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.