Association between maternal breastmilk microbiota composition and rotavirus vaccine response in African, Asian, and European infants: a prospective cohort study

Background Maternal breastmilk is a source of pre- and pro-biotics that impact neonatal gut microbiota colonisation. Since oral rotavirus vaccines (ORVs) are administered at a time when infants are often breastfed, breastmilk microbiota composition may have a direct or indirect influence on vaccine take and immunogenicity. Methods Using standardised methods across sites, we compared breastmilk microbiota composition in relation to geographic location and ORV response in cohorts prospectively followed up from birth to 18 weeks of age in India ( n = 307), Malawi ( n = 119), and the UK ( n = 60). Results Breastmilk microbiota diversity was higher in India and Malawi than the UK across three longitudinal samples spanning weeks of life 1 to 13. Dominant taxa such as Streptococcus and Staphylococcus were consistent across cohorts; however, significant geographic differences were observed in the prevalence and abundance of common and rare genera throughout follow-up. No significant associations were identified between breastmilk microbiota composition and ORV outcomes including seroconversion, post-dose 1 vaccine shedding, and/or post-vaccination rotavirus-specific IgA level. Conclusions Our findings suggest that breastmilk microbiota composition may not be a key factor in shaping trends in ORV response within or between countries. ### Competing Interest Statement M.I.G. has received research grants from GSK and Merck, and has provided expert advice to GSK. K.C.J. has received investigator-initiated research grant support from GSK. ### Funding Statement This work was supported by different funders per site. The UK and Malawi sites were funded by the UK Medical Research Council and the UK Department for International Development (Newton Fund MR/N006259/1). K.C.J. is funded by a Wellcome International Training Fellowship (number 201945/Z/16/Z). The site in India was funded by the Government of India Department of Biotechnology. ### 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 study was approved by the Institutional Review Board at the Christian Medical College in Vellore (IRB No. 9472/24.06.2015), the College of Medicine Research and Ethics Committee in Blantyre (P.01/16/1853), and the North West Liverpool Central Research Ethics Committee in Liverpool (15/NW/0924). 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 The raw sequence data for this study have been deposited in the European Nucleotide Archive under accession code PRJEB38948. Processed data and analysis code are available on Github (https://github.com/eparker12/RoVI) The datasets generated during and/or analyzed during the current study are available from the corresponding author following reasonable request.