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Background   Propionibacterium acnes  and  Staphylococcus epidermidis  live in close proximity on human skin, and both bacterial species can be isolated from normal and acne vulgaris-affected skin sites. The antagonistic interactions between the two species are poorly understood, as well as the potential significance of bacterial interferences for the skin microbiota. Here, we performed simultaneous antagonism assays to detect inhibitory activities between multiple isolates of the two species. Selected strains were sequenced to identify the genomic basis of their antimicrobial phenotypes.    Results  First, we screened 77  P. acnes  strains isolated from healthy and acne-affected skin, and representing all known phylogenetic clades (I, II, and III), for their antimicrobial activities against 12  S. epidermidis  isolates. One particular phylogroup (I-2) exhibited a higher antimicrobial activity than other  P. acnes  phylogroups. All genomes of type I-2 strains carry an island encoding the biosynthesis of a thiopeptide with possible antimicrobial activity against  S. epidermidis .  Second, 20  S. epidermidis  isolates were examined for inhibitory activity against 25  P. acnes  strains. The majority of  S. epidermidis  strains were able to inhibit  P. acnes . Genomes of  S. epidermidis  strains with strong, medium and no inhibitory activities against  P. acnes  were sequenced. Genome comparison underlined the diversity of  S. epidermidis  and detected multiple clade- or strain-specific mobile genetic elements encoding a variety of functions important in antibiotic and stress resistance, biofilm formation and interbacterial competition, including bacteriocins such as epidermin. One isolate with an extraordinary antimicrobial activity against  P. acnes  harbors a functional ESAT-6 secretion system that might be involved in the antimicrobial activity against  P. acnes  via the secretion of polymorphic toxins.    Conclusions  Taken together, our study suggests that interspecies interactions could potentially jeopardize balances in the skin microbiota. In particular,  S. epidermidis  strains possess an arsenal of different mechanisms to inhibit  P. acnes . However, if such interactions are relevant in skin disorders such as acne vulgaris remains questionable, since no difference in the antimicrobial activity against, or the sensitivity towards  S. epidermidis  could be detected between health- and acne-associated strains of  P. acnes .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2489-5) contains supplementary material, which is available to authorized users.

Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis