Faecal bacterial microbiome of native and invasive small mammal species across a urban-rural ecotone in Borneo

Samples from Sundamys muelleri, Rattus rattus, Rattus norvegicus and Suncus murinus were used in the study: "Host-microbiome associations of native and invasive small mammals across a tropical urban-rural ecotone". Abstract: Global change and urbanisation profoundly alter habitat conditions for wildlife, often forcing native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are commonly driven by the interplay of host traits and environmental features, but little is known about the plasticity in microbiome associations of native and invasive species that co-occur across urban-rural habitat ecotones. Here, we explored the host-gut microbiome associations of four sympatric small mammal species across a continuous urban-rural ecotone in Borneo, one of the planet's oldest rainforest regions with a relative recent onset of urban sprawl. Host species identity was the primary factor shaping host gut microbiomes when all the species were analysed, while land use and proximity between individuals played a more important role when only the three closest species were considered. However, despite the commensal rats Rattus rattus and Rattus norvegicus being closely related, the microbiome of the native rat Sundamys muelleri was more similar to that of Rattus rattus, while the microbiome of the congeneric R. norvegicus was more distinct, as was that of the commensal shrew Suncus murinus. The microbiome of urban-dwelling R. norvegicus was the most sensitive to land use intensity across the urban-rural ecotone, with the most distinct microbiome compositions in less urbanised environments and the largest number of bacteria shifting in abundance across the ecotone. Our finding suggests that native and invasive species with the strongest environmental niche overlap share most gastrointestinal bacteria. Even for omnivorous species with a worldwide distribution such as commensal Rattus rats, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes and whether plasticity and selective forces on gut microbiomes could limit the way native and invasive species are able to exploit novel environments.