A Pilot Study: Composition and Diversity of 16S rRNA Based Skin Bacterial Microbiome in Indonesian Atopic Dermatitis Population

References

• Simpson EL, Leung DYM, Eichenfield LF, et al. Atopic dermatitis. In: Kang S, Amagai M, Bruckner AL, Enk AH, Margolis DJ, McMichael AJ, editors. Fitzpatrick’s Dermatology. 9th ed. New York: McGraw Hill; 2019:363–384.
   Google Scholar
• Kapur S, Watson W, Carr S. Atopic dermatitis. Allergy Asthma Clin Immunol. 2018;14(2):43–52. doi:10.1186/s13223-018-0281-6
   Web of Science ®Google Scholar
• Barbeau M, Bpharm HL. Burden of atopic dermatitis in Canada. Int J Dermatol. 2006;45(1):31–36. doi:10.1111/j.1365-4632.2004.02345.x
   PubMed Web of Science ®Google Scholar
• Kim JK, Kim BE, Leung DYM. Pathophysiology of atopic dermatitis: clinical implications. Allergy Asthma Proc. 2019;40(2):84–92. doi:10.2500/aap.2019.40.4202
   PubMed Web of Science ®Google Scholar
• Kong HH, Oh J, Deming C. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res. 2012;22(5):850–859. doi:10.1101/gr.131029.111
   PubMed Web of Science ®Google Scholar
• Williams MR, Gallo RL. The role of the skin microbiome in atopic dermatitis. Curr Allergy Asthma Rep. 2015;15(11):65. doi:10.1007/s11882-015-0567-4
   PubMed Web of Science ®Google Scholar
• Flores GE, Seité S, Henley JB, et al. Microbiome of affected and unaffected skin of patients with atopic dermatitis before and after emollient treatment. J Drugs Dermatol. 2014;13(11):611–618.
   Web of Science ®Google Scholar
• Dekio I, Sakamoto M, Hayashi H. Characterization of skin microbiota in patients with atopic dermatitis and in normal subjects using 16S rRNA gene-based comprehensive analysis. J Med Microbiol. 2007;56:1675–1683.
   Web of Science ®Google Scholar
• Kim MH, Rho M, Choi JP, et al. A metagenomic analysis provides a culture-independent pathogen detection for atopic dermatitis. Allergy Asthma Immunol Res. 2017;9(5):453–461. doi:10.4168/aair.2017.9.5.453
   Web of Science ®Google Scholar
• Silverberg JI, Lei D, Yousaf M, et al. What are the best endpoints for eczema area and severity index and scoring atopic dermatitis in clinical practice? A prospective observational study. Br J Dermatol. 2021;184(5):888–895. doi:10.1111/bjd.19457
   PubMed Web of Science ®Google Scholar
• Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinform. 2011;27(21):2957–2963. doi:10.1093/bioinformatics/btr507
   PubMed Web of Science ®Google Scholar
• Bokulich NA, Subramanian S, Faith JJ, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013;10(1):57–59. doi:10.1038/nmeth.2276
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–336. doi:10.1038/nmeth.f.303
   PubMed Web of Science ®Google Scholar
• Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinform. 2011;27(16):2194–2200. doi:10.1093/bioinformatics/btr381
   PubMed Web of Science ®Google Scholar
• Haas BJ, Gevers D, Earl AM, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011;21(3):494–504. doi:10.1101/gr.112730.110
   PubMed Web of Science ®Google Scholar
• Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–998. doi:10.1038/nmeth.2604
   PubMed Web of Science ®Google Scholar
• Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–5267. doi:10.1128/AEM.00062-07
   PubMed Web of Science ®Google Scholar
• Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596.
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–1797. doi:10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Catinean A, Neag MA, Mitre AO, Bocsan CI, Buzoianu AD. Microbiota and immune-mediated skin diseases—An overview. Microorganisms. 2019;7(9):279. doi:10.3390/microorganisms7090279
   Web of Science ®Google Scholar
• Nørreslet LB, Agner T, Clausen ML. The skin microbiome in inflammatory skin diseases. Curr Dermatol Rep. 2020;9(2):141–151. doi:10.1007/s13671-020-00297-z
   Web of Science ®Google Scholar
• Fahlén A, Engstrand L, Baker BS, Powles A, Fry L. Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin. Arch Dermatol Res. 2012;304(1):15–22. doi:10.1007/s00403-011-1189-x
   PubMed Web of Science ®Google Scholar
• Ganju P, Nagpal S, Mohammed M, et al. Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects. Sci Rep. 2016;6(1):18761. doi:10.1038/srep18761
   Web of Science ®Google Scholar
• Gao Z, Tseng C, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci USA. 2007;104(8):2927–2932. doi:10.1073/pnas.0607077104
   PubMed Web of Science ®Google Scholar
• Grice EA, Kong HH, Renaud G, et al. A diversity profile of the human skin microbiota. Genome Res. 2008;18(7):1043–1050. doi:10.1101/gr.075549.107
   PubMed Web of Science ®Google Scholar
• Grice EA. Topographical and temporal diversity of the human skin microbiome. Science. 2009;3(24):1190–1192. doi:10.1126/science.1171700
   Web of Science ®Google Scholar
• Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA. 2008;105(17):994–999. doi:10.1073/pnas.0807920105
   Web of Science ®Google Scholar
• Towell AM, Feuillie C, Vitry P, et al. Staphylococcus aureus binds to the N-terminal region of corneodesmosin to adhere to the stratum corneum in atopic dermatitis. Proc Natl Acad Sci USA. 2021;118(1):e2014444118. doi:10.1073/pnas.2014444118
   Web of Science ®Google Scholar
• Olesen CM, Ingham AC, Thomsen SF, et al. Changes in skin and nasal microbiome and Staphylococcal species following treatment of atopic dermatitis with dupilumab. Microorganisms. 2021;9(7):1487. doi:10.3390/microorganisms9071487
   PubMed Web of Science ®Google Scholar
• Khadka VD, Key FM, Romo-González C, et al. The skin microbiome of patients with atopic dermatitis normalizes gradually during treatment. Front Cell Infect Microbiol. 2021:910. doi:10.3389/fcimb.2021.720674
   Web of Science ®Google Scholar
• Germida J, Casida LE. Ensifer adhaerens predatory activity against other bacteria in soil, as monitored by indirect phage analysis. Appl Environ Microbiol. 1983;45(4):1380–1388. doi:10.1128/aem.45.4.1380-1388.1983
   Web of Science ®Google Scholar
• Pratiwi C, Rahayu WP, Lioe HN, Herawati D, Broto W, Ambarwati S. The effect of temperature and relative humidity for Aspergillus flavus BIO 2237 growth and aflatoxin production on soybeans. Int Food Res J. 2015;22(1):82–87.
   Web of Science ®Google Scholar