Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants

The microbiome inherited at birth exerts marked effects on immune programming with long-term health consequences. Here, we demonstrated that the gut, vaginal, and oral microbial diversity of pregnant women with SARS-CoV-2 infection is reduced, and women with early infections exhibit a different vaginal microbiota composition compared to healthy controls at the time of delivery. Accordingly, infants born to pregnant women with early SARS-CoV-2 infection exhibit a unique oral microbiota dominated by Streptococcus species. Together, we demonstrated that SARS-CoV-2 infections during pregnancy, particularly early infections, are associated with lasting changes in the microbiome of pregnant women compromising the initial microbial seed of their infant. Our results highlight the importance of further exploring the impact of SARS-CoV-2 on the infant’s microbiome-dependent immune programming. One Sentence Summary Pregnant patients with SARS-CoV-2 infection early in pregnancy and with active infection exhibit an altered vaginal and oral microbiota that is passed on to infants. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement HL, AMM, and AMC received funding to execute this study from the COVID-19/Pandemic Research Fund at UMass Chan Medical School. HL is also funded by the Worcester Foundation Grant. Funding sources for AMM, GF, and CF were also provided by MassCPR Evergrande Award. AMM was supported through the National Institutes of Health, NCI Serological Sciences Network (U01 CA261276). AMC is funded by The Leona M. and Harry B. Helmsley Charitable Trust. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Institutional Review Board at the University of Massachusetts Chan Medical School. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Sequencing data are available in a public, open-access repository: the NCBI database, BioProject ID: PRJNA871082. Additional de-identified clinical metadata are available on reasonable request.