Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term.

Introduction There is compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome. Antibiotics cause profound changes in the microbiome. However, the effect of intrapartum and early-life antibiotics on the maternal intestinal and breast milk microbiome, and the infant oral and intestinal microbiome, and whether effects are only short term or persist long term remain uncertain. Methods and analyses In this prospective cohort study, we will use metagenomic sequencing to determine: (1) the effect of intrapartum antibiotics on the composition of the breast milk, and the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (2) the effect of antibiotic exposure in the first year of life on the composition of the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (3) the effect of disruption of the infant oral and intestinal microbiome on health outcomes and (4) the compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome. Ethics and dissemination The ABERRANT study has been approved by the commission cantonale d'ethique de la recherche sur l'etre humain (CER-VD) du Canton de Vaud (#2019-01567). Outcomes will be disseminated through publication and will be presented at scientific conferences. Trial registration number NCT04091282.