{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:22:40Z","timestamp":1785435760004,"version":"3.56.0"},"posted":{"date-parts":[[2025,12,23]]},"group-title":"Microbiology","reference-count":46,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["AR084058"],"award-info":[{"award-number":["AR084058"]}],"id":[{"id":"https:\/\/ror.org\/006zn3t30","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["UM1AI109565"],"award-info":[{"award-number":["UM1AI109565"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"crossref","award":["APP1146913"],"award-info":[{"award-number":["APP1146913"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"award":["Intramural Research Program"],"award-info":[{"award-number":["Intramural Research Program"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]},{"award":["Intramural Research Program"],"award-info":[{"award-number":["Intramural Research Program"]}],"id":[{"id":"https:\/\/ror.org\/00baak391","id-type":"ROR","asserted-by":"publisher"}]},{"name":"DHB foundation"},{"name":"Rotary Club of Camberwell"},{"name":"Isabel and John Gilberston Charitable Trust"},{"DOI":"10.13039\/501100003842","name":"Ilhan Food Allergy Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003842","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Kimberly Foundation Australia"},{"name":"Constantinou Foundation"},{"name":"NHMRC fellowship","award":["GNT2008911"],"award-info":[{"award-number":["GNT2008911"]}]},{"name":"Melbourne Childrens Clinician-Scientist Fellowship"},{"name":"Australian Government Research Training Program Scholarship"},{"name":"National Allergy Centre of Excellence PhD scholarship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,12,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>\n                    Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While\n                    <jats:italic>FLG<\/jats:italic>\n                    null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Objective<\/jats:title>\n                  <jats:p>To determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>\n                    We analyzed &gt;1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with\n                    <jats:italic>FLG<\/jats:italic>\n                    mutation status.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months,\n                    <jats:italic>Staphylococcus epidermidis<\/jats:italic>\n                    was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased\n                    <jats:italic>Staphylococcus hominis<\/jats:italic>\n                    and\n                    <jats:italic>Lactococcus<\/jats:italic>\n                    species, along with increased\n                    <jats:italic>Dermacoccus nishinomiyaensis<\/jats:italic>\n                    and\n                    <jats:italic>Malassezia slooffiae<\/jats:italic>\n                    . At 2-3 months, early skin dysbiosis characterized by enrichment of\n                    <jats:italic>Staphylococcus<\/jats:italic>\n                    species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD,\n                    <jats:italic>FLG<\/jats:italic>\n                    mutation carriers exhibited additional microbial shifts, including reduced\n                    <jats:italic>Streptococcus<\/jats:italic>\n                    species and increased\n                    <jats:italic>Malassezia slooffiae<\/jats:italic>\n                    . Strain-level analyses revealed mother\u2013infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Infant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2025.12.22.696050","type":"posted-content","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T04:25:11Z","timestamp":1766550311000},"source":"Crossref","is-referenced-by-count":0,"title":["Skin microbiome composition and function in the development of atopic diseases during infancy"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3870-1390","authenticated-orcid":false,"given":"Zeyang","family":"Shen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Eckert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Saffery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina J.","family":"Allen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Walsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"VITALITY team","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clay","family":"Deming","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Laky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny Min","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindsay","family":"Chatman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"NISC Comparative Sequencing Program","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heidi H.","family":"Kong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsten P.","family":"Perrett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia A.","family":"Segre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pamela A.","family":"Frischmeyer-Guerrerio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025122608100896000_2025.12.22.696050v1.1","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph15092043"},{"key":"2025122608100896000_2025.12.22.696050v1.2","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/S0140-6736(20)31286-1","article-title":"Atopic dermatitis","volume":"396","year":"2020","journal-title":"The Lancet"},{"key":"2025122608100896000_2025.12.22.696050v1.3","doi-asserted-by":"crossref","first-page":"936","DOI":"10.3390\/life11090936","article-title":"The Epidemiology and Global Burden of Atopic Dermatitis: A Narrative Review","volume":"11","year":"2021","journal-title":"Life"},{"key":"2025122608100896000_2025.12.22.696050v1.4","doi-asserted-by":"crossref","unstructured":"Napolitano M , Fabbrocini G , Martora F , Genco L , Noto M , Patruno C. 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