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Ruuskanen MO, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R, Lahti L. Towards standardized and reproducible research in skin microbiomes. Environ Microbiol 2022; 24:3840-3860. [PMID: 35229437 PMCID: PMC9790573 DOI: 10.1111/1462-2920.15945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022]
Abstract
Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.
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Affiliation(s)
- Matti O. Ruuskanen
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| | - Deepti Vats
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Renuka Potbhare
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Ameeta RaviKumar
- Institute of Bioinformatics and BiotechnologySavitribai Phule Pune UniversityPuneIndia
| | - Eveliina Munukka
- Microbiome Biobank, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Richa Ashma
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Leo Lahti
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
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Ogura K, Furuya H, Takahashi N, Shibata K, Endo M, Watanabe S, Cui L, Miyoshi-Akiyama T, Okamoto S, Ogai K, Sugama J. Interspecies Regulation Between Staphylococcus caprae and Staphylococcus aureus Colonized on Healed Skin After Injury. Front Microbiol 2022; 13:818398. [PMID: 35300478 PMCID: PMC8921658 DOI: 10.3389/fmicb.2022.818398] [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: 11/19/2021] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
Staphylococcus spp. colonize commensally on the human skin. Some commensal coagulase-negative staphylococci and Staphylococcus aureus are also involved in nosocomial infections. Bacteria were collected from skin healed from pressure injury (PI). After the collection time points, some patients suffered from recurrent PI (RPI). This study analyzed the characteristics of Staphylococcus spp. on healed skin before recurrence between healed skin that suffered from RPI within 6 weeks (RPI group) and healed skin that did not suffer within the duration (non-RPI group) by Staphylococcus spp.-specific sequencing. Of the seven patients in the RPI group, two were dominated by S. aureus and four by Staphylococcus caprae, coagulase-negative human commensal staphylococci in the RPI group. Using mouse models, both S. caprae and S. aureus, but not Staphylococcus epidermidis, colonized on skin healed from injury at significantly higher rates than normal skin. Although subcutaneous injection of S. caprae did not induce lesion formation, the bacterium exhibited high hemolytic activity on human red blood cells. Lesion formation by subcutaneous injection of S. aureus was significantly suppressed in the presence of S. caprae. The hemolytic activity of rabbit blood cells of S. aureus was suppressed by S. caprae, whereas the hemolytic activity of S. caprae was dramatically suppressed by S. aureus. Data indicated that each of the two Staphylococcus spp. suppresses the pathogenicity of the other and that the imbalance between the two is associated with RPI.
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Affiliation(s)
- Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Hiroka Furuya
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Natsuki Takahashi
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Kana Shibata
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Maho Endo
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Shinjuku, Japan
| | - Shigefumi Okamoto
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Junko Sugama
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Research Center for Implementation Nursing Science Initiative, School of Health Sciences, Fujita Health University, Toyoake, Japan
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Pistone D, Meroni G, Panelli S, D’Auria E, Acunzo M, Pasala AR, Zuccotti GV, Bandi C, Drago L. A Journey on the Skin Microbiome: Pitfalls and Opportunities. Int J Mol Sci 2021; 22:9846. [PMID: 34576010 PMCID: PMC8469928 DOI: 10.3390/ijms22189846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022] Open
Abstract
The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.
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Affiliation(s)
- Dario Pistone
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Gabriele Meroni
- Department of Biomedical Surgical and Dental Sciences-One Health Unit, University of Milan, 20133 Milan, Italy;
| | - Simona Panelli
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Enza D’Auria
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Miriam Acunzo
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Ajay Ratan Pasala
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Gian Vincenzo Zuccotti
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Claudio Bandi
- Pediatric Clinical Research Center “Invernizzi”, Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Lorenzo Drago
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
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