eLife assessment: Bacterial DNA on the skin surface overrepresents the viable skin microbiome

Résumé

The skin microbiome provides vital contributions to human health.However, the spatial organization and viability of its bacterial components remain unclear.Here, we apply culturing, imaging, and molecular approaches to human and mouse skin samples, and find that the skin surface is colonized by fewer viable bacteria than predicted by bacterial DNA levels.Instead, viable skin-associated bacteria are predominantly located in hair follicles and other cutaneous invaginations.Furthermore, we show that the skin microbiome has a uniquely low fraction of viable bacteria compared to other human microbiome sites, indicating that most bacterial DNA on the skin surface is not associated with viable cells Additionally, a small number of bacterial families dominate each skin site and traditional sequencing methods overestimate both the richness and diversity of the skin microbiome.Finally, we performed an in vivo skin microbiome perturbation-recovery study using human volunteers.Bacterial 16S rRNA gene sequencing revealed that, while the skin microbiome is remarkably stable even in the wake of aggressive perturbation, repopulation of the skin surface is driven by the underlying viable population.Our findings help explain the dynamics of skin microbiome perturbation as bacterial DNA on the skin surface can be transiently perturbed but is replenished by a stable underlying viable population.These results address multiple outstanding questions in skin microbiome biology with significant implications for future efforts to study and manipulate it. eLife assessmentIn this important study, the authors provide convincing evidence that current DNA-based microbial genomics for skin bacteria cannot always detect the source of sequenced DNA and whether it originated from viable or non-viable bacteria.Additionally, the authors demonstrated in humans and mice that most of the viable bacteria reside inside hair follicles rather than the surface of the skin per se.Overall, the work has significance beyond a single discipline and will be of interest to those studying microbiomes.

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