A gastrointestinal nematode in pregnant and lactating mice alters maternal and neonatal microbiomes

•Nematode infection increased beta-diversity and altered abundances of several species of bacteria in the maternal caecum.•Maternal nematode infection was associated with increased beta-diversity in the stomach of 2 days old pups.•Between postpartum days 2 and 7, the differential abundance of Lactobacillus increased in pups of infected dams.•Several putatively beneficial pathways were predicted to be up-regulated in the neonatal microbiome of infected dams.