The health and fitness of macroorganisms depends upon the complex and reciprocal feedbacks between the microbiome and its host. However, little is known about how processes operating at these two levels of biological organization interact to govern the assembly and stability of the microbiome in healthy vs. diseased organisms. We conducted a fully factorial tank experiment on fragments of the Staghorn coral Acropora cervicornis collected from the same location in Bocas del Toro, Panama to address this important issue by determining how (i) host genotype (8 genotypes), (ii) antibiotic exposure (control vs. exposed to antibiotics), and (iii) different sequences of double doses of disease vs. healthy microbiomes (healthy then healthy; diseased then diseased; healthy then diseased; diseased then healthy) affected the structure of the microbiome over (iv) time. We used 16s_v3v4 rRNA microbial tag sequencing to genetically profile the changes in the microbial communities and analyzed the data using multivariate methods (PERMANOVA and ordination).
Our analyses of the microbial community immediately following antibiotic exposure but prior to dosing revealed a significant interaction between host genotype and antibiotic exposure. This interaction became non-significant over time suggesting that the host’s ability to regulate its microbiome is weak and transient. We also saw a significant interaction between antibiotic exposure, dosing, and time suggesting that the effect of dosing depends on the initial microbiome and changes over time. Specifically, the effect of dosing on microbial community structure was initially weak but became stronger over time, with corals receiving a double dose of healthy microbiomes but no antibiotics clustering together but separately from those receiving a double dose of diseased microbiomes. Hence, corals whose microbiomes were reset via antibiotics were easier to convert to a diseased microbiome via dosing than those whose microbiomes remained intact. These results support the probiotic hypothesis whereby the microbiome plays an important role in warding off would-be invaders such as microbial pathogens. Interestingly, the intermediate dosing treatments (healthy then diseased; diseased then healthy) yielded intermediate microbiomes suggesting that there are no priority effects. Overall, our results show that competition plays an important role in microbiome assembly and, ultimately, the health of the host.