Feasibility of genetically mapping microbiome composition inA. mexicanus
Despite their distinct appearance and behavior, A. mexicanussurface and cave morphotypes have remained interfertile. F2 surface/cave hybrids have been used in numerous quantitative trait loci (QTL) mapping studies to identify genetic changes associated with cavefish evolution . Using microbiome composition as a trait for QTL mapping in mice has revealed genomic regions associated with abundance of bacterial taxa in the intestine . We next investigated the feasibility of using proportional abundance of taxa in the microbiome as a trait for QTL mapping in A. mexicanus by examining how stable bacterial taxa abundance is across time in individual fish. We reasoned that if the trait is highly plastic, it may be less likely to identify genetic markers associated with trait variance at the population level. We focused on Fusobacteriota since proportional abundance of this taxa was the most different between morphotypes.
We found that Fusobacteriota was at very low proportional abundance in 16s rRNA sequencing data from gut contents and pooled fecal samples of laboratory raised Pachón cavefish compared to other morphotypes (Figure 4A-B ). Discovering differences in abundance in fecal samples suggested that 1) feces can be used to quantify differences in Fusobacteriota between individuals, and that 2) an individual fish could be sampled over time. We collected feces from individual three-year-old surface fish and Pachón cavefish that were siblings of the six-month-old fish used for microbiome sequencing. Using quantitative PCR, we found that Fusobacteriota 16s rRNA was always detected in the feces of the surface fish (n = 6) and was undetectable (n = 2/6) or had a higher threshold for detection in the feces of most Pachón cavefish (n=3/4, Figure 4C ). Our data suggest that Fusobacteriota abundance varies between individual fish, but that lower abundance in Pachón compared to surface fish is a trait that persists through life. We also found that Fusobacteriota abundance was stable in individual fish sampled at different times; fish with high or low abundance consistently had high or low abundance (Figure 4D ). The results demonstrate the feasibility of using proportional abundance of Fusobacteriota as a trait for genetic mapping in A. mexicanusto identify host-driven molecular pathways that shape microbiome composition.