Fig. 3. Examples of how the gut microbiota composition depends on host sex, genotype (cross), and infection status, focusing on the relative abundance of microbial Orders.

To visualize these effects we first adjusted for variation due to rearing location (room), by calculating residuals from a quasibinomial general linear model of the focal Order’s read counts (out of the total reads per fish) regressed on rearing room. Here we plot the mean (and ±1 s.e. confidence intervals) for this residual abundance, for various groups of fish to illustrate infection and host effects. a Fusobacteriales exhibit a significant decrease in cestode-infected fish, both males (black) and females (gray). b Lactobacillales are more abundant in males (black) than in females (gray) regardless of infection status. c Clostridiales abundance is reduced in infected males, but not infected females (black = males, gray = females). d Rhodobacterales are more common in females for uninfected fish, but more common in males for infected fish (black = males, gray = females). e Caulobacterales are more abundant in F2 hybrids than in either backcross, regardless of infection status (black = uninfected, gray = infected). f Rhodobacterales are more abundant in fish with a greater fraction of Roberts lake ancestry, but only among uninfected fish; infection leads to a higher Rhodobacterales abundance that is similar across fish genotypes (black = uninfected, gray = infected). Supplementary Fig. 5 shows the same plots, but with all data points included to show the small effect size relative to high among-individual variation.