Adverse pregnancy outcomes in women with type 1 diabetes are associated with multiple alterations in the vaginal microbiome

Abstract

Acknowledgements: The authors thank S. A. Wilcox (Genomics Hub, Walter and Eliza Hall Institute of Medical Research) for advice with DNA sequencing and D. Huang for processing samples. We also gratefully acknowledge the participants and their families who contribute to the ENDIA Study. Data availability: The demultiplexed raw sequencing data supporting the findings of this study are publicly available in the NCBI Sequence Read Archive (SRA; https://www.ncbi.nlm.nih.gov/sra ) under project number PRJNA1037097. Code availability: All code used in the analyses is available on GitHub at https://github.com/RothSchulze/Adverse-pregnancy-outcomes-in-women-with-T1D-and-vaginal-microbiome , commit 8241215 (archived version used for this analysis). The repository includes Qiime2 command logs for sequence processing, R Markdown scripts and the associated R objects containing taxonomic profiles and metadata used for statistical analyses. Funding: Open Access funding enabled and organized by CAUL and its Member Institutions. This research was supported by Breakthrough T1D (formerly known as JDRF) Australia, a Commonwealth of Australia grant for Accelerated Research under the Medical Research Future Fund, and funding from the Leona M. and Harry B. Helmsley Charitable Trust (grant key 3-SRA-2020-966-M-N). In addition, support was provided by the National Health and Medical Research Council of Australia (NHMRC) Centre of Research Excellence for the Protection of Pancreatic Beta Cells (1078106) and JDRF International (1-SRA-2018-543-S-B). Additional support was provided by an NHMRC program grant (LCH 1037321), the Victorian State Government Operational Infrastructure Support, Diabetes South Australia, and the NHMRC Research Institute Infrastructure Support Scheme. LCH was supported by a NHMRC leadership investigator grant (APP1173945). Authors’ relationships and activities: The authors declare that there are no relationships or activities that might bias, or be perceived to bias, their work. Contribution statement: AJR-S performed bioinformatic analyses under the supervision of LCH and wrote the manuscript with LCH; EB-S performed DNA extraction and fungal sequencing and discussed the manuscript; KMN performed DNA extraction and sequencing and discussed the manuscript; GN performed DNA extraction and fungal sequencing; HO prepared maternal summary tables, advised on statistical analysis, and discussed and edited the manuscript; PA prepared maternal summary tables; GM analysed data. JDB prepared maternal summary tables; EZ-V contributed to bioinformatic analysis and discussion; RLT analysed dietary and physical activity data; PGC, JMW, GS and TH contributed to participant recruitment and sample collection; PJV contributed to study design, recruitment and sample collection; JJC contributed to participant recruitment and sample collection, and discussed and edited the manuscript; MASP contributed to study conception and design, compiled metadata and edited the manuscript; and LCH designed and supervised the study, analysed data and wrote the manuscript with AJR-S. All authors reviewed the draft manuscript and approved the final version of the manuscript. LCH is responsible for the integrity of the work as a whole and is the guarantor of the work.