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Background  Inferring the microbiota diversity of helminths enables depiction of evolutionarily established ecological and pathological traits that characterize a particular parasite-host interaction. In turn, these traits could provide valuable information for the development of parasitosis control and mitigation strategy. The parasite  Anisakis pegreffii  (Nematoda: Anisakidae) realizes the final stage of its life-cycle within gastric chambers of aquatic mammals, causing mild-to-moderate granulomatous gastritis with eosinophilic infiltrate, to severe ulcerative gastritis with mixed inflammatory infiltrate, often associated with bacterial colonies. However, its interaction with the host microbiota remains unknown, and might reveal important aspects of parasite colonization and propagation within the final host.    Methods  MySeq Illumina sequencing was performed for the  16S  rRNA gene from microbiota isolated from larvae, and uterus and gut of adult  A. pegreffii  parasitizing stranded striped dolphins ( Stenella coeruleoalba ). To assess the potential presence of  Brucella ceti  within isolated microbiota,  Brucella -targeted real-time PCR was undertaken. In addition, TEM of the gastrointestinal tract of the infective third-stage (L3) and transitioning fourth-stage larvae (L4) was performed to characterize the morphological differences and the level of larval feeding activity.    Results  In total, 230 distinct operational taxonomic units (OTUs) were identified across all samples ( n  = 20). The number of shared taxa was lower than the number of taxa found specifically in each parasite stage or organ. The dominant taxon was  Mycoplasmataceae  (genus  Mycoplasma ) in the gut and uterus of adult  A. pegreffii , whereas  Fusobacteriaceae  (genus  Cetobacterium ) was the most abundant in 40% of larvae, alongside  Mycoplasmataceae . No  B. ceti  DNA was detected in any of the microbiota isolates. TEM revealed differences in gut ultrastructure between L3 and L4, reflecting a feeble, most likely passive, level of feeding activity in L3.    Conclusions  Microbiota from L3 was more related to that of the gut rather than the uterus of adult  A. pegreffii . Taxa of the larval microbiota showed qualitative and quantitative perturbations, likely reflecting the propagation through different environments during its life-cycle. This suggests an ontogenetic shift in the alpha and beta diversity of microbial communities from uterus-derived towards cetacean-derived microbiota. Although TEM did not reveal active L3 feeding, microbiota of the latter showed similarity to that of an actively feeding adult nematode.    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3636-z) contains supplementary material, which is available to authorized users.

Microbiota and gut ultrastructure of Anisakis pegreffii isolated from stranded cetaceans in the Adriatic Sea