{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T05:52:25Z","timestamp":1791870745085,"version":"4.3.4"},"reference-count":46,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AR084058"],"award-info":[{"award-number":["AR084058"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["UM1AI109565"],"award-info":[{"award-number":["UM1AI109565"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1146913"],"award-info":[{"award-number":["APP1146913"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT2008911"],"award-info":[{"award-number":["GNT2008911"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Allergy"],"abstract":"ABSTRACT<\/jats:title>\n \n Background<\/jats:title>\n \n Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co\u2010occur in infancy, but the factors underlying distinct atopic phenotypes remain unclear. Although\n FLG<\/jats:italic>\n null mutations are major genetic risk factors for AD, they explain only part of disease heritability, suggesting a potential role for the skin microbiome. This study examined how early\u2010life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n We analyzed >\u20091000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2\u20133\u2009months (pre\u2010diagnosis) and 12\u2009months (post\u2010diagnosis). Differential abundance, strain\u2010level, and microbial genome\u2010wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, their co\u2010occurrence, and\n FLG<\/jats:italic>\n mutation status.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Within AD, microbial signatures differed by co\u2010occurring FA or FS. At 12\u2009months,\n \n Staphylococcus epidermidis<\/jats:italic>\n <\/jats:styled-content>\n was enriched in infants with AD alone, whereas infants with AD and FA showed decreased\n \n Staphylococcus hominis<\/jats:italic>\n <\/jats:styled-content>\n and\n Lactococcus<\/jats:italic>\n species, and increased\n \n Dermacoccus nishinomiyaensis<\/jats:italic>\n <\/jats:styled-content>\n and\n Malassezia slooffiae<\/jats:italic>\n . At 2\u20133\u2009months, early skin dysbiosis characterized by enrichment of\n Staphylococcus species<\/jats:italic>\n was associated with later development of AD with FS or FA, but not AD alone. Among infants with AD,\n FLG<\/jats:italic>\n mutation carriers showed additional microbial shifts, including reduced\n Streptococcus<\/jats:italic>\n species and increased\n M. slooffiae<\/jats:italic>\n . Strain\u2010level analyses revealed mother\u2013infant sharing of AD\u2010associated taxa, and microbial genome\u2010wide association analyses identified species\u2010specific genes linked to AD severity.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n Infant atopic phenotypes are associated with distinct, phenotype\u2010specific skin microbiome features that emerge before and after disease onset, highlighting the microbiome as a potential target for early risk stratification.<\/jats:p>\n <\/jats:sec>","DOI":"10.1111\/all.70449","type":"journal-article","created":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T03:26:46Z","timestamp":1784345206000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Shotgun Metagenomics Reveals Skin Microbiome Composition and Function in Infant Atopic Disease"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3870-1390","authenticated-orcid":false,"given":"Zeyang","family":"Shen","sequence":"first","affiliation":[{"name":"School of Molecular Biosciences, College of Veterinary Medicine Washington State University Pullman Washington USA"},{"name":"Microbial Genomics Section, Translational and Functional Genomics Branch National Human Genome Research Institute, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1616-7430","authenticated-orcid":false,"given":"Jana K.","family":"Eckert","sequence":"additional","affiliation":[{"name":"Population Allergy Murdoch Children's Research Institute Parkville Victoria Australia"},{"name":"Centre for Food and Allergy Research Murdoch Children's Research Institute Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Saffery","sequence":"additional","affiliation":[{"name":"Centre for Food and Allergy Research Murdoch Children's Research Institute Parkville Victoria Australia"},{"name":"Department of Paediatrics University of Melbourne Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina J.","family":"Allen","sequence":"additional","affiliation":[{"name":"Population Allergy Murdoch Children's Research Institute Parkville Victoria Australia"},{"name":"Centre for Food and Allergy Research Murdoch Children's Research Institute Parkville Victoria Australia"},{"name":"Department of Paediatrics University of Melbourne Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-0560-5599","authenticated-orcid":false,"given":"Audrey","family":"Walsh","sequence":"additional","affiliation":[{"name":"Population Allergy Murdoch Children's Research Institute Parkville Victoria Australia"},{"name":"Centre for Food and Allergy Research Murdoch Children's Research Institute Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"VITALITY team","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clay","family":"Deming","sequence":"additional","affiliation":[{"name":"Microbial Genomics Section, Translational and Functional Genomics Branch National Human Genome Research Institute, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiong","family":"Chen","sequence":"additional","affiliation":[{"name":"Microbial Genomics Section, Translational and Functional Genomics Branch National Human Genome Research Institute, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Laky","sequence":"additional","affiliation":[{"name":"Laboratory of Allergic Diseases National Institute of Allergy and Infectious Diseases, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8923-289X","authenticated-orcid":false,"given":"Jenny Min","family":"Li","sequence":"additional","affiliation":[{"name":"Laboratory of Allergic Diseases National Institute of Allergy and Infectious Diseases, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-9598-949X","authenticated-orcid":false,"given":"Lindsay","family":"Chatman","sequence":"additional","affiliation":[{"name":"Laboratory of Allergic Diseases National Institute of Allergy and Infectious Diseases, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"NISC Comparative Sequencing Program","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4424-064X","authenticated-orcid":false,"given":"Heidi H.","family":"Kong","sequence":"additional","affiliation":[{"name":"Dermatology Branch National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5683-996X","authenticated-orcid":false,"given":"Kirsten P.","family":"Perrett","sequence":"additional","affiliation":[{"name":"Population Allergy Murdoch Children's Research Institute Parkville Victoria Australia"},{"name":"Centre for Food and Allergy Research Murdoch Children's Research Institute Parkville Victoria Australia"},{"name":"Department of Paediatrics University of Melbourne Parkville Victoria Australia"},{"name":"Department of Allergy and Immunology Royal Children's Hospital Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6860-348X","authenticated-orcid":false,"given":"Julia A.","family":"Segre","sequence":"additional","affiliation":[{"name":"Microbial Genomics Section, Translational and Functional Genomics Branch National Human Genome Research Institute, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2259-5546","authenticated-orcid":false,"given":"Pamela A.","family":"Frischmeyer\u2010Guerrerio","sequence":"additional","affiliation":[{"name":"Laboratory of Allergic Diseases National Institute of Allergy and Infectious Diseases, NIH Bethesda Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,17]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"crossref","DOI":"10.3390\/ijerph15092043","article-title":"The Epidemiology of Food Allergy in the Global Context","volume":"15","author":"Loh W.","year":"2018","journal-title":"International Journal of Environmental Research and Public Health"},{"key":"e_1_2_9_3_1","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/S0140-6736(20)31286-1","article-title":"Atopic Dermatitis","volume":"396","author":"Langan S. 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O.","year":"2023","journal-title":"Journal of the European Academy of Dermatology and Venereology"},{"key":"e_1_2_9_7_1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.jaci.2021.05.034","article-title":"Polygenic Prediction of Atopic Dermatitis Improves With Atopic Training and Filaggrin Factors","volume":"149","author":"Arehart C. 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R.","year":"2016","journal-title":"Nature Microbiology"},{"key":"e_1_2_9_11_1","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1101\/gr.131029.111","article-title":"Temporal Shifts in the Skin Microbiome Associated With Disease Flares and Treatment in Children With Atopic Dermatitis","volume":"22","author":"Kong H. H.","year":"2012","journal-title":"Genome Research"},{"key":"e_1_2_9_12_1","doi-asserted-by":"crossref","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 T.","year":"2017","journal-title":"Science Translational Medicine"},{"key":"e_1_2_9_13_1","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aal4651","article-title":"Staphylococcus aureus and \n Staphylococcus epidermidis\n Strain Diversity Underlying Pediatric Atopic Dermatitis","volume":"9","author":"Byrd A. L.","year":"2017","journal-title":"Science Translational Medicine"},{"key":"e_1_2_9_14_1","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.chom.2023.03.010","article-title":"Staphylococcal Diversity in Atopic Dermatitis From an Individual to a Global Scale","volume":"31","author":"Saheb Kashaf S.","year":"2023","journal-title":"Cell Host & Microbe"},{"key":"e_1_2_9_15_1","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.00930-22","article-title":"The Ubiquitous Human Skin Commensal \n Staphylococcus hominis\n Protects Against Opportunistic Pathogens","volume":"13","author":"Severn M. M.","year":"2022","journal-title":"mBio"},{"key":"e_1_2_9_16_1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.jaci.2016.07.029","article-title":"Skin Microbiome Before Development of Atopic Dermatitis: Early Colonization With Commensal Staphylococci at 2 Months Is Associated With a Lower Risk of Atopic Dermatitis at 1 Year","volume":"139","author":"Kennedy E. A.","year":"2017","journal-title":"Journal of Allergy and Clinical Immunology"},{"key":"e_1_2_9_17_1","doi-asserted-by":"crossref","first-page":"1949","DOI":"10.1111\/all.15671","article-title":"The Skin Microbiome in the First Year of Life and Its Association With Atopic Dermatitis","volume":"78","author":"Rapin A.","year":"2023","journal-title":"Allergy"},{"key":"e_1_2_9_18_1","doi-asserted-by":"crossref","DOI":"10.3390\/nu13051682","article-title":"A Combined Analysis of Gut and Skin Microbiota in Infants With Food Allergy and Atopic Dermatitis: A Pilot Study","volume":"13","author":"\u0141o\u015b\u2010Rycharska E.","year":"2021","journal-title":"Nutrients"},{"key":"e_1_2_9_19_1","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aav2685","article-title":"The Nonlesional Skin Surface Distinguishes Atopic Dermatitis With Food Allergy as a Unique Endotype","volume":"11","author":"Leung D. Y. M.","year":"2019","journal-title":"Science Translational Medicine"},{"key":"e_1_2_9_20_1","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1016\/j.jaci.2019.04.025","article-title":"Association of \n Staphylococcus aureus\n Colonization With Food Allergy Occurs Independently of Eczema Severity","volume":"144","author":"Tsilochristou O.","year":"2019","journal-title":"Journal of Allergy and Clinical Immunology"},{"key":"e_1_2_9_21_1","doi-asserted-by":"crossref","DOI":"10.1136\/bmjopen-2015-009377","article-title":"VITALITY Trial: Protocol for a Randomised Controlled Trial to Establish the Role of Postnatal Vitamin D Supplementation in Infant Immune Health","volume":"5","author":"Allen K. J.","year":"2015","journal-title":"BMJ Open"},{"key":"e_1_2_9_22_1","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1111\/j.1365-2133.1994.tb08532.x","article-title":"The U.K. Working Party's Diagnostic Criteria for Atopic Dermatitis. III. Independent Hospital Validation","volume":"131","author":"Williams H. C.","year":"1994","journal-title":"British Journal of Dermatology"},{"key":"e_1_2_9_23_1","volume-title":"VITALITY Statistical Analysis Plan V1.0 9th September 2025","author":"Zannino D.","year":"2025"},{"key":"e_1_2_9_24_1","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1038\/s41591-018-0211-7","article-title":"Expanded Skin Virome in DOCK8\u2010Deficient Patients","volume":"24","author":"Tirosh O.","year":"2018","journal-title":"Nature Medicine"},{"key":"e_1_2_9_25_1","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1016\/j.chom.2025.07.002","article-title":"Restoration of the Human Skin Microbiome Following Immune Recovery After Hematopoietic Stem Cell Transplantation","volume":"33","author":"Che Y.","year":"2025","journal-title":"Cell Host & Microbe"},{"key":"e_1_2_9_26_1","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/s41564-021-01011-w","article-title":"Integrating Cultivation and Metagenomics for a Multi\u2010Kingdom View of Skin Microbiome Diversity and Functions","volume":"7","author":"Saheb Kashaf S.","year":"2021","journal-title":"Nature Microbiology"},{"key":"e_1_2_9_27_1","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/s13059-023-03090-w","article-title":"A Genome Catalog of the Early\u2010Life Human Skin Microbiome","volume":"24","author":"Shen Z.","year":"2023","journal-title":"Genome Biology"},{"key":"e_1_2_9_28_1","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/j.jaci.2009.07.034","article-title":"Filaggrin Mutations That Confer Risk of Atopic Dermatitis Confer Greater Risk for Eczema Herpeticum","volume":"124","author":"Gao P. 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N. A.","year":"2006","journal-title":"Nature Genetics"},{"key":"e_1_2_9_32_1","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-022-02630-0","article-title":"StrainGE: A Toolkit to Track and Characterize Low\u2010Abundance Strains in Complex Microbial Communities","volume":"23","author":"Van Dijk L. R.","year":"2022","journal-title":"Genome Biology"},{"key":"e_1_2_9_33_1","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-024-74513-2","article-title":"Mild Atopic Dermatitis Is Characterized by Increase in Non\u2010Staphylococcus Pathobionts and Loss of Specific Species","volume":"14","author":"Delanghe L.","year":"2024","journal-title":"Scientific Reports"},{"key":"e_1_2_9_34_1","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.biotechadv.2019.02.004","article-title":"Harnessing the Catabolic Versatility of Gordonia Species for Detoxifying Pollutants","volume":"37","author":"Sowani H.","year":"2019","journal-title":"Biotechnology Advances"},{"key":"e_1_2_9_35_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0282569","article-title":"Diisocyanates Influence Models of Atopic Dermatitis Through Direct Activation of TRPA1","volume":"18","author":"Yadav M.","year":"2023","journal-title":"PLoS One"},{"key":"e_1_2_9_36_1","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.ade8898","article-title":"Exposure to Isocyanates Predicts Atopic Dermatitis Prevalence and Disrupts Therapeutic Pathways in Commensal Bacteria","volume":"9","author":"Zeldin J.","year":"2023","journal-title":"Science Advances"},{"key":"e_1_2_9_37_1","doi-asserted-by":"crossref","first-page":"763","DOI":"10.3390\/nu12030763","article-title":"Effect of the \n Lactococcus lactis\n 11\/19\u2010B1 Strain on Atopic Dermatitis in a Clinical Test and Mouse Model","volume":"12","author":"Suzuki T.","year":"2020","journal-title":"Nutrients"},{"key":"e_1_2_9_38_1","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1111\/myc.12913","article-title":"Contribution of Malassezia spp. to the Development of Atopic Dermatitis","volume":"62","author":"Nowicka D.","year":"2019","journal-title":"Mycoses"},{"key":"e_1_2_9_39_1","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1111\/pai.12522","article-title":"Alterations in the Gut Microbiotas of Children With Food Sensitization in Early Life","volume":"27","author":"Chen C.","year":"2016","journal-title":"Pediatric Allergy and Immunology"},{"key":"e_1_2_9_40_1","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.1038876","article-title":"The Associations of Maternal and Children's Gut Microbiota With the Development of Atopic Dermatitis for Children Aged 2\u2009Years","volume":"13","author":"Fan X.","year":"2022","journal-title":"Frontiers in Immunology"},{"key":"e_1_2_9_41_1","doi-asserted-by":"crossref","first-page":"1636","DOI":"10.1016\/j.jaci.2018.11.034","article-title":"Effects of Diet on the Childhood Gut Microbiome and Its Implications for Atopic Dermatitis","volume":"143","author":"Mahdavinia M.","year":"2019","journal-title":"Journal of Allergy and Clinical Immunology"},{"key":"e_1_2_9_42_1","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1111\/all.16095","article-title":"Neonatal Skin Dysbiosis to Infantile Atopic Dermatitis: Mitigating Effects of Skin Care","volume":"79","author":"Aoyama R.","year":"2024","journal-title":"Allergy"},{"key":"e_1_2_9_43_1","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1159\/000520978","article-title":"The Skin and Nose Microbiome and Its Association With Filaggrin Gene Mutations in Pediatric Atopic Dermatitis","volume":"238","author":"Van Mierlo M. M. F.","year":"2022","journal-title":"Dermatology"},{"key":"e_1_2_9_44_1","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1001\/jamadermatol.2017.5440","article-title":"Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis","volume":"154","author":"Clausen M. L.","year":"2018","journal-title":"JAMA Dermatology"},{"key":"e_1_2_9_45_1","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2020.570423","article-title":"Dysbiotic Lesional Microbiome With Filaggrin Missense Variants Associate With Atopic Dermatitis in India","volume":"10","author":"Nath S.","year":"2020","journal-title":"Frontiers in Cellular and Infection Microbiology"},{"key":"e_1_2_9_46_1","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1016\/j.jid.2025.03.017","article-title":"Shifts in Infant Skin Microbiome at 2 Months After Short\u2010Term Emollient Use From Birth Are Associated With Reduced Prevalence of Atopic Dermatitis at 12 Months in a High\u2010Risk Cohort","volume":"145","author":"Stamatas G. 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