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Crepin DM, Chavignon M, Verhoeven PO, Laurent F, Josse J, Butin M. Staphylococcus capitis: insights into epidemiology, virulence, and antimicrobial resistance of a clinically relevant bacterial species. Clin Microbiol Rev 2024; 37:e0011823. [PMID: 38899876 PMCID: PMC11391707 DOI: 10.1128/cmr.00118-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
SUMMARYStaphylococcus capitis is divided into two subspecies, S. capitis subsp. ureolyticus (renamed urealyticus in 1992; ATCC 49326) and S. capitis subsp. capitis (ATCC 27840), and fits with the archetype of clinically relevant coagulase-negative staphylococci (CoNS). S. capitis is a commensal bacterium of the skin in humans, which must be considered an opportunistic pathogen of interest particularly as soon as it is identified in a clinically relevant specimen from an immunocompromised patient. Several studies have highlighted the potential determinants underlying S. capitis pathogenicity, resistance profiles, and virulence factors. In addition, mobile genetic element acquisitions and mutations contribute to S. capitis genome adaptation to its environment. Over the past decades, antibiotic resistance has been identified for S. capitis in almost all the families of the currently available antibiotics and is related to the emergence of multidrug-resistant clones of high clinical significance. The present review summarizes the current knowledge concerning the taxonomic position of S. capitis among staphylococci, the involvement of this species in human colonization and diseases, the virulence factors supporting its pathogenicity, and the phenotypic and genomic antimicrobial resistance profiles of this species.
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Affiliation(s)
- Deborah M Crepin
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal pathogenesis team, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Marie Chavignon
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal pathogenesis team, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Paul O Verhoeven
- CIRI, Centre International de Recherche en Infectiologie, GIMAP Team, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
- Faculté de Médecine, Université Jean Monnet, St-Etienne, France
- Service des agents infectieux et d'hygiène, Centre Hospitalier Universitaire de St-Etienne, St-Etienne, France
| | - Frédéric Laurent
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal pathogenesis team, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
- Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Jérôme Josse
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal pathogenesis team, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Marine Butin
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal pathogenesis team, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
- Service de Néonatologie et Réanimation Néonatale, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France
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Wilkinson HN, Stafford AR, Rudden M, Rocha NDC, Kidd AS, Iveson S, Bell AL, Hart J, Duarte A, Frieling J, Janssen F, Röhrig C, de Rooij B, Ekhart PF, Hardman MJ. Selective Depletion of Staphylococcus aureus Restores the Skin Microbiome and Accelerates Tissue Repair after Injury. J Invest Dermatol 2024; 144:1865-1876.e3. [PMID: 38307323 DOI: 10.1016/j.jid.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/02/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024]
Abstract
Our skin is home to a diverse community of commensal microorganisms integral to cutaneous function. However, microbial dysbiosis and barrier perturbation increase the risk of local and systemic infection. Staphylococcus aureus is a particularly problematic bacterial pathogen, with high levels of antimicrobial resistance and direct association with poor healing outcome. Innovative approaches are needed to selectively kill skin pathogens, such as S aureus, without harming the resident microbiota. In this study, we provide important data on the selectivity and efficacy of an S aureus-targeted endolysin (XZ.700) within the complex living skin/wound microbiome. Initial cross-species comparison using Nanopore long-read sequencing identified the translational potential of porcine rather than murine skin for human-relevant microbiome studies. We therefore performed an interventional study in pigs to assess the impact of endolysin administration on the microbiome. XZ.700 selectively inhibited endogenous porcine S aureus in vivo, restoring microbial diversity and promoting multiple aspects of wound repair. Subsequent mechanistic studies confirmed the importance of this microbiome modulation for effective healing in human skin. Taken together, these findings strongly support further development of S aureus-targeted endolysins for future clinical management of skin and wound infections.
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Affiliation(s)
- Holly N Wilkinson
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom; Skin Research Centre, Hull York Medical School, The University of York, Heslington, United Kingdom.
| | - Amber R Stafford
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom
| | - Michelle Rudden
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom; Skin Research Centre, Hull York Medical School, The University of York, Heslington, United Kingdom
| | - Nina D C Rocha
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom
| | - Alexandria S Kidd
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom
| | - Sammi Iveson
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom
| | | | | | - Ana Duarte
- Micreos Pharma B.V., Bilthoven, The Netherlands
| | | | | | | | | | | | - Matthew J Hardman
- Biomedical Institute for Multimorbidity, Centre for Biomedicine, Hull York Medical School, The University of Hull, Hull, United Kingdom; Skin Research Centre, Hull York Medical School, The University of York, Heslington, United Kingdom
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Maître M, Gravier E, Simcic-Mori A, Géniès C, Mias C, Alvarez-Georges S, Noustens A, Bouyer K, Bessou-Touya S, Carballido F, Duplan H. Characterization of the forehead skin microbiome in the early phase of acne. J Eur Acad Dermatol Venereol 2024; 38 Suppl 7:3-11. [PMID: 39051132 DOI: 10.1111/jdv.20203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/27/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND The skin microbiota is known to be imbalanced in acne vulgaris, but the changes occurring during the early stages of acne onset remain poorly described. OBJECTIVES To characterize the skin microbiome of subclinical stages of acne in adults and adolescents. METHODS The composition and diversity of the microbiota from non-lesional skin on the forehead of subjects with mild-to-moderate acne were compared to the ones from non-acne subjects. Analyses of skin swab samples were performed using high-throughput sequencing of the V1-V3 regions of the bacterial 16S ribosomal RNA gene, the tuf gene fragment of Staphylococcus species and the internal transcribed spacer (ITS1) region of the fungal rRNA gene to determine the relative abundance, alpha-diversity and beta-diversity of bacteria and fungi. RESULTS Compared with non-acne subjects, acne subjects had a higher abundance of Cutibacterium (72.4% vs. 57.8%) and lower abundances of Corynebacterium (2.8% vs. 4.8%) and Streptococcus (1.4% vs. 3.2%). Bacterial alpha- and beta-diversity indices also differed significantly between the two groups, reflecting differences in richness, evenness, abundance and phylogenetic distance between bacterial populations. Differences were also observed at the level of Staphylococcus species: S. capitis was predominant in skin samples from non-acne subjects (46.7%), whereas S. epidermidis was the most abundant Staphylococcus species in non-lesional forehead skin areas of acne subjects (44.2%). Conversely, no significant between-group differences were found for fungi, with Malasseziales being the predominant order in both subject groups. CONCLUSION Dysbiosis was observed very early in subclinical acne stages of the forehead skin, with the overall abundance, richness and evenness of the bacterial population being lower in acne than in non-acne skin samples. Dysbiosis was also found at the level of Staphylococcus species. The development of acne lesions could therefore be prevented by using a skin care product that rebalances facial skin microbiota at very early stages.
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Affiliation(s)
- M Maître
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - E Gravier
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - A Simcic-Mori
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - C Géniès
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - C Mias
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - S Alvarez-Georges
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - A Noustens
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - K Bouyer
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - S Bessou-Touya
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
| | - F Carballido
- Laboratoires A-Derma, Pierre Fabre Dermo-Cosmétique, Lavaur, France
| | - H Duplan
- Pierre Fabre Dermo-Cosmétique and Personal Care, Research & Development, Toulouse, France
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Imam MW, Luqman S. Unveiling the mechanism of essential oil action against skin pathogens: from ancient wisdom to modern science. Arch Microbiol 2024; 206:347. [PMID: 38985339 DOI: 10.1007/s00203-024-03986-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/28/2024] [Indexed: 07/11/2024]
Abstract
Essential oils are among the most well-known phyto-compounds, and since ancient times, they have been utilized in medicine. Over 100 essential oils have been identified and utilized as therapies for various skin infections and related ailments. While numerous commercial medicines are available in different dosage forms to treat skin diseases, the persisting issues include their side effects, toxicity, and low efficacy. As a result, researchers are seeking novel classes of compounds as substitutes for synthetic drugs, aiming for minimal side effects, no toxicity, and high efficacy. Essential oils have shown promising antimicrobial activity against skin-associated pathogens. This review presents essential knowledge and scientific information regarding essential oil's antimicrobial capabilities against microorganisms that cause skin infections. Essential oils mechanisms against different pathogens have also been explored. Many essential oils exhibit promising activity against various microbes, which has been qualitatively assessed using the agar disc diffusion experiment, followed by determining the minimum inhibitory concentration for quantitative evaluation. It has been observed that Staphylococcus aureus and Candida albicans have been extensively researched in the context of skin-related infections and their antimicrobial activity, including established modes of action. In contrast, other skin pathogens such as Staphylococcus epidermidis, Streptococcus pyogens, Propionibacterium acnes, and Malassezia furfur have received less attention or neglected. This review report provides an updated understanding of the mechanisms of action of various essential oils with antimicrobial properties. This review explores the anti-infectious activity and mode of action of essential against distinct skin pathogens. Such knowledge can be valuable in treating skin infections and related ailments.
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Affiliation(s)
- Md Waquar Imam
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201001, Uttar Pradesh, India
| | - Suaib Luqman
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201001, Uttar Pradesh, India.
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White EK, Uberoi A, Pan JTC, Ort JT, Campbell AE, Murga-Garrido SM, Harris JC, Bhanap P, Wei M, Robles NY, Gardner SE, Grice EA. Alcaligenes faecalis corrects aberrant matrix metalloproteinase expression to promote reepithelialization of diabetic wounds. SCIENCE ADVANCES 2024; 10:eadj2020. [PMID: 38924411 PMCID: PMC11204295 DOI: 10.1126/sciadv.adj2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Chronic wounds are a common and costly complication of diabetes, where multifactorial defects contribute to dysregulated skin repair, inflammation, tissue damage, and infection. We previously showed that aspects of the diabetic foot ulcer microbiota were correlated with poor healing outcomes, but many microbial species recovered remain uninvestigated with respect to wound healing. Here, we focused on Alcaligenes faecalis, a Gram-negative bacterium that is frequently recovered from chronic wounds but rarely causes infection. Treatment of diabetic wounds with A. faecalis accelerated healing during early stages. We investigated the underlying mechanisms and found that A. faecalis treatment promotes reepithelialization of diabetic keratinocytes, a process that is necessary for healing but deficient in chronic wounds. Overexpression of matrix metalloproteinases in diabetes contributes to failed epithelialization, and we found that A. faecalis treatment balances this overexpression to allow proper healing. This work uncovers a mechanism of bacterial-driven wound repair and provides a foundation for the development of microbiota-based wound interventions.
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Affiliation(s)
- Ellen K. White
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aayushi Uberoi
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie Ting-Chun Pan
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jordan T. Ort
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy E. Campbell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sofia M. Murga-Garrido
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jordan C. Harris
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Preeti Bhanap
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monica Wei
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nelida Y. Robles
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sue E. Gardner
- College of Nursing, The University of Iowa, Iowa City, IA 52242, USA
| | - Elizabeth A. Grice
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Na HH, Kim S, Kim JS, Lee S, Kim Y, Kim SH, Lee CH, Kim D, Yoon SH, Jeong H, Kweon D, Seo HW, Ryu CM. Facemask acne attenuation through modulation of indirect microbiome interactions. NPJ Biofilms Microbiomes 2024; 10:50. [PMID: 38902263 PMCID: PMC11190265 DOI: 10.1038/s41522-024-00512-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/28/2024] [Indexed: 06/22/2024] Open
Abstract
During the COVID-19 pandemic, facemasks played a pivotal role in preventing person-person droplet transmission of viral particles. However, prolonged facemask wearing causes skin irritations colloquially referred to as 'maskne' (mask + acne), which manifests as acne and contact dermatitis and is mostly caused by pathogenic skin microbes. Previous studies revealed that the putative causal microbes were anaerobic bacteria, but the pathogenesis of facemask-associated skin conditions remains poorly defined. We therefore characterized the role of the facemask-associated skin microbiota in the development of maskne using culture-dependent and -independent methodologies. Metagenomic analysis revealed that the majority of the facemask microbiota were anaerobic bacteria that originated from the skin rather than saliva. Previous work demonstrated direct interaction between pathogenic bacteria and antagonistic strains in the microbiome. We expanded this analysis to include indirect interaction between pathogenic bacteria and other indigenous bacteria classified as either 'pathogen helper (PH)' or 'pathogen inhibitor (PIn)' strains. In vitro screening of bacteria isolated from facemasks identified both strains that antagonized and promoted pathogen growth. These data were validated using a mouse skin infection model, where we observed attenuation of symptoms following pathogen infection. Moreover, the inhibitor of pathogen helper (IPH) strain, which did not directly attenuate pathogen growth in vitro and in vivo, functioned to suppress symptom development and pathogen growth indirectly through PH inhibitory antibacterial products such as phenyl lactic acid. Taken together, our study is the first to define a mechanism by which indirect microbiota interactions under facemasks can control symptoms of maskne by suppressing a skin pathogen.
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Affiliation(s)
- Han-Hee Na
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Department of Interdisciplinary Program in Biocosmetics, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Seil Kim
- Division of Metrology for Quality of Life, Center for Bioanalysis, Korea Research Institute of Standards and Science, 267 Gajeong-Ro, Yuseong-Gu, Daejeon, 34113, Republic of Korea
| | - Jun-Seob Kim
- Department of Nano-Bioengineering, Incheon National University, Incheon, 22012, South Korea
| | - Soohyun Lee
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Yeseul Kim
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Functional Genomics Program, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Su-Hyun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Republic of Korea
| | - Choong-Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Republic of Korea
- Research Institute for Bioactive-Metabolome Network, Konkuk University, Seoul, Republic of Korea
| | - Dohyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Republic of Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Daehyuk Kweon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Hwi Won Seo
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea.
| | - Choong-Min Ryu
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea.
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7
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Dreno B, Dekio I, Baldwin H, Demessant AL, Dagnelie MA, Khammari A, Corvec S. Acne microbiome: From phyla to phylotypes. J Eur Acad Dermatol Venereol 2024; 38:657-664. [PMID: 37777343 DOI: 10.1111/jdv.19540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/12/2023] [Indexed: 10/02/2023]
Abstract
Acne vulgaris is a chronic inflammatory skin disease with a complex pathogenesis. Traditionally, the primary pathophysiologic factors in acne have been thought to be: (1) altered sebum production, (2) inflammation, (3) excess keratinization and (4) colonization with the commensal Cutibacterium acnes. However, the role of C. acnes has been unclear, since virtually all adults have C. acnes on their skin yet not all develop acne. In recent years, understanding of the role of C. acnes has expanded. It is still acknowledged to have an important place in acne pathogenesis, but evidence suggests that an imbalance of individual C. acnes phylotypes and an alteration of the skin microbiome trigger acne. In addition, it is now believed that Staphylococcus epidermidis is also an actor in acne development. Together, C. acnes and S. epidermidis maintain and regulate homeostasis of the skin microbiota. Antibiotics, which have long been a staple of acne therapy, induce cutaneous dysbiosis. This finding, together with the long-standing public health edict to spare antibiotic use when possible, highlights the need for a change in acne management strategies. One fertile direction of study for new approaches involves dermocosmetic products that can support epidermal barrier function and have a positive effect on the skin microbiome.
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Affiliation(s)
- Brigitte Dreno
- Dermatology Department, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes Université, Nantes, France
| | - Itaru Dekio
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan
| | - Hilary Baldwin
- Acne Treatment and Research Center, Morristown, New Jersey, USA
| | | | - Marie-Ange Dagnelie
- Dermatology Department, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes Université, Nantes, France
| | - Amir Khammari
- Dermatology Department, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes Université, Nantes, France
| | - Stephane Corvec
- CHU Nantes, Bacteriology Department, INCIT, UMR 1302, University Nantes, Nantes, France
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Dong Q, Wang S, Miao Y, Luo H, Weng Z, Yu L. Novel antimicrobial peptides against Cutibacterium acnes designed by deep learning. Sci Rep 2024; 14:4529. [PMID: 38402320 PMCID: PMC10894229 DOI: 10.1038/s41598-024-55205-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/21/2024] [Indexed: 02/26/2024] Open
Abstract
The increasing prevalence of antibiotic resistance in Cutibacterium acnes (C. acnes) requires the search for alternative therapeutic strategies. Antimicrobial peptides (AMPs) offer a promising avenue for the development of new treatments targeting C. acnes. In this study, to design peptides with the specific inhibitory activity against C. acnes, we employed a deep learning pipeline with generators and classifiers, using transfer learning and pretrained protein embeddings, trained on publicly available data. To enhance the training data specific to C. acnes inhibition, we constructed a phylogenetic tree. A panel of 42 novel generated linear peptides was then synthesized and experimentally evaluated for their antimicrobial selectivity and activity. Five of them demonstrated their high potency and selectivity against C. acnes with MIC of 2-4 µg/mL. Our findings highlight the potential of these designed peptides as promising candidates for anti-acne therapeutics and demonstrate the power of computational approaches for the rational design of targeted antimicrobial peptides.
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Affiliation(s)
- Qichang Dong
- Shanghai MetaNovas Biotech Co., Ltd, Shanghai, 200120, China
| | - Shaohua Wang
- Shanghai MetaNovas Biotech Co., Ltd, Shanghai, 200120, China
| | - Ying Miao
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Heng Luo
- Shanghai MetaNovas Biotech Co., Ltd, Shanghai, 200120, China
| | - Zuquan Weng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Lun Yu
- Metanovas Biotech Inc., Foster City, 94404, USA.
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Amer MA, Darwish MM, Soliman NS, Amin HM. Resistome, mobilome, and virulome explored in clinical isolates derived from acne patients in Egypt: unveiling unique traits of an emerging coagulase-negative Staphylococcus pathogen. Front Cell Infect Microbiol 2024; 14:1328390. [PMID: 38371297 PMCID: PMC10869526 DOI: 10.3389/fcimb.2024.1328390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/10/2024] [Indexed: 02/20/2024] Open
Abstract
Coagulase-negative staphylococci (CoNS) are a group of gram-positive staphylococcal species that naturally inhabit the healthy human skin and mucosa. The clinical impact of CoNS-associated infections has recently been regarded as a challenge for diagnosis and therapeutic options. CoNS-associated infections are primarily caused by bacterial resistance to antibiotics and biofilm formation. As antibiotics are still the most used treatment, this problem will likely persist in the future. The present study aimed to investigate the resistance and virulence of CoNS recovered from various acne lesions and explore their genetic basis. Skin swab samples were collected from participants with acne and healthy skin. All samples underwent conventional culture for the isolation of CoNS, MALDI-TOF confirmation, antibiotic susceptibility, and biofilm formation testing. A total of 85 CoNS isolates were recovered from the samples and preliminarily identified as Staphylococcus epidermidis. Isolates from the acne group (n = 60) showed the highest rates of resistance to penicillin (73%), cefoxitin (63%), clindamycin (53.3%), and erythromycin (48%), followed by levofloxacin (36.7%) and gentamycin (31.7%). The lowest rates of resistance were observed against tetracycline (28.3%), doxycycline (11.7%), and minocycline (8.3%). CoNS isolated from mild, moderate acne and healthy isolates did not show strong biofilm formation, whereas the isolates from the severe cases of the acne group showed strong biofilm formation (76.6%). Four extensively drug-resistant and strong biofilm-forming staphylococcal isolates recovered from patients with severe acne were selected for whole-genome sequencing (WGS), and their genomes were investigated using bioinformatics tools. Three of the sequenced genomes were identified as S. epidermidis; however, isolate 29AM was identified as Staphylococcus warneri, which is a newly emerging pathogen that is not commonly associated with acne and was not detected by MALDI-TOF. All the sequenced strains were multidrug-resistant and carried multiple resistance genes, including blaZ, mecA, tet(K), erm(C), lnuA, vgaA, dfrC, fusB, fosBx1, norA, and vanT, which were found to be located on plasmids and chromosomes. Virulence features were detected in all genomes in the presence of genes involved in adherence and biofilm formation (icaA, icaB, icaC, sdrG, sdrH, atl, ebh, and ebp). Only the S. warneri isolate 29AM contained immune evasion genes (capB, capC, acpXL, and manA), an anti-phagocytosis gene (cdsA), and other unique features. As a result of their potential pathogenicity and antibiotic resistance, CoNS must be monitored as an emerging pathogen associated with acne infections. To the best of our knowledge, this is the first report to isolate, identify, and correlate S. warneri with severe acne infections among Egyptian patients using WGS and bioinformatic analysis.
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Affiliation(s)
- Mai A. Amer
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts, Giza, Egypt
| | - Manal M. Darwish
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts, Giza, Egypt
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Noha S. Soliman
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Heba M. Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts, Giza, Egypt
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10
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Glatthardt T, Lima RD, de Mattos RM, Ferreira RBR. Microbe Interactions within the Skin Microbiome. Antibiotics (Basel) 2024; 13:49. [PMID: 38247608 PMCID: PMC10812674 DOI: 10.3390/antibiotics13010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
The skin is the largest human organ and is responsible for many important functions, such as temperature regulation, water transport, and protection from external insults. It is colonized by several microorganisms that interact with each other and with the host, shaping the microbial structure and community dynamics. Through these interactions, the skin microbiota can inhibit pathogens through several mechanisms such as the production of bacteriocins, proteases, phenol soluble modulins (PSMs), and fermentation. Furthermore, these commensals can produce molecules with antivirulence activity, reducing the potential of these pathogens to adhere to and invade human tissues. Microorganisms of the skin microbiota are also able to sense molecules from the environment and shape their behavior in response to these signals through the modulation of gene expression. Additionally, microbiota-derived compounds can affect pathogen gene expression, including the expression of virulence determinants. Although most studies related to microbial interactions in the skin have been directed towards elucidating competition mechanisms, microorganisms can also use the products of other species to their benefit. In this review, we will discuss several mechanisms through which microorganisms interact in the skin and the biotechnological applications of products originating from the skin microbiota that have already been reported in the literature.
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Affiliation(s)
- Thaís Glatthardt
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (T.G.); (R.D.L.); (R.M.d.M.)
- Department of Physiology and Pharmacology, Health Research Innovation Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Pediatrics, Alberta Children Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Rayssa Durães Lima
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (T.G.); (R.D.L.); (R.M.d.M.)
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Raquel Monteiro de Mattos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (T.G.); (R.D.L.); (R.M.d.M.)
| | - Rosana Barreto Rocha Ferreira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (T.G.); (R.D.L.); (R.M.d.M.)
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
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11
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Dessinioti C, Katsambas A. The Microbiome and Acne: Perspectives for Treatment. Dermatol Ther (Heidelb) 2024; 14:31-44. [PMID: 38183614 PMCID: PMC10828138 DOI: 10.1007/s13555-023-01079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 01/08/2024] Open
Abstract
The skin microbiome consists of the microorganisms populating the human skin. Cutibacterium acnes (C. acnes, formerly named Propionibacterium acnes) is recognized as a key factor in acne development, regulating inflammatory and immune pathways. Dysbiosis has been described as the imbalance in skin microbiome homeostasis and may play a role in acne pathogenesis. Microbial interference has been shown to be a contributor to healthy skin homeostasis and staphylococcal strains may exclude acne-associated C. acnes phylotypes. In this review we present an update on the skin microbiome in acne and discuss how current acne treatments such as benzoyl peroxide, orally administered isotretinoin, and antibiotics may affect the skin microbiome homeostasis. We highlight the collateral damage of acne antibiotics on the skin microbiome, including the risk of antimicrobial resistance and the dysregulation of the microbiome equilibrium that may occur even with short-term antibiotic courses. Consequently, the interest is shifting towards new non-antibiotic pharmacological acne treatments. Orally administered spironolactone is an emerging off-label treatment for adult female patients and topical peroxisome proliferator-activated receptor gamma (PPARγ) modulation is being studied for patients with acne. The potential application of topical or oral probiotics, bacteriotherapy, and phage therapy for acne are further promising areas of future research.
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Affiliation(s)
- Clio Dessinioti
- 1st Department of Dermatology, Andreas Sygros Hospital, University of Athens, 5, Dragoumi Str, 16 121, Athens, Greece.
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12
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King AM, Zhang Z, Glassey E, Siuti P, Clardy J, Voigt CA. Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra. Nat Microbiol 2023; 8:2420-2434. [PMID: 37973865 DOI: 10.1038/s41564-023-01524-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.
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Affiliation(s)
- Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengan Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Piro Siuti
- Synthetic Biology Group, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, Kong HH, Segre JA. Integrated genomic and functional analyses of human skin-associated Staphylococcus reveal extensive inter- and intra-species diversity. Proc Natl Acad Sci U S A 2023; 120:e2310585120. [PMID: 37956283 PMCID: PMC10666031 DOI: 10.1073/pnas.2310585120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023] Open
Abstract
Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain-specific manners. To unlock the potential of engineering skin microbial communities, we aim to characterize the diversity of this genus within the context of the skin environment. We reanalyzed an extant 16S rRNA amplicon dataset obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant staphylococcal species present in all volunteers and were detected at all body sites. Pan-genome analysis of isolates from these three species revealed that the genus-core was dominated by central metabolism genes. Species-restricted-core genes encoded known host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.
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Affiliation(s)
- Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Shih-Queen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | | | - Heidi H. Kong
- Cutaneous Microbiome and Inflammation Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
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14
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Szekat C, Josten M, Rickmeyer J, Crüsemann M, Bierbaum G. A Staphylococcus capitis strain with unusual bacteriocin production. Microb Biotechnol 2023; 16:2181-2193. [PMID: 37850940 PMCID: PMC10616647 DOI: 10.1111/1751-7915.14356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Staphylococcus capitis is a member of the human and mammal skin microbiomes and is considered less harmful than Staphylococcus aureus. S. capitis subsp. urealyticus BN2 was isolated from a cat and expressed strong antibacterial activity against a range of Gram-positive species, most notably including S. aureus strains with resistance to methicillin (MRSA) and strains with intermediate resistance to vancomycin (VISA). These latter strains are normally relatively resistant to bacteriocins, due to cell wall and cell membrane modifications. Genomic sequencing showed that the strain harboured at least two complete gene clusters for biosynthesis of antagonistic substances. The complete biosynthetic gene cluster of the well-known lantibiotic gallidermin was encoded on a large plasmid and the mature peptide was present in isopropanol cell extracts. In addition, a chromosomal island contained a novel non-ribosomal peptide synthetase (NRPS) gene cluster. Accidental deletion of two NRPS modules and partial purification of the anti-VISA activity showed that this novel bacteriocin represents a complex of differently decorated, non-ribosomal peptides. Additionally, a number of phenol-soluble modulins (PSMs) was detected by mass spectrometry of whole cells. Producing these compounds, the strain was able to outcompete several S. aureus strains, including MRSA and VISA, in tube cultures.
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Affiliation(s)
- Christiane Szekat
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Michaele Josten
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of BonnBonnGermany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
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15
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Irfan B, Yaqoob A. Dermatological Implications of the Taqiyah and Imamah: Recommendations for Delivering Culturally Conscious Care. Cureus 2023; 15:e45528. [PMID: 37868539 PMCID: PMC10585659 DOI: 10.7759/cureus.45528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Background and objective The growing cultural and religious diversity in healthcare settings necessitates clinicians to integrate cultural competence and sensitivity into their practice. Despite significant research focusing on the hijab worn by Muslim women, there is a gap in understanding the dermatological implications of the taqiyah and imamah, worn by Muslim men. In light of this, this study aimed to offer insights into delivering culturally conscious dermatological care for Muslim men wearing these garments, thereby bridging a crucial knowledge gap. Materials and methods The study employed a comprehensive research strategy that encompassed both medical literature and foundational Islamic texts. PubMed, Web of Science, and Scopus were used for medical literature searches, while al-Maktabah al-Shamela and Sunnah.com, along with Quranic and Hadith translations were consulted for religious insights. A thematic analysis was employed to identify patterns, challenges, and unique points, ensuring a holistic understanding of the subject. Results Our findings revealed that wearing a taqiyah or imamah has both beneficial and detrimental dermatological effects, depending on factors such as climate, fabric, and hygiene practices. While the garments are rooted in Islamic tradition, their use varies based on cultural context rather than strict religious guidelines. Moreover, gender dynamics and the concept of privacy ('awrah) within Islamic teachings have implications for healthcare interactions. The study offers practical guidelines for dermatological care tailored to Muslim men wearing a taqiyah or imamah. It emphasizes the importance of material choice, hygiene practices, and the willingness of many Muslim men to be accommodating in medical settings, albeit with some reservations. The paper also discusses the role of telemedicine in culturally sensitive healthcare delivery, recommending measures such as secure communication channels and self-imaging options. Conclusion The paper provides comprehensive recommendations aimed at delivering culturally and religiously sensitive dermatological care to Muslim men wearing a taqiyah or imamah. By integrating both medical best practices and a nuanced understanding of Islamic customs, healthcare providers can foster a more trusting and effective care relationship, thereby improving patient satisfaction and dermatological outcomes.
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Affiliation(s)
- Bilal Irfan
- Microbiology and Immunology, University of Michigan, Ann Arbor, USA
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16
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Widaty S, Surachmiati L, Legiawati L, Sirait SP, Krisanti IA, Budianti WK, Miranda E, Rihatmadja R, Oktarina C. Scalp microbiome of healthy women wearing hijab compared to those not wearing hijab: a cross-sectional study. Sci Rep 2023; 13:11797. [PMID: 37479743 PMCID: PMC10361994 DOI: 10.1038/s41598-023-38903-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Use of hijab can influence the scalp's condition, including its microbiome. To date there has been no study comparing scalp microbiome in women wearing hijab to that in women not wearing hijab. This was a cross-sectional study conducted from August 2019 to April 2021. Healthy women aged 18 years old or older who had not undergone menopause were recruited. Those in the hijab group should wear hijab minimum 8 h a day for at least 5 years. After wash-out period, the sample was collected from the subject's scalp. Next Generation Sequencing (NGS) was performed with primer V3-V4 region of 16S rRNA and ITS1 DNA for bacteria and fungi, respectively. Alpha diversity and beta diversity were identified, along with functional analysis. Actinobacteria and Ascomycota were the most dominant phyla on the scalp. S. capitis was more prominent in the hijab group while S. cohnii was more prominent in non-hijab group. Additionally, M. restricta was more common in hijab group while M. globosa was more common in non-hijab group. This study emphasizes the difference of scalp microbiome in women wearing hijab compared to women not wearing hijab, which indicated that women wearing hijab are more prone to seborrheic dermatitis.
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Affiliation(s)
- Sandra Widaty
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia.
| | - Lis Surachmiati
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
| | - Lili Legiawati
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
| | - Sondang Pandjaitan Sirait
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
| | - Inge Ade Krisanti
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
| | - Windy Keumala Budianti
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
| | - Eliza Miranda
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
| | - Rahadi Rihatmadja
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
| | - Caroline Oktarina
- Department of Dermatology and Venereology, Faculty of Medicine Universitas Indonesia - Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, 10430, Indonesia
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17
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Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, Kong HH, Segre JA. Integrated genomic and functional analyses of human skin-associated Staphylococcus reveals extensive inter- and intra-species diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.22.546190. [PMID: 37503282 PMCID: PMC10370188 DOI: 10.1101/2023.06.22.546190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain specific manners. To unlock the potential of engineering skin microbial communities, we aim to fully characterize the functional diversity of this genus within the context of the skin environment. We conducted metagenome and pan-genome analyses of isolates obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant species present in all volunteers and were detected at all body sites. Pan-genome analysis of these three species revealed that the genus-core was dominated by central metabolism genes. Species-specific core genes were enriched in host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene-sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.
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Affiliation(s)
- Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Shih-Queen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | | | - Heidi H. Kong
- Cutaneous Microbiome and Inflammation Section, NIAMS, NIH, Bethesda, Maryland, USA
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
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18
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Huang C, Zhuo F, Han B, Li W, Jiang B, Zhang K, Jian X, Chen Z, Li H, Huang H, Dou X, Yu B. The updates and implications of cutaneous microbiota in acne. Cell Biosci 2023; 13:113. [PMID: 37344849 DOI: 10.1186/s13578-023-01072-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023] Open
Abstract
Acne is a chronic inflammatory skin disorder that profoundly impacts the quality of life of patients worldwide. While it is predominantly observed in adolescents, it can affect individuals across all age groups. Acne pathogenesis is believed to be a result of various endogenous and exogenous factors, but the precise mechanisms remain elusive. Recent studies suggest that dysbiosis of the skin microbiota significantly contributes to acne development. Specifically, Cutibacterium acnes, the dominant resident bacterial species implicated in acne, plays a critical role in disease progression. Various treatments, including topical benzoyl peroxide, systemic antibiotics, and photodynamic therapy, have demonstrated beneficial effects on the skin microbiota composition in acne patients. Of particular interest is the therapeutic potential of probiotics in acne, given its direct influence on the skin microbiota. This review summarizes the alterations in skin microbiota associated with acne, provides insight into its pathogenic role in acne, and emphasizes the potential of therapeutic interventions aimed at restoring microbial homeostasis for acne management.
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Affiliation(s)
- Cong Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Fan Zhuo
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Baoquan Han
- Department of Urology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Wenting Li
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Bin Jiang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Kaoyuan Zhang
- Biomedical Research Institute, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Xingling Jian
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Zhenzhen Chen
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Hui Li
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Haiyan Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Xia Dou
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Bo Yu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Shenzhen Key Laboratory for Translational Medicine of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China.
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19
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Nakatsuji T, Brinton SL, Cavagnero KJ, O'Neill AM, Chen Y, Dokoshi T, Butcher AM, Osuoji OC, Shafiq F, Espinoza JL, Dupont CL, Hata TR, Gallo RL. Competition between skin antimicrobial peptides and commensal bacteria in type 2 inflammation enables survival of S. aureus. Cell Rep 2023; 42:112494. [PMID: 37167061 DOI: 10.1016/j.celrep.2023.112494] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 05/13/2023] Open
Abstract
During inflammation, the skin deploys antimicrobial peptides (AMPs) yet during allergic inflammation it becomes more susceptible to Staphylococcus aureus. To understand this contradiction, single-cell sequencing of Il4ra-/- mice combined with skin microbiome analysis reveals that lower production of AMPs from interleukin-4 receptor α (IL-4Rα) activation selectively inhibits survival of antibiotic-producing strains of coagulase-negative Staphylococcus (CoNS). Diminished AMPs under conditions of T helper type 2 (Th2) inflammation enable expansion of CoNS strains without antibiotic activity and increase Staphylococcus aureus (S. aureus), recapitulating the microbiome on humans with atopic dermatitis. This response is rescued in Camp-/- mice or after topical steroids, since further inhibition of AMPs enables survival of antibiotic-producing CoNS strains. In conditions of Th17 inflammation, a higher expression of host AMPs is sufficient to directly inhibit S. aureus survival. These results show that antimicrobials produced by the host and commensal bacteria each act to control S. aureus on the skin.
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Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Samantha L Brinton
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kellen J Cavagnero
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alan M O'Neill
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yang Chen
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Tatsuya Dokoshi
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anna M Butcher
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Olive C Osuoji
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Faiza Shafiq
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Josh L Espinoza
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Tissa R Hata
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92037, USA.
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20
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The dynamic balance of the skin microbiome across the lifespan. Biochem Soc Trans 2023; 51:71-86. [PMID: 36606709 PMCID: PMC9988004 DOI: 10.1042/bst20220216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
For decades research has centered on identifying the ideal balanced skin microbiome that prevents disease and on developing therapeutics to foster this balance. However, this single idealized balance may not exist. The skin microbiome changes across the lifespan. This is reflected in the dynamic shifts of the skin microbiome's diverse, inter-connected community of microorganisms with age. While there are core skin microbial taxa, the precise community composition for any individual person is determined by local skin physiology, genetics, microbe-host interactions, and microbe-microbe interactions. As a key interface with the environment, the skin surface and its appendages are also constantly exchanging microbes with close personal contacts and the environment. Hormone fluctuations and immune system maturation also drive age-dependent changes in skin physiology that support different microbial community structures over time. Here, we review recent insights into the factors that shape the skin microbiome throughout life. Collectively, the works summarized within this review highlight how, depending on where we are in lifespan, our skin supports robust microbial communities, while still maintaining microbial features unique to us. This review will also highlight how disruptions to this dynamic microbial balance can influence risk for dermatological diseases as well as impact lifelong health.
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Smythe P, Wilkinson HN. The Skin Microbiome: Current Landscape and Future Opportunities. Int J Mol Sci 2023; 24:3950. [PMID: 36835363 PMCID: PMC9963692 DOI: 10.3390/ijms24043950] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.
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Affiliation(s)
- Paisleigh Smythe
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
| | - Holly N. Wilkinson
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
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22
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Lee SM, Keum HL, Sul WJ. Bacterial Crosstalk via Antimicrobial Peptides on the Human Skin: Therapeutics from a Sustainable Perspective. J Microbiol 2023; 61:1-11. [PMID: 36719618 DOI: 10.1007/s12275-022-00002-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 02/01/2023]
Abstract
The skin's epidermis is an essential barrier as the first guard against invading pathogens, and physical protector from external injury. The skin microbiome, which consists of numerous bacteria, fungi, viruses, and archaea on the epidermis, play a key role in skin homeostasis. Antibiotics are a fast-acting and effective treatment method, however, antibiotic use is a nuisance that can disrupt skin homeostasis by eradicating beneficial bacteria along with the intended pathogens and cause antibiotic-resistant bacteria spread. Increased numbers of antimicrobial peptides (AMPs) derived from humans and bacteria have been reported, and their roles have been well defined. Recently, modulation of the skin microbiome with AMPs rather than artificially synthesized antibiotics has attracted the attention of researchers as many antibiotic-resistant strains make treatment mediation difficult in the context of ecological problems. Herein, we discuss the overall insights into the skin microbiome, including its regulation by different AMPs, as well as their composition and role in health and disease.
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Affiliation(s)
- Seon Mi Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hye Lim Keum
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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23
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Chen H, Zhao Q, Zhong Q, Duan C, Krutmann J, Wang J, Xia J. Skin Microbiome, Metabolome and Skin Phenome, from the Perspectives of Skin as an Ecosystem. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:363-382. [PMID: 36939800 PMCID: PMC9712873 DOI: 10.1007/s43657-022-00073-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Accepted: 08/11/2022] [Indexed: 11/07/2022]
Abstract
Skin is a complex ecosystem colonized by millions of microorganisms, including bacteria, fungi, and viruses. Skin microbiota is believed to exert critical functions in maintaining host skin health. Profiling the structure of skin microbial community is the first step to overview the ecosystem. However, the community composition is highly individualized and extremely complex. To explore the fundamental factors driving the complexity of the ecosystem, namely the selection pressures, we review the present studies on skin microbiome from the perspectives of ecology. This review summarizes the following: (1) the composition of substances/nutrients in the cutaneous ecological environment that are derived from the host and the environment, highlighting their proposed function on skin microbiota; (2) the features of dominant skin commensals to occupy ecological niches, through self-adaptation and microbe-microbe interactions; (3) how skin microbes, by their structures or bioactive molecules, reshape host skin phenotypes, including skin immunity, maintenance of skin physiology such as pH and hydration, ultraviolet (UV) protection, odor production, and wound healing. This review aims to re-examine the host-microbe interactions from the ecological perspectives and hopefully to give new inspiration to this field.
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Affiliation(s)
- Huizhen Chen
- grid.8547.e0000 0001 0125 2443Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Qi Zhao
- grid.27255.370000 0004 1761 1174Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
- grid.435557.50000 0004 0518 6318IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, D-40225 Germany
| | - Qian Zhong
- grid.8547.e0000 0001 0125 2443Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Cheng Duan
- grid.8547.e0000 0001 0125 2443Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Guangzhou, 511458 China
| | - Jean Krutmann
- grid.435557.50000 0004 0518 6318IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, D-40225 Germany
| | - Jiucun Wang
- grid.8547.e0000 0001 0125 2443Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438 China
- grid.506261.60000 0001 0706 7839Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, 200438 China
| | - Jingjing Xia
- grid.8547.e0000 0001 0125 2443Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Guangzhou, 511458 China
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24
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Lee HJ, Kim M. Skin Barrier Function and the Microbiome. Int J Mol Sci 2022; 23:13071. [PMID: 36361857 PMCID: PMC9654002 DOI: 10.3390/ijms232113071] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 08/27/2023] Open
Abstract
Human skin is the largest organ and serves as the first line of defense against environmental factors. The human microbiota is defined as the total microbial community that coexists in the human body, while the microbiome refers to the collective genome of these microorganisms. Skin microbes do not simply reside on the skin but interact with the skin in a variety of ways, significantly affecting the skin barrier function. Here, we discuss recent insights into the symbiotic relationships between the microbiome and the skin barrier in physical, chemical, and innate/adaptive immunological ways. We discuss the gut-skin axis that affects skin barrier function. Finally, we examine the effects of microbiome dysbiosis on skin barrier function and the role of these effects in inflammatory skin diseases, such as acne, atopic dermatitis, and psoriasis. Microbiome cosmetics can help restore skin barrier function and improve these diseases.
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Affiliation(s)
| | - Miri Kim
- Department of Dermatology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, #10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea
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Mäenpää K, Wang S, Ilves M, El-Nezami H, Alenius H, Sinkko H, Karisola P. Skin microbiota of oxazolone-induced contact hypersensitivity mouse model. PLoS One 2022; 17:e0276071. [PMID: 36264944 PMCID: PMC9584374 DOI: 10.1371/journal.pone.0276071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Contact allergy is a common skin allergy, which can be studied utilising contact hypersensitivity (CHS) animal model. However, it is not clear, whether CHS is a suitable model to investigate skin microbiota interactions. We characterised the effect of contact dermatitis on the skin microbiota and studied the biological effects of oxazolone (OXA) -induced inflammation on skin thickness, immune cell numbers and changes of the microbiota in CHS mouse model (n = 72) for 28 days. Through 16S rRNA gene sequencing we defined the composition of bacterial communities and associations of bacteria with inflammation. We observed that the vehicle solution of acetone and olive oil induced bacterial community changes on day 1, and OXA-induced changes were observed mainly on day 7. Many of the notably enriched bacteria present in the OXA-challenged positive group represented the genus Faecalibaculum which were most likely derived from the cage environment. Additionally, skin inflammation correlated negatively with Streptococcus, which is considered a native skin bacterium, and positively with Muribacter muris, which is typical in oral environment. Skin inflammation favoured colonisation of cage-derived faecal bacteria, and additionally mouse grooming transferred oral bacteria on the skin. Due to the observed changes, we conclude that CHS model could be used for certain skin microbiome-related research set-ups. However, since vehicle exposure can alter the skin microbiome as such, future studies should include considerations such as careful control sampling and statistical tests to account for potential confounding factors.
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Affiliation(s)
- Kuunsäde Mäenpää
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Shuyuan Wang
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong
| | - Marit Ilves
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Hani El-Nezami
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong
| | - Harri Alenius
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
| | - Hanna Sinkko
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Piia Karisola
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- * E-mail:
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26
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Tham KC, Lefferdink R, Duan K, Lim SS, Wong XFCC, Ibler E, Wu B, Abu-Zayed H, Rangel SM, Del Duca E, Chowdhury M, Chima M, Kim HJ, Lee B, Guttman-Yassky E, Paller AS, Common JEA. Distinct skin microbiome community structures in congenital ichthyosis. Br J Dermatol 2022; 187:557-570. [PMID: 35633118 PMCID: PMC10234690 DOI: 10.1111/bjd.21687] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 03/28/2022] [Accepted: 05/21/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND The ichthyoses are rare genetic keratinizing disorders that share the characteristics of an impaired epidermal barrier and increased risk of microbial infections. Although ichthyotic diseases share a T helper (Th) 17 cell immune signature, including increased expression of antimicrobial peptides, the skin microbiota of ichthyoses is virtually unexplored. OBJECTIVES To analyse the metagenome profile of skin microbiome for major congenital ichthyosis subtypes. METHODS Body site-matched skin surface samples were collected from the scalp, upper arm and upper buttocks of 16 healthy control participants and 22 adult patients with congenital forms of ichthyosis for whole metagenomics sequencing analysis. RESULTS Taxonomic profiling showed significant shifts in bacteria and fungi abundance and sporadic viral increases across ichthyosis subtypes. Cutibacterium acnes and Malassezia were significantly reduced across body sites, consistent with skin barrier disruption and depletion of lipids. Microbial richness was reduced, with specific increases in Staphylococcus and Corynebacterium genera, as well as shifts in fungal species, including Malassezia. Malassezia globosa was reduced at all body sites, whereas M. sympodialis was reduced in the ichthyotic upper arm and upper buttocks. Malassezia slooffiae, by contrast, was strikingly increased at all body sites in participants with congenital ichthyosiform erythroderma (CIE) and lamellar ichthyosis (LI). A previously undescribed Trichophyton species was also detected as sporadically colonizing the skin of patients with CIE, LI and epidermolytic ichthyosis subtypes. CONCLUSIONS The ichthyosis skin microbiome is significantly altered from healthy skin with specific changes predominating among ichthyosis subtypes. Skewing towards the Th17 pathway may represent a response to the altered microbial colonization in ichthyosis. What is already known about this topic? The skin microbiome of congenital ichthyoses is largely unexplored. Microbes play an important role in pathogenesis, as infections are common. The relative abundances of staphylococci and corynebacteria is increased in the cutaneous microbiome of patients with Netherton syndrome, but extension of these abundances to all congenital ichthyoses is unexplored. What does this study add? A common skin microbiome signature was observed across congenital ichthyoses. Distinct microbiome features were associated with ichthyosis subtypes. Changes in microbiome may contribute to T helper 17 cell immune polarization. What is the translational message? These data provide the basis for comparison of the microbiome with lipidomic and transcriptomic alterations in these forms of ichthyosis and consideration of correcting the dysbiosis as a therapeutic intervention.
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Affiliation(s)
- Khek-Chian Tham
- A*STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-10 Immunos, Singapore, 138648, Singapore
| | - Rachel Lefferdink
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kaibo Duan
- Singapore Immunology Network, Agency for Science, Technology and Research, 8A Biomedical Grove, #03 Immunos, Singapore, 138648, Singapore
| | - Seong Soo Lim
- A*STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-10 Immunos, Singapore, 138648, Singapore
| | - X F Colin C Wong
- A*STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-10 Immunos, Singapore, 138648, Singapore
| | - Erin Ibler
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benedict Wu
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hajar Abu-Zayed
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Ester Del Duca
- Icahn School of Medicine at Mount Sinai Medical Center, New York, NY, USA
| | - Mashkura Chowdhury
- Icahn School of Medicine at Mount Sinai Medical Center, New York, NY, USA
| | - Margot Chima
- Icahn School of Medicine at Mount Sinai Medical Center, New York, NY, USA
| | - Hee Jee Kim
- Icahn School of Medicine at Mount Sinai Medical Center, New York, NY, USA
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, 8A Biomedical Grove, #03 Immunos, Singapore, 138648, Singapore
| | | | - Amy S Paller
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John E A Common
- A*STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-10 Immunos, Singapore, 138648, Singapore
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27
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Chong CE, Bengtsson RJ, Horsburgh MJ. Comparative genomics of Staphylococcus capitis reveals species determinants. Front Microbiol 2022; 13:1005949. [PMID: 36246238 PMCID: PMC9563023 DOI: 10.3389/fmicb.2022.1005949] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Staphylococcus capitis is primarily described as a human skin commensal but is now emergent as an opportunistic pathogen isolated from the bloodstream and prosthetic joint infections, and neonatal intensive care unit (NICU)-associated sepsis. We used comparative genomic analyses of S. capitis to provide new insights into commensal scalp isolates from varying skin states (healthy, dandruff lesional, and non-lesional), and to expand our current knowledge of the species populations (scalp isolates, n = 59; other skin isolates, n = 7; publicly available isolates, n = 120). A highly recombinogenic population structure was revealed, with genomes including the presence of a range of previously described staphylococcal virulence factors, cell wall-associated proteins, and two-component systems. Genomic differences between the two described S. capitis subspecies were explored, which revealed the determinants associated exclusively with each subspecies. The subspecies ureolyticus was distinguished from subspecies capitis based on the differences in antimicrobial resistance genes, β-lactam resistance genes, and β-class phenol soluble modulins and gene clusters linked to biofilm formation and survival on skin. This study will aid further research into the classification of S. capitis and virulence-linked phylogroups to monitor the spread and evolution of S. capitis.
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28
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Ahle CM, Stødkilde K, Poehlein A, Bömeke M, Streit WR, Wenck H, Reuter JH, Hüpeden J, Brüggemann H. Interference and co-existence of staphylococci and Cutibacterium acnes within the healthy human skin microbiome. Commun Biol 2022; 5:923. [PMID: 36071129 PMCID: PMC9452508 DOI: 10.1038/s42003-022-03897-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/25/2022] [Indexed: 12/12/2022] Open
Abstract
Human skin is populated by trillions of microbes collectively called the skin microbiome. Staphylococcus epidermidis and Cutibacterium acnes are among the most abundant members of this ecosystem, with described roles in skin health and disease. However, knowledge regarding the health beneficial effects of these ubiquitous skin residents is still limited. Here, we profiled the staphylococcal and C. acnes landscape across four different skin sites of 30 individuals (120 skin samples) using amplicon-based next-generation sequencing. Relative abundance profiles obtained indicated the existence of phylotype-specific co-existence and exclusion scenarios. Co-culture experiments with 557 staphylococcal strains identified 30 strains exhibiting anti-C. acnes activities. Notably, staphylococcal strains were found to selectively exclude acne-associated C. acnes and co-exist with healthy skin-associated phylotypes, through regulation of the antimicrobial activity. Overall, these findings highlight the importance of skin-resident staphylococci and suggest that selective microbial interference is a contributor to healthy skin homeostasis. The dynamic interaction between the common resident skin microbes Staphylococcus epidermidis and Cutibacterium acnes is uncovered, showing that S. epidermidis can selectively exclude acne-associated C. acnes strains from the human skin.
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Affiliation(s)
- Charlotte Marie Ahle
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany. .,Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
| | | | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37073, Göttingen, Germany
| | - Mechthild Bömeke
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37073, Göttingen, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Horst Wenck
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Jörn Hendrik Reuter
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Jennifer Hüpeden
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Holger Brüggemann
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark.
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Transitory Shifts in Skin Microbiota Composition and Reductions in Bacterial Load and Psoriasin following Ethanol Perturbation. mSphere 2022; 7:e0017122. [PMID: 35727021 PMCID: PMC9429936 DOI: 10.1128/msphere.00171-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Personal care and hygiene regimens may substantially alter the composition of the skin microbiota through direct and indirect mechanisms. An understanding of the timescales of commensal skin microbiota reestablishment following perturbation is required to inform consumer safety risk assessment, and support product development. In the current investigation, the microbiota of the volar and dorsal forearm of 10 volunteers was sampled immediately before and after wiping with 70% ethanol and at up to 24 h afterwards. Quantitative PCR and amplicon sequencing were used to measure microbial load and composition, and concentrations of the antimicrobial peptide psoriasin were measured using an enzyme-linked immunosorbent assay (ELISA). Ethanol wiping significantly reduced the total bacterial abundance at 2 h post-wipe. Recovery was observed after 6 h for total bacterial populations and for Staphylococcus epidermidis depending on the site tested. Microbiome diversity recovered by 6 h after wiping. Psoriasin concentrations were highly variable between volunteers, ranging from 42 to 1,569 ng/mL, and dorsal concentrations were significantly higher than volar concentrations (P < 0.05). For most of the volunteers, the application of ethanol decreased psoriasin concentrations, particularly for the dorsal samples, but the overall effect was not significant. This work extends observations of skin microbiome stability and demonstrates resilience in a key antimicrobial peptide. IMPORTANCE An understanding of the timescales of commensal skin microbiota reestablishment following perturbation is required to inform consumer safety risk assessment and support product development. Following ethanol exposure, total bacterial populations and microbiome diversity recovered after 6 h. For most of the volunteers, the application of ethanol decreased psoriasin concentrations, but the overall effect was not significant. This work extends observations of skin microbiome stability and demonstrates resilience in a key antimicrobial peptide.
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Lin X, Li YZ, Chen T, Min SH, Wang DF, Ding MM, Jiang G. Effects of wearing personal protective equipment during COVID-19 pandemic on composition and diversity of skin bacteria and fungi of medical workers. J Eur Acad Dermatol Venereol 2022; 36:1612-1622. [PMID: 35538594 PMCID: PMC9348071 DOI: 10.1111/jdv.18216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/21/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND During the COVID-19 pandemic, wearing PPE can induce skin damage such as erythema, pruritus, erosion, and ulceration among others. Although the skin microbiome is considered important for skin health, the change of the skin microbiome after wearing PPE remain unknown. OBJECTIVE The present study aimed to characterize the diversity and structure of bacterial and fungal flora on skin surfaces of healthcare workers wearing personal protective equipment (PPE) during the COVID-19 pandemic using metagenomic next-generation sequencing (mNGS). METHODS A total of 10 Chinese volunteers were recruited and the microbiome of their face, hand, and back were analyzed before and after wearing PPE. Moreover, VISIA was used to analyze skin features. RESULTS Results of alpha bacterial diversity showed that there was statistically significant decrease in alpha diversity indice in the skin samples from face, hand, and three sites after wearing PPE as compared with the indice in the skin samples before wearing PPE. Further, the results of evaluated alpha fungal diversity show that there was a statistically significant decrease in alpha diversity indices in the skin samples from hand after wearing PPE as compared with the indices in the skin samples before wearing PPE (P<0.05). Results of the current study found that the main bacteria on the face, hand, and back skin samples before wearing the PPE were Propionibacterium spp. (34.04%), Corynebacterium spp. (13.12%), and Staphylococcus spp. (38.07%). The main bacteria found on the skin samples after wearing the PPE were Staphylococcus spp. (31.23%), Xanthomonas spp. (26.21%), and Cutibacterium spp. (42.59%). The fungal community composition was similar in three skin sites before and after wearing PPE. CONCLUSION It was evident that wearing PPE may affect the skin microbiota, especially bacteria. Therefore, it was evident that the symbiotic microbiota may reflect the skin health of medical workers during the COVID-19 pandemic.
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Affiliation(s)
- X Lin
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Y Z Li
- Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - T Chen
- Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - S H Min
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - D F Wang
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - M M Ding
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - G Jiang
- Department of dermatology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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31
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Dagnelie MA, Poinas A, Dréno B. What is new in adult acne for the last 2 years: focus on acne pathophysiology and treatments. Int J Dermatol 2022; 61:1205-1212. [PMID: 35521784 DOI: 10.1111/ijd.16220] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/07/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022]
Abstract
Acne affects more than 640 million people worldwide, including about 85% of adolescents. This inflammatory dermatosis affects the entire population, from teenagers to adults, which reinforces the need to investigate it. Furthermore, in adults, acne has serious consequences, including a psychological impact, low self-esteem, social isolation, and depression. Over the last years, the understanding of acne pathophysiology has improved, mainly thanks to the identification of the pivotal role of the microbiota. The aim of this review was to screen the most recent scientific literature on adult acne and the newly tested treatments. Clinically, therapeutic innovations for the treatment of acne have been recently developed, including pre/probiotics, new molecules, and innovative formulations associated, however, with fewer side effects. Moreover, clinical trials are underway to use off-label molecules that seem to be proving their value in the fight against adult acne.
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Affiliation(s)
- Marie-Ange Dagnelie
- Nantes Université, Univ Angers, INSERM, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302, Nantes, France
| | - Alexandra Poinas
- Nantes Université, Univ Angers, INSERM, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302, Nantes, France
| | - Brigitte Dréno
- Nantes Université, Univ Angers, INSERM, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302, Nantes, France
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Stødkilde K, Nielsen JT, Petersen SV, Paetzold B, Brüggemann H, Mulder FAA, Andersen CBF. Solution Structure of the Cutibacterium acnes-Specific Protein RoxP and Insights Into Its Antioxidant Activity. Front Cell Infect Microbiol 2022; 12:803004. [PMID: 35223541 PMCID: PMC8873378 DOI: 10.3389/fcimb.2022.803004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Cutibacterium acnes is a predominant bacterium on human skin and is generally regarded as commensal. Recently, the abundantly secreted protein produced by C. acnes, RoxP, was shown to alleviate radical-induced cell damage, presumably via antioxidant activity, which could potentially be harnessed to fortify skin barrier function. The aim of this study was to determine the structure of RoxP and elucidate the mechanisms behind its antioxidative effect. Here, we present the solution structure of RoxP revealing a compact immunoglobulin-like domain containing a long flexible loop which, in concert with the core domain, forms a positively charged groove that could function as a binding site for cofactors or substrates. Although RoxP shares structural features with cell-adhesion proteins, we show that it does not appear to be responsible for adhesion of C. acnes bacteria to human keratinocytes. We identify two tyrosine-containing stretches located in the flexible loop of RoxP, which appear to be responsible for the antioxidant activity of RoxP.
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Affiliation(s)
| | | | | | | | | | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
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Cobian N, Garlet A, Hidalgo-Cantabrana C, Barrangou R. Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications. Front Microbiol 2021; 12:758749. [PMID: 34803983 PMCID: PMC8595920 DOI: 10.3389/fmicb.2021.758749] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022] Open
Abstract
Cutibacterium acnes is an important member of the human skin microbiome and plays a critical role in skin health and disease. C. acnes encompasses different phylotypes that have been found to be associated with different skin phenotypes, suggesting a genetic basis for their impact on skin health. Here, we present a comprehensive comparative analysis of 255 C. acnes genomes to provide insights into the species genetic diversity and identify unique features that define various phylotypes. Results revealed a relatively small and open pan genome (6,240 genes) with a large core genome (1,194 genes), and three distinct phylogenetic clades, with multiple robust sub-clades. Furthermore, we identified several unique gene families driving differences between distinct C. acnes clades. Carbohydrate transporters, stress response mechanisms and potential virulence factors, potentially involved in competitive growth and host colonization, were detected in type I strains, which are presumably responsible for acne. Diverse type I-E CRISPR-Cas systems and prophage sequences were detected in select clades, providing insights into strain divergence and adaptive differentiation. Collectively, these results enable to elucidate the fundamental differences among C. acnes phylotypes, characterize genetic elements that potentially contribute to type I-associated dominance and disease, and other key factors that drive the differentiation among clades and sub-clades. These results enable the use of comparative genomics analyses as a robust method to differentiate among the C. acnes genotypes present in the skin microbiome, opening new avenues for the development of biotherapeutics to manipulate the skin microbiota.
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Affiliation(s)
- Natalia Cobian
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | | | - Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021; 19:726-739. [PMID: 34075213 DOI: 10.1038/s41579-021-00569-w] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
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Affiliation(s)
- Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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35
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O'Neill AM, Worthing KA, Kulkarni N, Li F, Nakatsuji T, McGrosso D, Mills RH, Kalla G, Cheng JY, Norris JM, Pogliano K, Pogliano J, Gonzalez DJ, Gallo RL. Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius. eLife 2021; 10:66793. [PMID: 34664551 PMCID: PMC8592530 DOI: 10.7554/elife.66793] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/02/2021] [Indexed: 12/13/2022] Open
Abstract
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important emerging zoonotic pathogen that causes severe skin infections. To combat infections from drug-resistant bacteria, the transplantation of commensal antimicrobial bacteria as a therapeutic has shown clinical promise. We screened a collection of diverse staphylococcus species from domestic dogs and cats for antimicrobial activity against MRSP. A unique strain (S. felis C4) was isolated from feline skin that inhibited MRSP and multiple gram-positive pathogens. Whole genome sequencing and mass spectrometry revealed several secreted antimicrobials including a thiopeptide bacteriocin micrococcin P1 and phenol-soluble modulin beta (PSMβ) peptides that exhibited antimicrobial and anti-inflammatory activity. Fluorescence and electron microscopy revealed that S. felis antimicrobials inhibited translation and disrupted bacterial but not eukaryotic cell membranes. Competition experiments in mice showed that S. felis significantly reduced MRSP skin colonization and an antimicrobial extract from S. felis significantly reduced necrotic skin injury from MRSP infection. These findings indicate a feline commensal bacterium that could be utilized in bacteriotherapy against difficult-to-treat animal and human skin infections.
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Affiliation(s)
- Alan M O'Neill
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Kate A Worthing
- College of Veterinary Medicine, University of Arizona, Oro Valley, United States
| | - Nikhil Kulkarni
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Fengwu Li
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Dominic McGrosso
- Department of Pharmacology, University of California, San Diego, San Diego, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, United States
| | - Robert H Mills
- Department of Pharmacology, University of California, San Diego, San Diego, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, United States
| | - Gayathri Kalla
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | - Joyce Y Cheng
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Jacqueline M Norris
- Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, San Diego, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, United States
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, San Diego, United States
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Lunjani N, Ahearn-Ford S, Dube FS, Hlela C, O'Mahony L. Mechanisms of microbe-immune system dialogue within the skin. Genes Immun 2021; 22:276-288. [PMID: 33993202 PMCID: PMC8497273 DOI: 10.1038/s41435-021-00133-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/09/2021] [Accepted: 04/26/2021] [Indexed: 02/01/2023]
Abstract
The prevalence and severity of dermatological conditions such as atopic dermatitis have increased dramatically during recent decades. Many of the factors associated with an altered risk of developing inflammatory skin disorders have also been shown to alter the composition and diversity of non-pathogenic microbial communities that inhabit the human host. While the most densely microbial populated organ is the gut, culture and non-culture-based technologies have revealed a dynamic community of bacteria, fungi, viruses and mites that exist on healthy human skin, which change during disease. In this review, we highlight some of the recent findings on the mechanisms through which microbes interact with each other on the skin and the signalling systems that mediate communication between the immune system and skin-associated microbes. In addition, we summarize the ongoing clinical studies that are targeting the microbiome in patients with skin disorders. While significant efforts are still required to decipher the mechanisms underpinning host-microbe communication relevant to skin health, it is likely that disease-related microbial communities, or Dermatypes, will help identify personalized treatments and appropriate microbial reconstitution strategies.
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Affiliation(s)
- Nonhlanhla Lunjani
- Department of Dermatology, University of Cape Town, Cape Town, South Africa
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Felix S Dube
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Carol Hlela
- Department of Dermatology, University of Cape Town, Cape Town, South Africa
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
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37
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Early development of the skin microbiome: therapeutic opportunities. Pediatr Res 2021; 90:731-737. [PMID: 32919387 PMCID: PMC7952468 DOI: 10.1038/s41390-020-01146-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/23/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023]
Abstract
As human skin hosts a diverse microbiota in health and disease, there is an emerging consensus that dysregulated interactions between host and microbiome may contribute to chronic inflammatory disease of the skin. Neonatal skin is a unique habitat, structurally similar to the adult but with a different profile of metabolic substrates, environmental stressors, and immune activity. The surface is colonized within moments of birth with a bias toward maternal strains. Initial colonists are outcompeted as environmental exposures increase and host skin matures. Nonetheless, early life microbial acquisitions may have long-lasting effects on health through modulation of host immunity and competitive interactions between bacteria. Microbial ecology and its influence on health have been of interest to dermatologists for >50 years, and an explosion of recent interest in the microbiome has prompted ongoing investigations of several microbial therapeutics for dermatological disease. In this review, we consider how recent insight into the host and microbial factors driving development of the skin microbiome in early life offers new opportunities for therapeutic intervention. IMPACT: Advancement in understanding molecular mechanisms of bacterial competition opens new avenues of investigation into dermatological disease. Primary development of the skin microbiome is determined by immunological features of the cutaneous habitat. Understanding coordinated microbial and immunological development in the pediatric patient requires a multidisciplinary synthesis of primary literature.
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38
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Mechanisms for control of skin immune function by the microbiome. Curr Opin Immunol 2021; 72:324-330. [PMID: 34537476 DOI: 10.1016/j.coi.2021.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
The skin represents the largest area for direct contact between microbes and host immunocytes and is a site for constant communication between the host and this diverse and essential microbial community. Coagulase-negative staphylococci are an abundant bacterial genus on the human skin and are regulated through various mechanisms that include the epidermal barrier environment and innate and adaptive immune systems within the epidermis and dermis. In turn, some species and strains of these bacteria produce beneficial products that augment host immunity by exerting specifically targeted antimicrobial, anti-inflammatory, or anti-neoplastic activity while also promoting broad innate and adaptive immune responses. The use of selected skin commensals as a therapeutic has shown promise in recent human clinical trials. This emerging concept of bacteriotherapy is defining mechanisms of action and validating the dependence on the microbiome for maintenance of immune homeostasis.
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Ahle CM, Stødkilde-Jørgensen K, Poehlein A, Streit WR, Hüpeden J, Brüggemann H. Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin. BMC Microbiol 2021; 21:221. [PMID: 34320945 PMCID: PMC8320028 DOI: 10.1186/s12866-021-02284-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/21/2021] [Indexed: 02/08/2023] Open
Abstract
Background Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution. Results Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis. Conclusions Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02284-1.
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Affiliation(s)
- Charlotte Marie Ahle
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany.,Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | | | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37073, Göttingen, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Jennifer Hüpeden
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Holger Brüggemann
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark.
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40
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Rademacher F, Gläser R, Harder J. Antimicrobial peptides and proteins: Interaction with the skin microbiota. Exp Dermatol 2021; 30:1496-1508. [PMID: 34310774 DOI: 10.1111/exd.14433] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/25/2021] [Accepted: 07/14/2021] [Indexed: 12/18/2022]
Abstract
The cutaneous microbiota comprises all living skin microorganisms. There is increasing evidence that the microbiota plays a crucial role in skin homeostasis. Accordingly, a dysbiosis of the microbiota may trigger cutaneous inflammation. The need for a balanced microbiota requires specific regulatory mechanisms that control and shape the microbiota. In this review, we highlight the present knowledge suggesting that antimicrobial peptides (AMPs) may exert a substantial influence on the microbiota by controlling their growth. This is supported by own data showing the differential influence of principal skin-derived AMPs on commensal staphylococci. Vice versa, we also illuminate how the cutaneous microbiota interacts with skin-derived AMPs by modulating AMP expression and how microbiota members protect themselves from the antimicrobial activity of AMPs. Taken together, the current picture suggests that a fine-tuned and well-balanced AMP-microbiota interplay on the skin surface may be crucial for skin health.
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Affiliation(s)
| | - Regine Gläser
- Department of Dermatology, Kiel University, Kiel, Germany
| | - Jürgen Harder
- Department of Dermatology, Kiel University, Kiel, Germany
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41
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Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes. Anaerobe 2021; 71:102411. [PMID: 34265438 DOI: 10.1016/j.anaerobe.2021.102411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/23/2021] [Accepted: 06/27/2021] [Indexed: 11/22/2022]
Abstract
In 2016, a new species name Cutibacterium acnes was coined for the well-documented species, Propionibacterium acnes, one of the most successful and clinically important skin commensals. The nomenclatural changes were brought about through creation of the genus Cutibacterium, when a group of propionibacteria isolates from the skin were transferred from the genus Propionibacterium and placed in the phylum Actinobacteria. Almost simultaneously, the discovery of two novel species of Cutibacterium occurred and the proposal of three subspecies of C. acnes were reported. These dramatic changes that occurred in a long-established taxon made it challenging for the non-specialist to correlate the huge volume of hitherto published work with current findings. In this review, we aim to correlate the eco-specificity and pathophysiological properties of these newly circumscribed taxa. We envisage that this information will shed light on the pathogenic potential of new isolates and enable better assessment of their clinical importance in the foreseeable future. Currently, five species are recognized within the genus: Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, Cutibacterium modestum (previously, "Propionibacterium humerusii"), and Cutibacterium namnetense. These reside in different niches reflecting their uniqueness in their genetic makeup. Their pathogenicity includes acne inflammation, sarcoidosis, progressive macular hypomelanosis, prostate cancer, and infections (bone, lumbar disc, and heart). This is also the case for the three newly described subspecies of C. acnes, which are C. acnes subspecies acnes (C. acnes type I), subspecies defendens (C. acnes type II), and subspecies elongatum (C. acnes type III). C. acnes subspecies acnes is related to inflamed acne and sarcoidosis, while subspecies defendens to prostate cancer and subspecies elongatum to progressive macular hypomelanosis. Because the current nomenclature is based upon polyphasic analyses of the biochemical and pathogenic characteristics and comparative genomics, it provides a sound basis studying the pathophysiological roles of these species.
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42
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Abstract
The skin microbiome is an ecosystem comprised of a multitude of microbial species interacting with their surroundings, including other microbes and host epithelial and immune cells. These interactions are the basis of important roles within the skin microbiome that provide benefit to the host, boosting multiple aspects of barrier function, a critical function of this essential organ. However, with reward always comes risk; resident skin microbes function in a context-dependent manner, set on the backdrop of a dynamic host and microbial milieu. Here, we discuss the reward of hosting a microbial ecosystem on the skin, including protection from pathogens and tuning of the skin microenvironment. We also give consideration to how these skin residents, often termed "commensals" can cause disorder, damage, and promote skin disease.
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Affiliation(s)
- Laurice Flowers
- Department of Dermatology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth A Grice
- Department of Dermatology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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43
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Nakatsuji T, Hata TR, Tong Y, Cheng JY, Shafiq F, Butcher AM, Salem SS, Brinton SL, Rudman Spergel AK, Johnson K, Jepson B, Calatroni A, David G, Ramirez-Gama M, Taylor P, Leung DYM, Gallo RL. Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial. Nat Med 2021; 27:700-709. [PMID: 33619370 PMCID: PMC8052297 DOI: 10.1038/s41591-021-01256-2] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 01/15/2021] [Indexed: 01/31/2023]
Abstract
Staphylococcus aureus colonizes patients with atopic dermatitis (AD) and exacerbates disease by promoting inflammation. The present study investigated the safety and mechanisms of action of Staphylococcus hominis A9 (ShA9), a bacterium isolated from healthy human skin, as a topical therapy for AD. ShA9 killed S. aureus on the skin of mice and inhibited expression of a toxin from S. aureus (psmα) that promotes inflammation. A first-in-human, phase 1, double-blinded, randomized 1-week trial of topical ShA9 or vehicle on the forearm skin of 54 adults with S. aureus-positive AD (NCT03151148) met its primary endpoint of safety, and participants receiving ShA9 had fewer adverse events associated with AD. Eczema severity was not significantly different when evaluated in all participants treated with ShA9 but a significant decrease in S. aureus and increased ShA9 DNA were seen and met secondary endpoints. Some S. aureus strains on participants were not directly killed by ShA9, but expression of mRNA for psmα was inhibited in all strains. Improvement in local eczema severity was suggested by post-hoc analysis of participants with S. aureus directly killed by ShA9. These observations demonstrate the safety and potential benefits of bacteriotherapy for AD.
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Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Tissa R Hata
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Yun Tong
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Joyce Y Cheng
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Faiza Shafiq
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Anna M Butcher
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Secilia S Salem
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Samantha L Brinton
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda K Rudman Spergel
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keli Johnson
- Rho Federal Systems Division, Inc., Durham, NC, USA
| | - Brett Jepson
- Rho Federal Systems Division, Inc., Durham, NC, USA
| | | | - Gloria David
- Rho Federal Systems Division, Inc., Durham, NC, USA
| | - Marco Ramirez-Gama
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Patricia Taylor
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Donald Y M Leung
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA.
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44
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Nakamura K, O'Neill AM, Williams MR, Cau L, Nakatsuji T, Horswill AR, Gallo RL. Short chain fatty acids produced by Cutibacterium acnes inhibit biofilm formation by Staphylococcus epidermidis. Sci Rep 2020; 10:21237. [PMID: 33277548 PMCID: PMC7718897 DOI: 10.1038/s41598-020-77790-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Biofilm formation by bacterial pathogens is associated with numerous human diseases and can confer resistance to both antibiotics and host defenses. Many strains of Staphylococcus epidermidis are capable of forming biofilms and are important human pathogens. Since S. epidermidis coexists with abundant Cutibacteria acnes on healthy human skin and does not typically form a biofilm in this environment, we hypothesized that C. acnes may influence biofilm formation of S. epidermidis. Culture supernatants from C. acnes and other species of Cutibacteria inhibited S. epidermidis but did not inhibit biofilms by Pseudomonas aeruginosa or Bacillus subtilis, and inhibited biofilms by S. aureus to a lesser extent. Biofilm inhibitory activity exhibited chemical properties of short chain fatty acids known to be produced from C. acnes. The addition of the pure short chain fatty acids propionic, isobutyric or isovaleric acid to S. epidermidis inhibited biofilm formation and, similarly to C. acnes supernatant, reduced polysaccharide synthesis by S. epidermidis. Both short chain fatty acids and C. acnes culture supernatant also increased sensitivity of S. epidermidis to antibiotic killing under biofilm-forming conditions. These observations suggest the presence of C. acnes in a diverse microbial community with S. epidermidis can be beneficial to the host and demonstrates that short chain fatty acids may be useful to limit formation of a biofilm by S. epidermidis.
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Affiliation(s)
- Kouki Nakamura
- Department of Dermatology, University of California San Diego, 9500 Gillman Dr. #0869, La Jolla, CA, 92093, USA
| | - Alan M O'Neill
- Department of Dermatology, University of California San Diego, 9500 Gillman Dr. #0869, La Jolla, CA, 92093, USA
| | - Michael R Williams
- Department of Dermatology, University of California San Diego, 9500 Gillman Dr. #0869, La Jolla, CA, 92093, USA
| | - Laura Cau
- Department of Dermatology, University of California San Diego, 9500 Gillman Dr. #0869, La Jolla, CA, 92093, USA
- SILAB, R&D Department, Brive, France
| | - Teruaki Nakatsuji
- Department of Dermatology, University of California San Diego, 9500 Gillman Dr. #0869, La Jolla, CA, 92093, USA
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, USA
| | - Richard L Gallo
- Department of Dermatology, University of California San Diego, 9500 Gillman Dr. #0869, La Jolla, CA, 92093, USA.
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Abstract
Multidisciplinary investigations into the pathogenesis of acne have significantly progressed over the past three years. Studies of the etiology of acne from the perspectives, for example, of sebaceous gland biology, sebum, genetics, keratinization, differentiation, hair cycles, immunology, bacteriology, and wound healing have elucidated its pathogenesis. This has led to the development of new therapies and paved the way for advanced studies that will enable the further evolution of acne treatment.
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Affiliation(s)
- Ichiro Kurokawa
- Department of Dermatology, Acne Clinical Research Center, Meiwa Hospital, Nishinomiya, Hyogo, 663-8186, Japan
| | - Keisuke Nakase
- Department of Microbiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
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