Infection with a small intestinal helminth, Heligmosomoides polygyrus bakeri, consistently alters microbial communities throughout the murine small and large intestine

•Heligmosomoides polygyrus bakeri (Hpb) impacts murine intestinal bacterial communities.•The impact on the bacterial community is not restricted to the site of infection.•The impact depends on the initial microbiome and other factors such as worm genetic variations.•A bacterium is highly associated with H. polygyrus bakeri infection across experimental conditions.•The bacterium is not carried over in the intestine by infective H. polygyrus bakeri larvae.