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.

Haemosporidians are among the most common parasites in birds and often impact negatively host fitness and consequently can affect entire host populations. It is therefore important to determine what factors influence parasite prevalence, particularly if they are caused by anthropogenic activities. Here we explore the effect of temperature, forest cover, and proximity to anthropogenic disturbance on haemosporidian prevalence and host-parasite networks on a horizontal spatial scale, comparing four fragmented forest patches and five localities within a continuous forest in Papua New Guinea. We find that the majority of Haemosporidian infections are caused by the genus Haemoproteus and that avian-haemosporidian networks are more specialized in continuous forests. At the community level, only forest cover was negatively associated with Haemoproteus infections, while abiotic and anthropogenic effects on parasite prevalence differed between bird species. We further tested if prevalence and host-parasite networks differed between the canopy and the understorey (vertical stratification) and found significantly higher Haemoproteus prevalence levels in the canopy, and the opposite trend for Plasmodium prevalence. This implies that birds experience distinct parasite pressures depending on the stratum they inhabit, likely driven by differences in vector communities. These three-dimensional analyses of avian-haemosporidians at horizontal and vertical scales provides a deeper understanding of the environmental factors driving haemosporidian prevalence in tropical lowland forests of New Guinea. Collectively, our results suggest that the effect of abiotic variables on haemosporidian infections are species specific, and that factors influencing community-level infections are primarily driven by host community composition.