traits to the endogenous microbiome, including opportunistic bacteria. These findings suggest that MP1-producing S. chromogenes strains combine antimicrobial functionality with low virulence potential, highlighting their potential ecological role as protective commensals on the teat skin and in the broader mammary ecosystem of dairy ruminants.

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Rahmdel, S., Türkoglu, T., Nikjoo, N., Babaali, E., Moradi Mirhesari, D., Nega, M., Brüggemann, H., Huang, L., Witte Paz, M., Nieselt, K., Götz, F.. 2025-08-04. Beyond commensalism: Genomic insights into micrococcin P1-producing Staphylococcus chromogenes. https://doi.org/10.1101/2025.08.01.668193

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