{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:59:55Z","timestamp":1785405595361,"version":"3.56.0"},"reference-count":31,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T00:00:00Z","timestamp":1785110400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Korea government","award":["IITP-2026-RS-2023-00254592"],"award-info":[{"award-number":["IITP-2026-RS-2023-00254592"]}]},{"name":"Catholic University of Korea\u2019s Uijeongbu St. Mary\u2019s Hospital Clinical Research Laboratory Foundation"},{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Nummular eczema (NE) and atopic dermatitis (AD) share clinical features, yet their skin microbiomes remain insufficiently characterized. This exploratory pilot study evaluated the taxonomic composition and functional potential of the skin microbiome across NE, a mixed NE\/AD phenotype (Mixed NE_AD), and AD using shotgun metagenomics. Lesional swabs from Korean patients with NE (n = 8), Mixed NE_AD (n = 6), and AD (n = 5) were sequenced to assess microbial diversity, taxonomy, and functional pathways. Staphylococcus aureus predominated across all groups. NE samples were characterized by the higher relative abundance of environmental taxa, wherein Delftia acidovorans was observed only in NE samples in this cohort, and Kocuria palustris diminished sequentially across the Mixed NE_AD and AD phenotypes. Mixed NE_AD exhibited greater intra-genus Staphylococcus diversity. Despite non-significant overall diversity differences, partial ecological separation was noted. Functionally, descriptive differences in metabolic potential were observed, with NE showing trends toward biosynthetic and oxidative stress-associated pathways and AD showing trends toward degradation-related pathways. Mixed NE_AD showed intermediate characteristics. Although these differences did not reach statistical significance after correction for multiple testing, these findings provide preliminary evidence for microbiome-based stratification of eczematous disorders, warranting larger cohort validation.<\/jats:p>","DOI":"10.3390\/microorganisms14081631","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T08:15:56Z","timestamp":1785140156000},"page":"1631","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Taxonomic and Functional Skin Microbiome Profiles in Nummular Eczema, Atopic Dermatitis, and Mixed Phenotypes: An Exploratory Shotgun Metagenomic Pilot Study"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-2690-9476","authenticated-orcid":false,"given":"Mingyu","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Dermatology, Uijeongbu St. Mary\u2019s Hospital, The Catholic University of Korea, Uijeongbu 11765, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8379-1873","authenticated-orcid":false,"given":"You Kyung","family":"Koh","sequence":"additional","affiliation":[{"name":"Department of Industrial Pharmacy, Dongguk University, Seoul 04620, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seong Joo","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Industrial Pharmacy, Dongguk University, Seoul 04620, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyung Hyun","family":"Min","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Uijeongbu St. Mary\u2019s Hospital, The Catholic University of Korea, Uijeongbu 11765, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2711-3112","authenticated-orcid":false,"given":"Hyun Jeong","family":"Ju","sequence":"additional","affiliation":[{"name":"Department of Dermatology, St. Vincent\u2019s Hospital, College of Medicine, The Catholic University of Korea, Suwon 16247, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0168-9546","authenticated-orcid":false,"given":"Minho","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Life Science, Dongguk University, Goyang 10326, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8642-2479","authenticated-orcid":false,"given":"Young Bok","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Uijeongbu St. Mary\u2019s Hospital, The Catholic University of Korea, Uijeongbu 11765, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"146","DOI":"10.2174\/22122710MTA59MDEa0","article-title":"Nummular Eczema: An Updated Review","volume":"14","author":"Leung","year":"2020","journal-title":"Recent Pat. Inflamm. Allergy Drug Discov."},{"key":"ref_2","unstructured":"Robinson, C.A., Love, L.W., Saleh, H.M., and Farci, F. (2026). Nummular Dermatitis. StatPearls, StatPearls Publishing."},{"key":"ref_3","first-page":"36","article-title":"Clinical features and aggravating factors in nummular eczema in Thais","volume":"31","author":"Jiamton","year":"2013","journal-title":"Asian Pac. J. Allergy Immunol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"189","DOI":"10.2340\/0001555549189196","article-title":"Nummular eczema--clinical and statistical data","volume":"49","author":"Hellgren","year":"1969","journal-title":"Acta Derm.-Venereol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1111\/j.1365-2133.2012.11072.x","article-title":"Features of Staphylococcus aureus colonization in patients with nummular eczema","volume":"168","author":"Kim","year":"2013","journal-title":"Br. J. Dermatol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2397","DOI":"10.1080\/09546634.2021.1966356","article-title":"The atopic dermatitis spectrum disorder. Recognizing the clinical heterogeneity in patients with atopic related skin conditions in order to improve therapeutic decision-making and outcomes: An expert panel consensus statement","volume":"33","author":"Butler","year":"2022","journal-title":"J. Dermatol. Treat."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1016\/j.jaci.2023.04.009","article-title":"The neglected twin: Nummular eczema is a variant of atopic dermatitis with codominant TH2\/TH17 immune response","volume":"152","author":"Bohner","year":"2023","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/s11882-015-0567-4","article-title":"The role of the skin microbiome in atopic dermatitis","volume":"15","author":"Williams","year":"2015","journal-title":"Curr. Allergy Asthma Rep."},{"key":"ref_9","first-page":"e48803","article-title":"Managing the Skin Microbiome as a New Bacteriotherapy for Inflammatory Atopic Dermatitis","volume":"15","author":"Dewi","year":"2023","journal-title":"Cureus"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/s41591-021-01256-2","article-title":"Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial","volume":"27","author":"Nakatsuji","year":"2021","journal-title":"Nat. Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"284","DOI":"10.2340\/00015555-3089","article-title":"Changes in Lesional and Non-lesional Skin Microbiome During Treatment of Atopic Dermatitis","volume":"99","author":"Kwon","year":"2019","journal-title":"Acta Derm. Venereol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Ogai, K., Nagase, S., Mukai, K., Iuchi, T., Mori, Y., Matsue, M., Sugitani, K., Sugama, J., and Okamoto, S. (2018). A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02812"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1016\/j.jid.2016.10.033","article-title":"Performing Skin Microbiome Research: A Method to the Madness","volume":"137","author":"Kong","year":"2017","journal-title":"J. Investig. Dermatol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1111\/j.1365-2133.1974.tb06447.x","article-title":"Staphylococcus aureus in the lesions of atopic dermatitis","volume":"90","author":"Leyden","year":"1974","journal-title":"Br. J. Dermatol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1016\/j.jid.2018.03.1517","article-title":"Patients with Atopic Dermatitis Colonized with Staphylococcus aureus Have a Distinct Phenotype and Endotype","volume":"138","author":"Simpson","year":"2018","journal-title":"J. Investig. Dermatol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1155\/2015\/973284","article-title":"Delftia acidovorans: A rare pathogen in immunocompetent and immunocompromised patients","volume":"26","author":"Bilgin","year":"2015","journal-title":"Can. J. Infect. Dis. Med. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.2147\/IDR.S457781","article-title":"Retrospective Cohort Study on Delftia acidovorans Infections in Patients: A Rare and Significant Infection","volume":"17","author":"Lu","year":"2024","journal-title":"Infect. Drug Resist."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Scaglione, V., Stefanelli, L.F., Mazzitelli, M., Cattarin, L., De Giorgi, L., Naso, E., Maraolo, A.E., Cattelan, A., and Nalesso, F. (2025). Delftia acidovorans Infections in Immunocompetent and Immunocompromised Hosts: A Case Report and Systematic Literature Review. Antibiotics, 14.","DOI":"10.3390\/antibiotics14040365"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.4269\/ajtmh.23-0377","article-title":"Case Report: Case Series of Kocuria palustris Bacteremia among Immunocompromised Patients","volume":"109","author":"Varghese","year":"2023","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1111\/php.13218","article-title":"Skin Microbiome Compositional Changes in Atopic Dermatitis Accompany Dead Sea Climatotherapy","volume":"96","author":"Brandwein","year":"2020","journal-title":"Photochem. Photobiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"215","DOI":"10.25100\/cm.v50i3.4025","article-title":"Delftia acidovorans pneumonia with lung cavities formation","volume":"50","author":"Yildiz","year":"2019","journal-title":"Colomb. Medica"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Tejman-Yarden, N., Robinson, A., Davidov, Y., Shulman, A., Varvak, A., Reyes, F., Rahav, G., and Nissan, I. (2019). Delftibactin-A, a Non-ribosomal Peptide with Broad Antimicrobial Activity. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02377"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nchembio.1179","article-title":"Gold biomineralization by a metallophore from a gold-associated microbe","volume":"9","author":"Johnston","year":"2013","journal-title":"Nat. Chem. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"eaah4680","DOI":"10.1126\/scitranslmed.aah4680","article-title":"Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis","volume":"9","author":"Nakatsuji","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Traisaeng, S., Herr, D.R., Kao, H.J., Chuang, T.H., and Huang, C.M. (2019). A Derivative of Butyric Acid, the Fermentation Metabolite of Staphylococcus epidermidis, Inhibits the Growth of a Staphylococcus aureus Strain Isolated from Atopic Dermatitis Patients. Toxins, 11.","DOI":"10.3390\/toxins11060311"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ohkubo, T., Matsumoto, Y., Cho, O., Ogasawara, Y., and Sugita, T. (2021). Delftia acidovorans secretes substances that inhibit the growth of Staphylococcus epidermidis through TCA cycle-triggered ROS production. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0253618"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e00437-13","DOI":"10.1128\/mBio.00437-13","article-title":"A dysfunctional tricarboxylic acid cycle enhances fitness of Staphylococcus epidermidis during \u03b2-lactam stress","volume":"4","author":"Thomas","year":"2013","journal-title":"mBio"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1007\/s00430-018-0573-y","article-title":"Interaction of host and Staphylococcus aureus protease-system regulates virulence and pathogenicity","volume":"208","author":"Singh","year":"2019","journal-title":"Med. Microbiol. Immunol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4239","DOI":"10.1128\/IAI.70.8.4239-4246.2002","article-title":"Variation in extracellular protease production among clinical isolates of Staphylococcus aureus due to different levels of expression of the protease repressor sarA","volume":"70","author":"Karlsson","year":"2002","journal-title":"Infect. Immun."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1089\/dna.2024.0134","article-title":"Staphylococcus aureus Proteases: Orchestrators of Skin Inflammation","volume":"43","author":"Kline","year":"2024","journal-title":"DNA Cell Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nrmicro.2017.157","article-title":"The human skin microbiome","volume":"16","author":"Byrd","year":"2018","journal-title":"Nat. Rev. Microbiol."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/8\/1631\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T08:28:46Z","timestamp":1785140926000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/8\/1631"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,27]]},"references-count":31,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["microorganisms14081631"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14081631","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,27]]}}}