New Insight Into Stability of Two Skin Microbiome Species

Researchers have detected a new dynamic in the transmission and migration of Cutibacterium acnes and Staphylococcus epidermis by reconstructing the in-person evolutionary history of adult facial skin microbiomes (FSMs). “Measuring the dynamics of strain communities can identify the nature of” uncertain ecological barriers, which hinder the colonization of new strains, “as evidenced by the difficulty of achieving durable engraftment of topically applied C. acnes,” the researchers noted.

The results were published in Cell Host & Microbe.

Studying the dynamics of microbial strain communities helps reveal whether ecological barriers to transmission are neutral or selective. Neutral barriers allow colonization mainly during early life or disturbances, whereas selective barriers maintain individual-specific microbial communities despite ongoing strain changes. Tracking strain transmission and within-person strain changes can help distinguish between these two types of ecological forces.

Thus, the researchers examined the dynamics of the FSM from childhood through adulthood, focusing on microbial changes at both species and lineage levels. During this time, anaerobic bacteria like C. acnes surge, alongside a 100-fold increase in aerobic bacteria. Using both genomic and metagenomic methods, the researchers investigated whether this transition reduces early-life colonization barriers (priority effects) and enables new strain colonization, potentially affecting the stability of existing microbial lineages.

Researchers collected over 4,000 isolates of S. epidermidis and C. acnes from 57 individuals (8 families in total) along with metagenomic data, allowing detailed analysis from species to genotype level. They found that though there is limited lineage sharing within families and mostly neutral evolution on individuals, species behave differently. S. epidermidis shows high lineage turnover and selective transmission barriers, limiting long-term probiotic use. In contrast, C. acnes has low turnover and a strong ability to establish during adolescence, likely due to relaxed early-life colonization barriers, making it a better candidate for durable probiotic therapy.

The dominance of multi-cell transmission in C. acnes aligns with earlier findings that each sebaceous follicle is colonized independently, forming a community structure like an archipelago, which allows diverse genotypes to coexist by minimizing direct competition. In contrast, it’s still unclear whether S. epidermidis has an anatomical structure that supports the coexistence of multiple transmitted genotypes, as its fine-scale spatial distribution on skin remains poorly understood. Phylogenetically, C. acnes shows a more “comb-like” tree with many unique mutations, unlike S. epidermidis, which suggests more efficient mixing within S. epidermidis populations. Still, the lack of single-cell transmission bottlenecks in both species points to a spatially organized environment that enables the stable presence of multiple genotypes.

“Here, we reveal previously hidden lineage-level assembly dynamics and report distinct models of community assembly for the two most dominant bacteria of the sebaceous skin microbiome, with implications for therapeutic design,” the researchers concluded.

Reference

Baker JS, et al. Cell Host & Microbe. 2025 Apr 25:S1931-3128(25)00143-X. doi: 10.1016/j.chom.2025.04.010.