An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension-feeding bivalves

Suspension-feeding bivalves are critical members of aquatic ecosystems worldwide, which is why research into their host-associated microbiota is growing. Experiments that artificially diminish the native microbial communities of bivalves in vivo will be increasingly necessary to evaluate the functional role of microbes within their hosts. Previous methods to manipulate the microbiome of bivalves lack standardization and, often, verification of successful disturbance. The goal of this study was to evaluate antibiotic administration as a method for perturbing the gut microbiome of bivalves in two separate, but related, experiments. In the first, a mixture of antibiotics was delivered to eastern oysters for 4 days to probe effects on gut microbial carbon usage, diversity, and taxonomic composition. In the second, the same antibiotic mixture was administered to blue mussels for 21 days to probe effects on microbial abundance, diversity, and taxonomic composition. In both experiments, animals were administered antibiotics in isolation, and stringent sterilization methods were employed, which included sterilized seawater and microalgal food. The results of the oyster experiment revealed that antibiotics substantially reduced microbial carbon usage and perturbed community composition. In the mussel experiment, antibiotics lowered microbial abundance and species richness and significantly altered community composition. Taken together, results from the two experiments demonstrate that antibiotics can be used to effectively alter the function and composition of the gut microbial community of bivalves. Future research that aims to perturb the microbiomes of suspension-feeding animals should incorporate aspects similar to the protocols described herein. Additionally, future studies must include verification, ideally high-throughput DNA sequencing coupled with microbial quantification, that the antibiotic perturbation was successful.