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Microorganisms
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Skin Microbiome
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Skin Microbiome

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 30 November 2026 | Viewed by 18335

Special Issue Editor

Prof. Dr. Zhe-Xue Quan

E-Mail Website
Guest Editor
Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
Interests: nitrification; comammox; enrichment; skin microbiome; metatranscriptome

Special Issue Information

Dear Colleagues,

The skin, our largest organ, is the first line of defense against the external environment. Beneath its surface lies a complex and diverse community: the skin microbiome. This network of microorganisms, including bacteria, fungi, viruses, and mites, plays a key role in maintaining skin health and influences conditions ranging from acne to eczema, psoriasis, and even broader systemic diseases. Recent advances in multi-omics and bioinformatics have greatly expanded our understanding of the diversity and functions of skin microbes, altering how we perceive their interactions with the host and the environment.

This Special Issue of Microorganisms gathers cutting-edge research and in-depth reviews that explore the essential components of the skin microbiota, examine host-microbe relationships, and address the possibilities of modifying the skin microbiome for health benefits. With contributions from experts around the globe, this collection seeks to extend current knowledge and encourage a deeper exploration of the skin microbiome’s role in health and disease.

We are excited to present this Special Issue and hope the diverse range of topics will inspire further research and cooperation in this promising field.

Prof. Dr. Zhe-Xue Quan
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • skin health
  • skin microbes
  • multi-omics and bioinformatics
  • host-microbe relationship

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Published Papers (7 papers)

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Research

Jump to: Review, Other

17 pages, 1666 KB  
Article
Shotgun Metagenomic Characterization of Acne Microbiota Before and After Treatment with a Topical Biotechnological Phytocomplex: Understanding Skin Dysbiosis
by Adrià Cruells, Cristina Eguren, Aymée Robainas Barcia, Helena Martínez, Mohammed Sharaf, Carlos Ruiz, Antonio Sánchez-Baos, Nerea Carrón, Lola Bou, Montse Pérez, Raúl De Lucas and Aurora Guerra-Tapia
Microorganisms 2026, 14(4), 915; https://doi.org/10.3390/microorganisms14040915 - 18 Apr 2026
Viewed by 181
Abstract
This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, [...] Read more.
This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris. Full article
(This article belongs to the Special Issue Skin Microbiome)
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21 pages, 8603 KB  
Article
Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area
by Ping Hu, Andrew N. Carr, Mirjana Parlov, Dionne Swift, Jay P. Tiesman, Nivedita Ramji, Jennifer J. Schoch and Amber G. Teufel
Microorganisms 2025, 13(11), 2632; https://doi.org/10.3390/microorganisms13112632 - 20 Nov 2025
Cited by 1 | Viewed by 1389
Abstract
Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, [...] Read more.
Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions. Full article
(This article belongs to the Special Issue Skin Microbiome)
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18 pages, 3289 KB  
Article
Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability
by Xibei Fan, Ning Lv and Zhexue Quan
Microorganisms 2025, 13(3), 549; https://doi.org/10.3390/microorganisms13030549 - 28 Feb 2025
Viewed by 1882
Abstract
The composition of the human microbiome is a critical health indicator, and culture-independent methodologies have substantially advanced our understanding of human-associated microorganisms. However, precise identification and characterization of microbial strains require culture-based techniques. Recently, the resurgence of culturomics, combined with high-throughput sequencing technology, [...] Read more.
The composition of the human microbiome is a critical health indicator, and culture-independent methodologies have substantially advanced our understanding of human-associated microorganisms. However, precise identification and characterization of microbial strains require culture-based techniques. Recently, the resurgence of culturomics, combined with high-throughput sequencing technology, has reduced the high labor demand of pure culture methods, facilitating a more efficient and comprehensive acquisition of culturable microbial strains. This study employed an integrated approach combining culturomic and high-throughput sequencing to identify culturable microorganisms on the human scalp and in human saliva and feces. Several Staphylococcus strains were identified from the scalp, whereas anaerobic microorganisms were dominant in the saliva and fecal samples. Additionally, the study highlighted the beneficial effects of transportation conditions (liquid nitrogen treatment, dry ice transport, and dimethyl sulfoxide [DMSO] buffer) in preserving culturable microorganisms. A robust methodology was developed for the large-scale acquisition of culturable microorganisms with optimized transport conditions that enhance the potential for isolating a greater diversity of culturable strains. Full article
(This article belongs to the Special Issue Skin Microbiome)
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12 pages, 2179 KB  
Article
Distinct Intraspecies Variation of Cutibacterium acnes and Staphylococcus epidermidis in Acne Vulgaris and Healthy Skin
by Tina Hamann, Holger Brüggemann, Cecilie Feidenhansl, Erinda Rruci, Julia Gallinger, Stefan Gallinat and Jennifer Hüpeden
Microorganisms 2025, 13(2), 299; https://doi.org/10.3390/microorganisms13020299 - 29 Jan 2025
Cited by 11 | Viewed by 5529
Abstract
Human skin hosts a diverse array of microorganisms that contribute to its health. Key players in the facial skin microbiome include Cutibacterium acnes and staphylococci, whose colonization patterns may influence dermatological conditions like acne vulgaris. This study examined the facial microbiome composition of [...] Read more.
Human skin hosts a diverse array of microorganisms that contribute to its health. Key players in the facial skin microbiome include Cutibacterium acnes and staphylococci, whose colonization patterns may influence dermatological conditions like acne vulgaris. This study examined the facial microbiome composition of 29 individuals, including 14 with moderate to severe acne and 15 with healthy skin, using single locus sequence typing (SLST) amplicon sequencing. The results showed a shift in the relative abundances of C. acnes phylotypes: SLST types A, C, and F were increased in acne, while types H, K, and L were reduced compared to healthy skin. Among staphylococci, the relative abundance of S. epidermidis, S. capitis, and S. saphrophyticus increased in acne, while S. saccharolyticus and S. hominis decreased. The amplicon sequencing approach could also identify a population shift of S. epidermidis: a specific S. epidermidis phylogenetic lineage (type 3) was reduced in acne, while two abundant lineages (types 1 and 2) were elevated. These findings suggest that distinct phylogenetic lineages of both C. acnes and S. epidermidis are linked to healthy versus diseased skin, highlighting a potential role for both microorganisms in disease prevention and aggravation, respectively. Full article
(This article belongs to the Special Issue Skin Microbiome)
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21 pages, 5649 KB  
Article
Bidirectional Mendelian Randomization Analysis to Study the Relationship Between Human Skin Microbiota and Radiation-Induced Skin Toxicity
by Hui Chen, Xiaojie Xia, Kexin Shi, Tianyi Xie, Xinchen Sun, Zhipeng Xu and Xiaolin Ge
Microorganisms 2025, 13(1), 194; https://doi.org/10.3390/microorganisms13010194 - 17 Jan 2025
Viewed by 2029
Abstract
Radiation-induced skin toxicity, resulting from ionizing or nonionizing radiation, is a common skin disorder. However, the underlying relationship between skin microbiota and radiation-induced skin toxicity remains largely unexplored. Herein, we uncover the microbiota–skin interaction based on a genome-wide association study (GWAS) featuring 150 [...] Read more.
Radiation-induced skin toxicity, resulting from ionizing or nonionizing radiation, is a common skin disorder. However, the underlying relationship between skin microbiota and radiation-induced skin toxicity remains largely unexplored. Herein, we uncover the microbiota–skin interaction based on a genome-wide association study (GWAS) featuring 150 skin microbiota and three types of skin microenvironment. Summary datasets of human skin microbiota were extracted from the GWAS catalog database, and summary datasets of radiation-induced skin toxicity from the FinnGen biobank. Mendelian Randomization (MR) analysis was leveraged to sort out the causal link between skin microbiota and radiation-induced skin toxicity. We identified 33 causal connections between human skin microbiota and radiation-induced skin toxicity, including 19 positive and 14 negative causative directions. Among these potential associations, the genus Staphylococcus could serve as a common risk factor for radiation-induced skin toxicity, especially for radiodermatitis. And Streptococcus salivarius was identified as a potential protective factor against radiation-induced skin toxicity. Additional analysis indicated no pleiotropy, heterogeneity, or reverse causal relationship in the results. We comprehensively assessed potential associations of skin microbiota with radiation-induced skin toxicity and identified several suggestive links. Our results provide promising targets for the prevention and treatment of radiation-induced skin toxicity. Full article
(This article belongs to the Special Issue Skin Microbiome)
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Review

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26 pages, 7022 KB  
Review
Microbial Interventions for Inflammatory Skin Diseases: A Systematic Review and Meta-Analysis of Atopic Dermatitis and Psoriasis
by Yamil Liscano, Daniel Muñoz Morales, Fernanda Suarez Daza, Sinthia Vidal Cañas, Darly Martinez Guevara and Esteban Artunduaga Cañas
Microorganisms 2025, 13(11), 2416; https://doi.org/10.3390/microorganisms13112416 - 22 Oct 2025
Cited by 2 | Viewed by 4901
Abstract
Inflammatory dermatological diseases represent a significant global health burden, with emerging evidence suggesting that modulation of the gut–skin axis microbial interventions may offer therapeutic benefits. However, current evidence is fragmented, with considerable heterogeneity limiting definitive conclusions. A systematic review and a meta-analysis were [...] Read more.
Inflammatory dermatological diseases represent a significant global health burden, with emerging evidence suggesting that modulation of the gut–skin axis microbial interventions may offer therapeutic benefits. However, current evidence is fragmented, with considerable heterogeneity limiting definitive conclusions. A systematic review and a meta-analysis were conducted following PRISMA guidelines, registered in PROSPERO (CRD42024629809). Seven databases were searched for randomized controlled trials evaluating probiotics, synbiotics, or postbiotics in inflammatory skin conditions. Primary outcomes included disease severity scores (SCORAD for atopic dermatitis, PASI for psoriasis). Statistical analysis employed random-effect models with standardized mean differences (SMDs) and Hedges’ g as effect size measures, using R software. Heterogeneity among studies was assessed using Q statistics and the I2 index. Results: In total, 19 studies encompassing 1104 participants met the inclusion criteria. For atopic dermatitis, a meta-analysis of 12 studies (n = 817) demonstrated significant clinical improvement with microbial interventions versus placebo (SMD = −0.72; 95% CI: −1.26 to −0.17; p = 0.015), though substantial heterogeneity in the treatment effects was observed across studies (I2 = 85.1%). The psoriasis results were more variable, with five studies (n = 287) showing non-significant pooled effects (SMD = −0.63; 95% CI: −1.74 to 0.48; p = 0.192). Multi-strain formulations and synbiotic combinations appeared to show greater efficacy compared to single-strain preparations. Safety profiles remained consistently favorable across all interventions. Microbial interventions represent a promising adjunctive therapeutic approach for inflammatory dermatological diseases, particularly atopic dermatitis, acting via gut–skin axis mechanisms. The substantial heterogeneity between the included studies emphasizes the need for standardized protocols and personalized medicine approaches integrating microbiome profiling to optimize clinical outcomes. Full article
(This article belongs to the Special Issue Skin Microbiome)
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Other

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10 pages, 1173 KB  
Brief Report
Skin Microbiome Patterns Associated with Basal Cell Carcinoma: A Case Series
by Mavra Masood, David Ozog, Tengfei Ma, Marissa Ceresnie, Aunna Pourang, Christine C. Johnson, Xinyue Qiu, Albert Levin and Jesse Veenstra
Microorganisms 2026, 14(4), 822; https://doi.org/10.3390/microorganisms14040822 - 3 Apr 2026
Viewed by 330
Abstract
Basal cell carcinoma (BCC) is the most common malignancy worldwide, yet the role of the skin microbiome in BCC remains poorly defined. In this cross-sectional observational case series, we compared the cutaneous microbiome of BCC lesions with matched perilesional and control skin using [...] Read more.
Basal cell carcinoma (BCC) is the most common malignancy worldwide, yet the role of the skin microbiome in BCC remains poorly defined. In this cross-sectional observational case series, we compared the cutaneous microbiome of BCC lesions with matched perilesional and control skin using whole-genome shotgun sequencing in an intra-patient, multi-site sampling design. BCC samples demonstrated reduced microbial richness and significant shifts in community composition compared with matched control skin. Specifically, BCC lesions exhibited significantly lower Chao1 diversity (β = −484.6, 95% CI: −772.1 to −197.2, p = 0.003). Differences in overall microbial composition were confirmed by PERMANOVA analysis based on Bray–Curtis and Jaccard distance metrics (R2 = 12.6% and 9.7%, respectively; both p = 0.01). At the species level, Cutibacterium acnes was significantly reduced in BCC samples compared with controls (β = −0.31, 95% CI: −0.45 to −0.16, p = 0.0004), corresponding to an approximately 27% lower geometric mean relative abundance. Functional profiling suggested shifts in microbial metabolic potential, with pathways related to redox balance and lipid-associated processes differentially represented in BCC samples relative to controls. Together, these findings demonstrate that BCC lesions are associated with localized alterations in microbial diversity, community composition, and inferred functional potential. These results support the presence of a tumor-associated microbiome signature in BCC; however, further studies in larger and more diverse cohorts are needed to determine whether these changes contribute to tumor development or reflect adaptation to the tumor microenvironment. Full article
(This article belongs to the Special Issue Skin Microbiome)
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