Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacteria in wild non-primate mammals. Here we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate, and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. Civetta, while in Genetta spp. we observed an opposite pattern. We further found that individuals with similar diets have similar gut bacterial communities in both species. This association tended to be driven by specific associations of dietary items to specific gut bacterial taxa, rather than entire communities, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of wild mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat change.

Microbial communities in guts flexibly adjust to changes in host dietary intakes, but the relationship between diet and gut microbiome is still poorly studied in wild animals. DNA metabarcoding approaches are frequently used to characterise diets or gut microbiomes of diverse species. However, to date, no study has combined these approaches to investigate diet-gut microbiome associations in wild mammals with diverse and fluctuating dietary intakes, such as omnivores. Here, we do this for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. We characterised bacterial communities and identified taxonomic groups within diet by sequencing vertebrate, invertebrate and plant markers on faecal samples. This led us to establish diet compositions that diverged from what has previously been found using visual identification methods for these species. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal-based diets in C. Civetta, and higher proportions of plants consumed by Genetta spp. Diet similarity correlated with gut microbiome similarity in Genetta spp., indicating that plant consumption may be an important driver of gut microbiome structure. The novel insights we provide into the omnivorous diet of C. civetta and Genetta spp. highlight the importance of detailed identification of the dietary guild of species, not only for ecology and conservation, but also when researching how diet shapes the gut microbiome.

It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. But evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones between related species provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with forecrown colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 79 individuals, measuring spectral reflectance of forecrown feathers as well as scoring colours from photographs. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird that we assembled. Admixture mapping using 104,933 SNPs identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score. The hybrid zone was bimodal with asymmetric backcrossing, consistent with the hypothesis that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males may reinforce species divergence and is consistent with the hypothesis that converted carotenoids are an honest signal of quality.