Dataset Information

Highly-resolved within-species dynamics in the human facial skin microbiome.

ABSTRACT: Human facial skin microbiomes (FSMs) on adults are dominated by just two bacterial species, Cutibacterium acnes and Staphylococcus epidermidis. Underlying this apparent simplicity, each FSM harbors multiple strains of both species whose assembly dynamics on individuals are unknown. Here, we use 4,055 isolate genomes and 360 metagenomes to trace the dynamics of strains on individuals and their transmission. Strains are shared amongst family members of all ages, but each individual harbors unique strain consortia. Strain stability changes upon formation of the adult-type FSM: S. epidermidis lineage turnover slows, and the rate of C. acnes colonization increases before stabilizing, suggesting this transitional window could facilitate engraftment of therapeutic strains. Our work reveals previously undetectable community dynamics and informs the design of therapeutic interventions.

SUBMITTER: Baker JS

PROVIDER: S-EPMC10802602 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species.

Baker Jacob S JS Qu Evan E Mancuso Christopher P CP Tripp A Delphine AD Conwill Arolyn A Lieberman Tami D TD

bioRxiv : the preprint server for biology 20250131

Adult human facial skin microbiomes are remarkably similar at the species-level, dominated by <i>Cutibacterium acnes</i> and <i>Staphylococcus epidermidis,</i> yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 360 metagenomes, we reconstruct on-person evolutionary history to reveal on and between-person strain dynamics. We find that multiple cell ...[more]

PMID: 38260404

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Project description:BackgroundSequencing of the human skin microbiome revealed that Corynebacterium is an ubiquitous and abundant bacterial genus on human skin. Shotgun sequencing further highlighted the microbial "dark matter" of the skin microbiome, consisting of microorganisms, including corynebacterial species that were not cultivated and genome-sequenced so far. In this pilot project, facial human skin swabs of 13 persons were cultivated to selectively obtain corynebacteria. 54 isolates were collected and 15 of these were genome-sequenced and the pan-genome was determined. The strains were biochemically characterized and antibiotic susceptibility testing (AST) was performed.ResultsAmong the 15 sequenced strains, nine different corynebacterial species were found, including two so far undescribed species, tentatively named "Corynebacterium vikingii" and "Corynebacterium borealis", for which closed genome sequences were obtained. Strain variability beyond the species level was determined in biochemical tests, such as the variable presence of urease activity and the capacity to ferment different sugars. The ability to grow under anaerobic conditions on solid agar was found to be species-specific. AST revealed resistances to clindamycin in seven strains. A Corynebacterium pseudokroppenstedtii strain showed additional resistance towards beta-lactam and fluoroquinolone antibiotics; a chromosomally located 17 kb gene cluster with five antibiotic resistance genes was found in the closed genome of this strain.ConclusionsTaken together, this pilot study identified an astonishing diversity of cutaneous corynebacterial species in a relatively small cohort and determined species- and strain-specific individualities regarding biochemical and resistance profiles. This further emphasizes the need for cultivation-based studies to be able to study these microorganisms in more detail, in particular regarding their host-interacting and, potentially, -beneficial and/or -detrimental properties.

Project description:PurposeEveryone pursues perfect skin, but there exist significant differences between cultures, and no commonly accepted standards have been established. Therefore, our study attempted to define the "ideal skin" of oriental women and analyze the relationship between different skin physiological parameters and microbiomes.Patients and methodsBased on our customized grading standard, the VISIA CR photos of 111 young women aged from 18 to 25 in Shanghai were collected and scored by the severity of pores, acne, spots, and wrinkles. The volunteers were then divided into "ideal skin" (W1), "normal skin" (W2), and "undesirable skin" (W3) groups. The physiological parameters of facial skin were measured by non-invasive instrumental methods, and the skin microbiome was analyzed by 16S rRNA and ITS high-throughput sequencing.ResultsFrom "ideal skin" to "undesirable skin", the skin physiological parameters, α-diversity, and composition of the facial microbiome showed noticeable regular changes. Compared with the "normal skin" (W2) and "undesirable skin" (W3), the "ideal skin" (W1) group had lower sebum content, TEWL, melanin, hemoglobin, and roughness but higher hydration content and skin pH value. Furthermore, the Shannon index of skin bacteria was significantly increased in W1 (P = 0.004), suggesting that the ideal skin had higher species diversity. From W1 to W3, the species composition was changed significantly. The abundance of Actinobacteria was increased, while Proteobacteria and Bacteroidetes were decreased. Correspondingly, the abundances of lipophilic Propionibacterium and Malassezia were increased, while the abundances of Stenotrophomonas, Pseudomonas, Ralstonia, and Streptococcus, were significantly decreased. Additionally, Spearman correlation analysis revealed strong correlations between the physiological parameters and the microbiota. Notably, the Shannon index of skin bacteria was significantly positively correlated with skin hydration (P = 0.03) but negatively correlated with the abundance of Cutibacterium (P = 0.000), hemoglobin content (P = 0.025), and sebum content (P = 0.5). Therefore, the skin hydration content and the abundance of Cutibacterium played an important role in maintaining the α-diversity and skin homeostasis.ConclusionIdeal skin had better water-oil balance and barrier function, higher microbial diversity, and more reasonable species distribution. Therefore, daily skincare needs to control skin oil and maintain skin microecological balance to achieve ideal skin conditions for young women aged 18-25 years old.

Dataset Information

Highly-resolved within-species dynamics in the human facial skin microbiome.

Publications

Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species.

Similar Datasets

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