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Alpha diversity (richness, inverse Simpson evenness) was analysed by generalised linear mixed models, beta diversity was analysed by Bray\u2013Curtis dissimilarities and PERMANOVA, and differential abundance was analysed by limma. Additionally, we examined associations with maternal genetic risk score (GRS), maternal HLA type, glycaemic management (HbA\n                      <jats:sub>1c<\/jats:sub>\n                      ) and breastmilk secretory IgA (sIgA), and performed a parallel analysis for the infant stool microbiome.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A significant interaction between type 1 diabetes status and timepoint was observed for alpha diversity, both richness (\n                      <jats:italic>p<\/jats:italic>\n                      =0.01) and inverse Simpson diversity (\n                      <jats:italic>p<\/jats:italic>\n                      =0.003), indicating distinct temporal trajectories between women with and without type 1 diabetes. In those without type 1 diabetes, richness increased significantly between birth and 1\u00a0week postpartum, but this early increase was delayed in women with type 1 diabetes to between 1\u00a0week and 3\u00a0months postpartum (\n                      <jats:italic>p<\/jats:italic>\n                      =0.002). Beta diversity analysis revealed earlier and more extensive compositional shifts in women without type 1 diabetes compared to those with type 1 diabetes. These differences persisted after adjusting for Caesarean delivery, BMI, parity and infant sex, and were not attributable to a delay in initiating breastfeeding. Taxa with delayed enrichment in women with type 1 diabetes included\n                      <jats:italic>Streptococcus<\/jats:italic>\n                      spp. and\n                      <jats:italic>Rothia mucilaginosa<\/jats:italic>\n                      , which metabolise human milk oligosaccharides to short-chain fatty acids to promote development of the infant\u2019s gut barrier and immune system. Maternal GRS, HLA, HbA\n                      <jats:sub>1c<\/jats:sub>\n                      or sIgA were not associated with milk microbiota diversity trajectories. In infant stool samples, alpha diversity did not differ between exposure groups, and showed no evidence of delayed maturation. Beta diversity revealed an early compositional shift between birth and 1\u00a0week postpartum only in infants born to women without type 1 diabetes. Similarly, significant taxonomic changes between birth and 1\u00a0week postpartum were detected only in infants born to women without type 1 diabetes, but with some taxa differing between exposure groups at 1\u00a0week.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions\/interpretation<\/jats:title>\n                    <jats:p>Maternal type 1 diabetes is associated with delayed early maturation of the breastmilk microbiome. Early compositional differences in microbiota restructuring were also observed in the infant gut, partially mirroring the pattern in the milk microbiome; however, sustained differences in infant gut microbiota diversity were not detected. Further investigation could determine whether these changes affect development of the infant\u2019s gut and immune system.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s00125-026-06791-6","type":"journal-article","created":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T23:55:15Z","timestamp":1782863715000},"page":"2833-2846","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Delayed maturation of the milk microbiome in women with type 1 diabetes"],"prefix":"10.1007","volume":"69","author":[{"given":"Alexandra J.","family":"Roth-Schulze","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina M.","family":"Ngui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guinevere","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pat","family":"Ashwood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca L.","family":"Thomson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrique","family":"Zozaya-Valdes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M.","family":"Wentworth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria E.","family":"Craig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Huynh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer J.","family":"Couper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan A. 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They also thank S.A. Wilcox (Genomics Hub, Walter and Eliza Hall Institute) for advice with DNA sequencing and D. Huang and D. Huynh (ENDIA Study Biospecimen Coordinators) for processing samples.","order":1,"name":"Ethics","label":"Acknowledgements","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"Demultiplexed raw sequencing datasets supporting the conclusions of this study have been publicly available since 5 May 2026 and can be accessed through the NCBI Sequence Read Archive (\n                      \n                      ; BioProject PRJNA1356526). Data are available without access restrictions for secondary analyses and research use.","order":2,"name":"Ethics","label":"Data availability","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"All R code used to perform statistical analyses has been publicly available since 18 April 2026 through GitHub (\n                      \n                      ). The repository includes QIIME2 command logs for sequence processing, R Markdown scripts and associated R objects containing taxonomic profiles and metadata used for statistical analyses. These resources are openly available without access restrictions.","order":3,"name":"Ethics","label":"Code availability","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"Open Access funding enabled and organized by CAUL and its Member Institutions. The research reported in this publication was funded by Breakthrough T1D through the Type 1 Diabetes Clinical Research Network (T1DCRN), supported by the Commonwealth of Australia and the Leona M. and Harry B. Helmsley Charitable Trust (3-SRA-2023-1374-M-N, 3-SRA-2020-966-M-N, 1-SRA-2019-871-M-B, 4-SRA-2015-127-M-B and G-2112-04908). Additional support was provided by the National Health and Medical Research Council of Australia (APP1078106, APP1025083 and APP1173945).","order":4,"name":"Ethics","label":"Funding","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"The authors declare that there are no relationships or activities that might bias, or be perceived to bias, their work.","order":5,"name":"Ethics","label":"Authors\u2019 relationships and activities","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"AJR-S performed bioinformatic and statistical analyses under the supervision of LCH, and wrote the manuscript with LCH; GM prepared maternal summary tables; PA prepared maternal summary tables; KMN performed DNA extraction and sequencing and discussed the manuscript; EZ-V and YG contributed to bioinformatics discussion and analysis; RLT provided summary of early feeding issues and edited the manuscript; JMW, MEC and AH contributed to participant recruitment and sample collection; JJC contributed to participant recruitment and sample collection, and edited the manuscript; MASP contributed to study conception and design, compiled metadata and edited the manuscript; LCH designed and supervised the study, analysed data and wrote the manuscript with AJR-S. All authors reviewed the manuscript and approved the final version to be published. LCH takes responsibility for the contents of the article.","order":6,"name":"Ethics","label":"Contribution statement","group":{"name":"EthicsHeading","label":"Ethics"}}]}}