Sex, Contraceptives, and Social Grouping Shape the Structure of Dolphin Reproductive Microbiota

The reproductive microbiota is important for host’s health and breeding success. Cetaceans (whales, dolphins, porpoises) are aquatic-obligate mammals inhabiting microbe-rich water environments, posing unique challenges for establishing and maintaining healthy microbiota. Limited research has explored cetacean reproductive microbiomes, with no studies characterizing mammary and placental microbiota within the infraorder. We used 16S rRNA metabarcoding of 272 samples to characterize the genital, mammary, gastrointestinal, and respiratory microbiomes of 60 common bottlenose dolphins (Tursiops truncatus) and 4 rough-toothed dolphins (Steno bredanensis) housed under human care, in addition to milk and placenta samples from one common bottlenose dolphin. Microbiome composition differed profoundly between the two dolphin species and across body sites. Reproductive microbiomes were lower in species richness compared to gastric and respiratory microbiomes. Body site patterns were relatively conserved within dolphin species, although genital microbiomes tended to cluster by facility and respiratory microbiome varied geographically. Dolphins housed together off contraceptives exhibited similar vaginal and penile microbiomes, suggesting bacteria exchange between the sexes through socio-sexual contact. Contraceptive intake did not alter vaginal, mammary, gastric, rectal, and respiratory microbial profiles. Dolphin mammary slit hosted a microbiome distinct from other body sites. Mammary and milk microbiomes were similar, indicating that dolphin mammary slit may play a role in milk colonization. Staphylococcus, Enterococcus, Streptococcus, and Corynebacterium were detected in the placenta and corresponding deceased neonate, yet absent in mother’s vagina and habitat water, suggesting vertical transmission of potential pathogens occurred during gestation. Our findings reveal novel species- and body site-specific microbiome patterns that shed light on the interplay between host biology, social behavior, and microbial communities in dolphins.