Early-life gut microbiome associates with positive vaccine take and shedding in neonatal schedule of the human neonatal rotavirus vaccine RV3-BB

Josef Wagner ORCID logo ; Amanda Handley ; Celeste M Donato ; Eleanor A Lyons ORCID logo ; Daniel Pavlic ; Darren Suryawijaya Ong ORCID logo ; Rhian Bonnici ; Nada Bogdanovic-Sakran ; Edward PK Parker ORCID logo ; Christina Bronowski ORCID logo ; +17 more... Jarir At Thobari ; Cahya Dewi Satria ; Hera Nirwati ; Desiree Witte ; Khuzwayo C Jere ORCID logo ; Ashley Mpakiza ; Emma Watts ; Ann Turner ; Karen Boniface ; Jonathan Mandolo ; Frances Justice ; Naor Bar-Zeev ; Miren Iturriza-Gomara ; Jim P Buttery ; Nigel A Cunliffe ; Yati Soenarto ; Julie E Bines ORCID logo ; (2025) Early-life gut microbiome associates with positive vaccine take and shedding in neonatal schedule of the human neonatal rotavirus vaccine RV3-BB. Nature communications, 16 (1). 3432-. ISSN 2041-1723 DOI: 10.1038/s41467-025-58632-6
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Abstract

Rotavirus vaccines are less effective in high mortality regions. A rotavirus vaccine administered at birth may overcome challenges to vaccine uptake posed by a complex gut microbiome. We investigated the association between the microbiome and vaccine responses following RV3-BB vaccine (G3P[6]) administered in a neonatal schedule (dose 1: 0-5 days), or infant schedule (dose 1: 6-8 weeks) in Indonesia (Phase 2b efficacy study) (n = 478 samples/193 infants) (ACTRN12612001282875) and in Malawi (Immunigenicity study) (n = 355 samples/186 infants) (NCT03483116). Vaccine responses assessed using anti-rotavirus IgA seroconversion (IgA), stool shedding of vaccine virus and vaccine take (IgA seroconversion and/or shedding). Here we report, high alpha diversity, beta diversity differences and high abundance of Bacteroides is associated with positive vaccine take and shedding following RV3-BB administered in the neonatal schedule, but not with IgA seroconversion, or in the infant schedule. Higher alpha diversity was associated with shedding after three doses of RV3-BB in the neonatal schedule compared to non-shedders, or the placebo group. High abundance of Streptococcus and Staphylococcus is associated with no shedding in the neonatal schedule group. RV3-BB vaccine administered in a neonatal schedule modulates the early microbiome environment and presents a window of opportunity to optimise protection from rotavirus disease.


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