Antibiotic exposure can significantly disrupt the microbiota of a host, potentially impacting host health. Functionally important species may be lost, which could reduce nutrient availability for the host, increase susceptibility to pathogens, and more. It is unclear whether chronic antibiotic exposure permanently alters microbiota composition or if the microbiota is able to recover after antibiotic exposure ceases.
To address this question, we used Daphnia magna, a keystone zooplankton with a microbiota dominated by relatively few bacterial species. We used shotgun metagenomic sequencing to characterize the species present within the D. magna microbiota and to identify potential functions from gene content. To understand how the microbiota responds to antibiotic exposure and how it subsequently recovers, we used an antibiotic cocktail of aztreonam, erythromycin, and sulfamethoxazole. We exposed D. magna to the cocktail for five generations, removing half of each generation’s offspring and placing them in an antibiotic-free treatment. We quantified microbiota composition using 16S sequencing, comparing the microbiota of individuals in antibiotic-exposed and antibiotic-recovery treatments to the microbiota of individuals in an antibiotic-free control treatment. We quantified the fitness effects of antibiotic exposure and recovery by measuring growth, survival, and reproduction of Daphnia.
Results/Conclusions
The D. magna microbiota is dominated by five novel bacterial species: two from the Limnohabitans genus, one from Pedobacter, one from Polaromonas, and one that was unidentifiable past the Burkholderiaceae family. The two Limnohabitans species are the most abundant, comprising >80% of the D. magna microbiota. There is significant functional redundancy among these species: only 742 of 7453 coding regions are unique to one species. Functional analysis indicates that one Limnohabitans species may be able to provide the essential amino acid arginine to the host D. magna.
We found that multi-generational antibiotic exposure significantly reduced host growth and survival, but had no effect on host reproduction. This exposure also shifted the D. magna microbiota, reducing the relative abundance of Burkholderiales (Limnohabitans, Polaromonas) and increasing the abundance of Sphingobacteria (Pedobacter) and other taxa in the Proteobacteria phylum. The microbiota was able to recover 1-2 generations after exposure, and more generations of antibiotic exposure did not reduce the rate of recovery. However, hosts exposed to antibiotics for more generations grew less than those not exposed. These results suggest that important species in the D. magna microbiota are acquired from the environment, and long-term antibiotic exposure does not permanently alter a species’ microbiota.