As urban development continues to creep further into Earth’s oldest and most diverse rainforests, a Swansea University-led study reveals native and invasive small mammals aren't just adapting to their changing habitats—they may also be sharing their microbes.
Published in Molecular Ecology , the study explores the gut microbial communities of hundreds of small mammals—three rats and one shrew species—across habitat areas from city to rainforest in Borneo.
Swansea PhD student Alessandra Giacomini led the study, supervised by Dr Tamsyn Uren Webster and Dr Konstans Wells, who oversee the University’s research in biodiversity and animal health.
Working with international collaborators, the team discovered the black rat ( Rattus rattus ), an invasive species commonly found in cities and towns, had a gut microbiome more similar to the native rainforest rat ( Sundamys muelleri )—the only local species to have successfully adapted to urban life—than to its close invasive relative, the Norway rat ( Rattus norvegicus ).
Ms Giacomini said: “Our findings suggest that shared environmental use can drive microbiome similarity as much or even more than the genetic relatedness of host species.”
The shrew ( Suncus murinus ), also an urban dweller, stood out with a distinctly different microbiome profile, highlighting the diversity of microbial responses among species adapting to human-altered landscapes.
Microbiomes in invasive Norway rats were found to be most different between those living in urban areas and those in suburban areas. This suggests that the type of environment and how the rats use it not only influence how microbiomes are shared between different species, but also how habitat and diet can shape the microbiomes of individuals within the same species.
Dr Wells explained: "This raises important questions about the role of gut microbiomes in helping animals adapt to new and changing environments.”
The team’s research offers fresh insight into the impact of urbanisation on wildlife, not just in terms of where animals live, but also how it can influence their relationships with the microbial organisms living inside them, with potential implications for their health and the spread of associated infectious diseases.
Understanding these shifts could help predict which native and invasive species thrive—and which struggle—in rapidly changing environments.
Dr Uren Webster and Dr Wells’ research groups are now expanding on this work to explore a range of other species and ecosystems.
Molecular Ecology
Experimental study
Animals
Host-Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
28-Apr-2025
The authors declare no conflicts of interest.