Abstract
Skin is the first line of defense of human body against infections where many diverse microbes, including fungi, viruses, bacteria are surviving. These microbes exists in/on a different layer of skin like epidermis, dermis, etc. These skin microbiomes prevent invasion of such pathogen in association with the immune system, while a few skin microbiomes can also react as opportunistic pathogens. Culture-dependent and culture-independent methodologies are useful for the identification and characterization of disease associated with skin microbiome. 16s RNA gene sequencing techniques are useful for skin disease determination, but these techniques have certain limitations as they dont accurately predict microorganism present on flora of skin. However, methods such as NGS, shotgun sequencing, Illumina’s sequencing, etc. have capability to give precise details about the skin microbiome. There are some challenges regarding skin microbiome samples, advantages and disadvantages of the sequencing methodologies, and probable future prospect for the discipline.
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References
Alexander H, Paller AS, Traidl-Hoffmann C, Beck LA, De Benedetto A, Dhar S et al (2020) The role of bacterial skin infections in atopic dermatitis: expert statement and review from the International Eczema Council Skin Infection Group. Br J Dermatol 182(6):1331–1342
Bates M (2022) The role of the skin microbiome in health and disease. IEEE Pulse 13(4):8–13
Ducarmon QR, Zwittink RD, Hornung BVH, Van Schaik W, Young VB, Kuijper EJ (2019) Gut microbiota and colonization resistance against bacterial enteric infection. Microbiol Mol Biol Rev 83(3):10–1128
El Bairi K, Azzam F, Amrani M (2020) The arrival of next-generation sequencing: an overview of current technologies. In: Illuminating colorectal cancer genomics by next-generation sequencing: a big chapter in the tale. Springer, Cham, pp 73–89
Fadiji AE, Babalola OO (2020) Metagenomics methods for the study of plant-associated microbial communities: a review. J Microbiol Methods 170:105860
Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE et al (2020) Multi-platform assessment of DNA sequencing performance using human and bacterial reference genomes in the ABRF next-generation sequencing study. bioRxiv, 2020-07
Hu T, Chitnis N, Monos D, Dinh A (2021) Next-generation sequencing technologies: an overview. Hum Immunol 82(11):801–811
Kelly J (2013) Metagenomic and genomic analysis of the skin microbiota. Doctoral dissertation, University of Liverpool
Knetsch CW, van der Veer EM, Henkel C, Taschner P (2019) DNA sequencing. In: Molecular diagnostics: part 1: technical backgrounds and quality aspects. Springer, pp 339–360
Liu S, Moon CD, Zheng N, Huws S, Zhao S, Wang J (2022) Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. Microbiome 10(1):76
Lopatkin AJ, Collins JJ (2020) Predictive biology: modelling, understanding and harnessing microbial complexity. Nat Rev Microbiol 18(9):507–520
Meera Krishna B, Khan MA, Khan ST (2019) Next-generation sequencing (NGS) platforms: an exciting era of genome sequence analysis. In: Microbial genomics in sustainable agroecosystems, vol 2. Springer, Singapore, pp 89–109
Mikheenko A, Prjibelski AD, Joglekar A, Tilgner HU (2022) Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns. Genome Res 32(4):726–737
Mitchell SL, Simner PJ (2019) Next-generation sequencing in clinical microbiology: are we there yet? Clin Lab Med 39(3):405–418
Mukherjee A, Reddy MS (2020) Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech 10(2):71
Nash MV, Anesio AM, Barker G, Tranter M, Varliero G, Eloe-Fadrosh EA, Nielsen T, Turpin-Jelfs T, Benning LG, Sánchez-Baracaldo P (2018) Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol 94(9):fiy114. https://doi.org/10.1093/femsec/fiy114. PMID: 29901729; PMCID: PMC6054269
Lopez-Ojeda W, Pandey A, Alhajj M, Oakley AM (2020) Anatomy, skin (integument)[Internet]. Treasure Island: StatPearls Publishing
Quince C, Walker AW, Simpson JT, Loman NJ, Segata N (2017) Shotgun metagenomics, from sampling to analysis. Nat Biotechnol 35(9):833–844
Rana S, Kumar M, Maurya DK, Singh SK (2024) Fungal metagenomics: an emerging approach to determine the imperceptible facets of fungal diversity. In: Applied mycology for agriculture and foods. Apple Academic Press, pp 19–36
Roux PF, Oddos T, Stamatas G (2022) Deciphering the role of skin surface microbiome in skin health: an integrative multiomics approach reveals three distinct metabolite–microbe clusters. J Invest Dermatol 142(2):469–479.e5. https://doi.org/10.1016/j.jid.2021.07.159. Epub 2021 Jul 31. PMID: 34343557
Skowron K, Bauza-Kaszewska J, Kraszewska Z, Wiktorczyk-Kapischke N, Grudlewska-Buda K, Kwiecinska-Piróg J, Wałecka-Zacharska E, Radtke L, Gospodarek-Komkowska E (2021) Human skin microbiome: impact of intrinsic and extrinsic factors on skin microbiota. Microorganisms 9:543. https://doi.org/10.3390/microorganisms9030543
Sui HY, Weil AA, Nuwagira E, Qadri F, Ryan ET, Mezzari MP et al (2020) Impact of DNA extraction method on variation in human and built environment microbial community and functional profiles assessed by shotgun metagenomics sequencing. Front Microbiol 11:953
Thye AYK, Bah YR, Law JWF, Tan LTH, He YW, Wong SH et al (2022) Gut–skin axis: unravelling the connection between the gut microbiome and psoriasis. Biomedicines 10(5):1037
Tsuchiya KD, Funke B, Hegde M, Santani A, Souers RJ, Szelinger S et al (2023) Implementation, evolution, and laboratory performance of methods-based proficiency testing for next-generation sequencing detection of germline sequence variants. Arch Pathol Lab Med 1:1–9
Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X et al (2022) Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm 3(1):e116
Zhang L, Chen F, Zeng Z, Xu M, Sun F, Yang L et al (2021) Advances in metagenomics and its application in environmental microorganisms. Front Microbiol 12:766364
Zhu Y, Yu X, Cheng G (2023) Human skin bacterial microbiota homeostasis: a delicate balance between health and disease. mLife 2(2):107–120
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Joshi, K., Panchasara, M., Goswami, H., Bishoyi, A.K., Sanghvi, G. (2024). Multi-omics in Study of Skin Microbiome. In: Mani, I., Singh, V. (eds) Multi-Omics Analysis of the Human Microbiome. Springer, Singapore. https://doi.org/10.1007/978-981-97-1844-3_10
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DOI: https://doi.org/10.1007/978-981-97-1844-3_10
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