Pinworm microbiomes are distinct from their chipmunk host gut microbiota

Abstract Mammals house a complex community of gut bacteria, known as the microbiome, as well as endoparasitic helminths. Very little is known about how much of helminth microbiota are derived or distinct from their hosts. Helminths that inhabit the gastrointestinal tract, a microbially rich environment, would likely have many opportunities to derive a microbial community from their host. We characterized and compared the gut microbiome of chipmunk hosts and the internal microbiome of their endoparasitic pinworms, a type of nematode. We sampled fresh feces and used 16S rRNA sequencing to characterize the microbiomes of the Crater Yellow-pine Chipmunk (Tamias amoenus cratericus) and their pinworms (Heteroxynema cucullatum). Microbiomes differed in bacterial species composition between chipmunks and pinworms. Pinworm gut microbiomes also had less diverse bacterial communities than their chipmunk host microbiome. Pinworms and the chipmunks they inhabited shared few bacterial taxa, demonstrating that pinworms have a microbiota distinct from their chipmunk host. Chipmunks collected from different localities showed minor differences in relative abundances of bacterial composition, indicating that locality may have an influence on microbial makeup. Our findings demonstrate that pinworms, although residing and interacting inside the gut of a chipmunk, house their own distinct microbial communities.