Data from: Host genetics and the skin microbiome independently predict parasite resistance

Host responses to parasite infection involve several interacting systems.
Host genetics determine much of the response, but it is increasingly clear
that the host-associated microbiome also plays a role. Genetically
determined systems and the microbiome can also interact; for example, the
microbiome can modulate the immune response, and vice versa. However, it
remains unclear how such interactions between the host immune system and
the microbiome may influence the host’s overall response to parasites. To
investigate how host genetics and the microbiome interact to shape
responses to parasites, we imposed truncation selection on Trinidadian
guppies (Poecilia reticulata) for low and high resistance to the
specialist ectoparasite Gyrodactylus turnbulli. After 3-6 generations of
breeding without parasites, we sampled the skin-associated microbiome and
infected fish from each line. We applied Dirichlet Multinomial Modeling
(DMM) machine-learning to identify bacterial community types across lines
and evaluated how selection line and community type explained variations
in infection severity. Our findings showed that among females, the
resistant line had significantly lower infection severity, while the
susceptible line had higher infection severity. Among males, only the
susceptible line experienced higher infection severity compared to the
other lines. Line did not explain skin microbial diversity, structure or
composition. Our DMM analysis revealed three distinct bacterial community
types, independent of artificial selection lines, which explained just as
much variation in infection load as selection line. Overall, we found that
the microbiome and host genetics independently predict infection severity,
highlighting the microbiome's active role in host-parasite
interactions.