Genomic characterization of Staphylococcus epidermidis Se252 isolated from the rhizosphere of a Brazilian endemic plant

Abstract

Background: Staphylococcus epidermidis (Se) is commonly regarded as a commensal organism; however, under specific conditions, it may act as an opportunistic pathogen. Here, we report the whole-genome sequencing and comparative genomic analysis of Se strain 252 (Se252), isolated from the rhizosphere of an endemic Brazilian plant.

Results: Se252 exhibits a unique repertoire of genes associated with environmental adaptation and virulence. These include two putative Type VII secretion system (T7SS) effectors and thirteen proteins involved in adhesion, toxin production, and immune evasion—among them, IsaB, which has not been previously reported in Se. Gene family expansions were observed in loci related to phenol-soluble modulins (PSMs), TLpps, LPXTG-motif proteins, nonribosomal peptide synthetases (NRPS), and siderophore biosynthesis (staphylopine, staphyloferrin), as well as quorum-sensing autoinducing peptides. In contrast, Se252 harbors relatively few antibiotic resistance genes.

Conclusions: The genomic profile of Se252 reflects adaptations to a plant-associated environment, yet harbors multiple features potentially enhancing human pathogenicity. These findings highlight the relevance of environmental Se lineages as possible reservoirs of virulence traits with implications for public health.

Graphical Abstract:

Supplementary Information: The online version contains supplementary material available at 10.1186/s12864-025-12211-7.

Keywords: Staphylococcus epidermidis; Comparative genomics; Emerging pathogens; Horizontal gene transfer; Rhizosphere; Type VII secretion system; Virulence factors.

Fig. 1

Comparative genomic analysis of 36 S. epidermidis genomes. (a) Flower plot showing shared and unique protein-coding genes among strains. The center indicates the core genome (orthologous groups present in all strains); the pink halo represents accessory genes. Numbers near strain codes denote unique genes (black: single-copy; blue: multi-copy). Red numbers indicate gene families shared exclusively with Se252. Icons depict isolation sources, created with BioRender.com (see Table S1). (b) Rooted phylogenomic tree based on core genomes, using S. aureus Sa8325 as outgroup. Clades I–III show strong bootstrap support (red circles). Inverted triangles indicate putative gain events of orthologous families, with protein counts noted. (c) MUMmer matrix showing genomic similarity (red) and dissimilarity (green) among strains (Sa8325 was excluded). (d) Functional classification of strain-specific singletons. WAF: with assigned function; Hyp: hypothetical; Ψ: pseudogene; Tn-ase: transposase. “Plasmid” column shows number of extrachromosomal replicons. Genes linked to virulence/adaptation are in pink squares; shared ones in purple squares. Paralogous genes are marked with copy numbers > 1. “p” indicates plasmid-encoded genes.

Fig. 2

Synteny and structural analysis of type VII secretion system (T7SS) proteins in S. epidermidis genomes. (a) Presence/absence matrix of structural and effector genes encoding T7SS components. The cladogram reflects the phylogenomic relationships shown in Fig. 1b. T7SS genes are entirely absent in clade III, partially present in clade I, and fully conserved in clade II. Ψ: pseudogene; numbers > 1 indicate paralogs. Numbers in matrix cells represent gene copy number; cell colors correspond to gene/protein labels in panels B and D. TVIIne: two newly identified orthologous protein families (1 and 2) potentially secreted by T7SS. (b) Synteny and gene cluster organization of T7SS in Se252, plant-associated Se (Se2.9 and Se4.7), and S. aureus (ATCC8235) genomes. Background colors indicate conserved or rearranged gene blocks. Modules represent conserved gene clusters encoding core or accessory proteins of the system: Green arrows: putative structural components; red arrows: putative secreted effectors. (c) Evolutionary analysis of TVIIne proteins using EsxA (ESAT-6) and EsxB (ESAT-7) as references; Se252 LXG (colicin IA) serves as outgroup. (d) Predicted 3D structures of selected T7SS-associated proteins The structures identified from 1 to 6 correspond to the respective proteins with the same numbering shown in panel C.

Fig. 3

Virulence factors in S. epidermidis strains. (a) Presence/absence matrix of genes associated with adherence, exotoxin and exoenzyme production, biofilm formation, and immune evasion. Comparative strains from S. haemolyticus JSJC1435, S. saprophyticus ATCC 15,305, and S. epidermidis RP62A (highlighted in blue) were included based on VFDB data. Color codes are indicated in the figure legend. The cladogram corresponds to the phylogenomic clustering shown in Fig. 1b. Ψ: pseudogene; numbers > 1 indicate paralogs. (b) Pairwise alignment of IsaB from Sa8325 and IsaB-like from Se252. Sp: signal peptide; Id: sequence identity. Below is an analysis of confidence, conservation, and quality of the amino acid residues composing IsaB-like proteins in S. epidermidis genomes. It can be observed that regions with the highest degree of conservation correspond to positions forming α-helices (red) and β-sheets (green) identified in the structure. (c) Predicted 3D structures of IsaB (Sa8325) and IsaB-like (Se252) proteins using Robetta. (d) Error estimation (Å) of structural predictions shown in panel C. (e) Structural superposition of IsaB (green) and IsaB-like (orange) proteins from panel C using Dali. (f) Syntenic organization of genomic regions flanking isaB (Sa8325) and isaB-like (Se252). Gene abbreviations: aur – aureolysin; clfB – clumping factor B; PM – phenol-soluble modulins; IS6 – transposase family IS6; arcCDBRargR – arginine deiminase pathway. Background shading indicates homologous genes.

Fig. 4

Genomic regions associated with secondary metabolite biosynthesis in S. epidermidis. (a) Presence/absence matrix of biosynthetic gene clusters (BGCs) across S. epidermidis strains, identified using antiSMASH. The cladogram reflects the phylogenomic clustering from Fig. 1b. Conserved BGCs across all strains are marked in red. The number inside each square indicates the total number of paralogous copies. (b) Structural and functional characterization of the sactipeptide BGC. Left: protein domain architecture of genes in the hycABCDEF cluster. TM – transmembrane domain; C – cytoplasmic domain; SAM – S-adenosylmethionine domain; ABCt – ABC transporter domain; M16 – M16 domain. Right: amino acid sequence of the subtilosin (bacteriocin) encoded by hycS, with multiple alignment and consensus comparison to homologs in Staphylococcus and Bacillus genomes. (c) Gene cluster (Crt) organization involved in staphyloxanthin biosynthesis. Each gene present in the cluster participates in a reaction involved in the biosynthesis of staphyloxanthin or 4,4′-diapolycopenedial. (d) Spectrophotometric detection of staphyloxanthin in S. aureus and Se252, with absorbance peaks at 455 and 475 nm indicating pigment presence. (e) Classification of autoinducing peptides (AIPs) based on agrD sequences, with clade-specific color coding as in the AgrD phylogeny. TI and TV indicate the classification of the identified AIPs with their respective amino acid variants, along with the model organisms from which the S. epidermidis strains were isolated. (f) Phylogenetic analysis of the identified AIPs. Note that clades I, II, and III are more closely related to each other than to types IV and V.

Fig. 5

Distribution and genomic context of antibiotic resistance genes in S. epidermidis genomes. (a) Presence/absence matrix of antibiotic resistance genes. Ψ: pseudogene; numbers > 1 indicate paralogs; p: gene located on a plasmid; /p: paralogs split between plasmid and chromosome; x/yΨ: x intact and y frameshifted paralogs. The purple color was used solely to indicate the reference genes employed in the search for orthologous copies, while the red color highlights Sa8325. Icons were obtained from BioRender. Arrows above the matrix denote tandem gene arrangements. The vrgGFgraSRX cluster is associated with bacitracin resistance. Genes conserved across all strains (putative vertically inherited) are marked in black; genes likely acquired via horizontal gene transfer (HGT) are marked in green. (b) Genomic context of reference resistance genes (purple in A), showing co-localization with flanking genes (± 10 kbp). Colored backgrounds indicate functional categories of neighboring genes (see legend). (c) Synteny and organization of resistance loci potentially acquired via HGT, with gene functions summarized in the figure legend. The general function of the genes (indicated by different colors) is shown in the figure legend.

Fig. 6

Metal resistance and metabolism in S. epidermidis genomes. (a) Overview of metal-related metabolic pathways in Se genomes. Presence/absence analysis of each gene is detailed in Fig. S12. Genes likely acquired via horizontal gene transfer (HGT) are indicated with a white background, including those in the kdp (potassium uptake) and mer/met (mercury metabolism) systems. Ni – nickel; K – potassium; Fe – iron; S – sulfur; Cu – copper; Cd – cadmium; Hg – mercury; Zn – zinc; P – phosphorus; N – nitrogen. Two gene clusters are highlighted: the mer cluster, associated with Hg transport in the ATCC12228 genome, and the kdp and lar clusters, associated with K and Ni transport in the M0026 genome. Both are located in putative HGT islands flanked by transposable elements. (b) Arsenic metabolism in strain Se252. (c) In vitro arsenic removal assay. Strain Mc250 (Alcaligenes faecalis) was used as a removal efficiency control. (d) Indirect plant growth promotion assay in the presence of arsenite (As³⁺) and arsenate (As⁵⁺), with or without Se252 inoculation. Bar graphs show mean plant elongation. *p ≤ 0.05; **p ≤ 0.01. # Previously published data on growth promotion by other strains.

Fig. 7

Metabolic profile of S. epidermidisSe252in soil, plant-associated niches, and as a potential opportunistic human pathogen