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.