UC San Diego

Gut microbiota influence their host’s health through pathogenic resistance and immunological responses, nutrient uptake, metabolism, and digestion. A fish’s gut microbiome can be affected by its diet, environment, and host genetics and adaptation. The hybrids of the Owens River Tui Chub and the Lahontan Tui Chub live in freshwater stream and lake habitats within the eastern Sierra Nevada mountains. Fish living in flowing versus still water environments often experience divergent selective pressures leading to differences in behavior, morphology, physiology and diet. My thesis compares gut microbiomes of lake and river populations of wild hybrids of the Owens River Tui Chub and the Lahontan Tui Chub. Five lake populations and two stream populations were sampled and their gut microbiomes were characterized by sequencing the 16s gene. Stream sites had a higher abundance of Firmicutes and Cyanobacteria, while lake sites had a higher abundance of Fusobacteriota. The microbial community composition varied between lake and stream habitats, with habitat type explaining 6% of the variation. However, the population of origin explained 25% of the variation, indicating that population is more important than habitat type for gut microbiomes. In addition to sampling wild fish, a reciprocal transplant experiment was performed where fish were placed in lake or stream mesocosms to ask whether the fish’s microbiome is plastic in response to habitat shifts or determined mainly by the fish’s population of origin. The experiment found that transplanting Tui Chub between lakes and streams resulted in a significant change within the composition of the fish’s gut microbiome, suggesting that the microbiome is highly plastic in response to habitat shifts. These data suggest that gut microbiomes vary between lake and stream populations of Tui Chub, but that geographic location is more important than habitat type. In addition, the gut microbiome is a plastic trait that is under stronger control by host habitat than host phenotype or genotype.