Development of an ex vivo skin model for quantitative recovery and preservation of donor-specific human microbiota
Abstract
BACKGROUND: Through multi-omics approaches, our understanding of skin microbiota has substantially advanced. However, the development of reliable and physiologically relevant experimental models would greatly accelerate progress in microbiome-targeted science. Most investigations of skin microbiota rely on in vitro 2D models or reconstructed epidermis colonized with a limited number of strains, which do not reflect the complexity and the spatial microbial organization observed on in vivo skin. To overcome these limitations, we developed a model based on perfused human skin explants (Perfex model), that enables the transfer of complex bacterial communities from human volunteers onto ex vivo skin. RESULTS: After quantitative validation of recovered microbial DNA by qPCR from volunteers (V1-V2-V3) and corresponding inoculated explants (MV1-MV3), 16S rRNA gene sequencing was performed to assess whether microbiota transfer influenced community structure and diversity. No statistically significant differences in alpha-diversity were observed between original and transferred microbiota at the genus level, suggesting that the transfer procedure did not substantially alter overall community diversity. Clustering analysis revealed distinct grouping of samples according to donor origin, indicating that donor-specific microbial signatures were largely maintained on the explants after 48 hours. Control samples formed separate clusters, suggesting minimal background signal and supporting the absence of cross-contamination. These observations indicate that the model enables clear discrimination between the endogenous microbiota of the explants and the transferred microbiota, supporting the integrity of the experimental conditions. Beta-diversity analysis based on Bray-Curtis supported these findings. Across samples, microbial communities were characterized by the recurrent presence of common skin-associated genera such as Cutibacterium, Staphylococcus, and Corynebacterium. Histological analyses demonstrated preserved tissue architecture, while immunostaining revealed modulation of selected innate immune markers consistent with a localized skin response to microbial transfer. CONCLUSIONS: The Perfex model enables transfer of donor-specific skin microbiota to ex vivo human skin while preserving tissue integrity over short-term culture. This model provides a human-relevant platform for studying host-microbiota interactions under controlled conditions and for preclinical evaluation of microbiome-targeted therapies and dermo-cosmetic treatments.
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BibTeX
@article{patatian2026development,
title = {{Development of an ex vivo skin model for quantitative recovery and preservation of donor-specific human microbiota}},
author = {Angela Patatian and Chrisse Ngari and Caroline Durand and Delhia Romain and Christelle Guéré and Katell Vie and Valérie Poulet and Giuseppe Percoco and Damien Seyer},
journal = {BMC Microbiology},
year = {2026},
month = jun,
doi = {10.1186/s12866-026-05316-w},
url = {https://hal.science/hal-05778110v1},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Development of an ex vivo skin model for quantitative recovery and preservation of donor-specific human microbiota
AU - Angela Patatian
AU - Chrisse Ngari
AU - Caroline Durand
AU - Delhia Romain
AU - Christelle Guéré
AU - Katell Vie
AU - Valérie Poulet
AU - Giuseppe Percoco
AU - Damien Seyer
PY - 2026
DA - 2026/06/22
JO - BMC Microbiology
DO - 10.1186/s12866-026-05316-w
UR - https://hal.science/hal-05778110v1
AB - BACKGROUND: Through multi-omics approaches, our understanding of skin microbiota has substantially advanced. However, the development of reliable and physiologically relevant experimental models would greatly accelerate progress in microbiome-targeted science. Most investigations of skin microbiota rely on in vitro 2D models or reconstructed epidermis colonized with a limited number of strains, which do not reflect the complexity and the spatial microbial organization observed on in vivo skin. To overcome these limitations, we developed a model based on perfused human skin explants (Perfex model), that enables the transfer of complex bacterial communities from human volunteers onto ex vivo skin. RESULTS: After quantitative validation of recovered microbial DNA by qPCR from volunteers (V1-V2-V3) and corresponding inoculated explants (MV1-MV3), 16S rRNA gene sequencing was performed to assess whether microbiota transfer influenced community structure and diversity. No statistically significant differences in alpha-diversity were observed between original and transferred microbiota at the genus level, suggesting that the transfer procedure did not substantially alter overall community diversity. Clustering analysis revealed distinct grouping of samples according to donor origin, indicating that donor-specific microbial signatures were largely maintained on the explants after 48 hours. Control samples formed separate clusters, suggesting minimal background signal and supporting the absence of cross-contamination. These observations indicate that the model enables clear discrimination between the endogenous microbiota of the explants and the transferred microbiota, supporting the integrity of the experimental conditions. Beta-diversity analysis based on Bray-Curtis supported these findings. Across samples, microbial communities were characterized by the recurrent presence of common skin-associated genera such as Cutibacterium, Staphylococcus, and Corynebacterium. Histological analyses demonstrated preserved tissue architecture, while immunostaining revealed modulation of selected innate immune markers consistent with a localized skin response to microbial transfer. CONCLUSIONS: The Perfex model enables transfer of donor-specific skin microbiota to ex vivo human skin while preserving tissue integrity over short-term culture. This model provides a human-relevant platform for studying host-microbiota interactions under controlled conditions and for preclinical evaluation of microbiome-targeted therapies and dermo-cosmetic treatments.
SN - 1471-2180
ER -