It is a popular belief that exposure to microbes and pathogens in the environment strengthens the immune system. In amphibians, the community of microbes on the skin, called the microbiome, may have antibacterial and antifungal properties. These skin microbes can play a key role in battling the deadly chytrid fungus Batrachochytrium dendrobatidis (Bd), which has affected more than 500 amphibian species and contributed to nearly 90 extinctions over the past five decades. In a new study published in Proceedings of the National Academy of Sciences (PNAS), researchers at the Smithsonian Tropical Research Institute (STRI), the Pennsylvania State University and other institutions discovered that connecting distinct types of habitats enhances the ability of amphibian's skin microbiome to defend it from diseases, by increasing the presence of beneficial bacteria.
Scientists sampled 40 sites in Brazil's Atlantic Forest. The sites were either forest fragments — unconnected patches of forest — or continuous forests, which varied in the degree of habitat loss. At each site they measured the natural land cover, the density of the forest edge and the distance between natural forest fragments and aquatic habitats, a.k.a habitat split. They also studied the skin bacterial community of four frog species which vary in the use of aquatic environments, and consequently in their exposure to Bd's waterborne zoospores. For instance, species with young stages (eggs and tadpoles) that require water bodies are forced to migrate from forest fragments through degraded habitats (e.g. caw pastures) to reach their breeding sites.
Scientists found that higher levels of habitat split are related to a reduced ability of amphibian skin bacteria to inhibit Bd in all four species.
"Our study provides evidence that connectivity among habitats is essential for maintaining multiple levels of biodiversity, from host-associated bacteria with protective functions to their respective host species, thus, highlighting a critical link between environmental disturbance, microbial defenses, and disease dynamics," said lead author Daniel Medina, STRI research associate and resident lecturer at the Center for Tropical Island Biodiversity Studies (TIBS) of the School for Field Studies (SFS).
"These results suggest that connected landscapes allow animals to maintain microbiomes that are better equipped to fight pathogens," associate professor of biology at Penn State and senior author of the study Gui Becker added.
The effects of habitat split on host-associated microbiomes and disease susceptibility are likely to occur in other animal species that migrate across large areas, especially those requiring different types of habitats to complete their life cycles. "Many species (from migratory birds to fish such as salmon and large mammals) move among different habitats as they feed, breed, or disperse," Becker said. "When those habitats become disconnected, it may not only affect movement but also alter how animals interact with microbes and pathogens."
Habitat fragmentation is widely known to be a major cause of biodiversity loss. This study exposes a deeper effect resulting from natural forests becoming divided into smaller areas by agriculture, development, or other land uses: the decrease of bacterial diversity in host-associated microbiomes.
"Conserving habitat connectivity is vital for preserving wildlife's natural defenses and maintaining multiple levels of biodiversity, including protective bacteria, helping to prevent population declines and reduce extinction risks," said Medina.
"Protecting habitat connectivity may help preserve multiple layers of biodiversity," wrote the authors, "from the animals we see to the microbial communities that help keep them healthy."
Recent research shows that it's also better for kids to spend time in microbially biodiverse environments; it is possible that we all may benefit from the same rule of thumb that applies to amphibians.
Reference: Medina, D., Martins, R. A., Prist, P., Lyra, M. L., Kearns, P. J., Woodhams, D. C., Buttimer, S., Neely, W. J., Schuck, L. K., Greenspan, S. E., Bletz, M. C., São‑Pedro, V. A., Haddad, C. F. B., & Becker, C. G. 2026. Connecting Habitats, Boosting Disease Resistance: Spatial Connectivity Enhances Amphibian Microbiome Defenses Against Fungal Pathogen. Proceedings of the National Academy of Sciences (PNAS): 123 (17) e2520745123. https://doi.org/10.1073/pnas.252074512
About the Smithsonian Tropical Research Institute
Headquartered in Panama City, Panama, STRI is a unit of the Smithsonian Institution. Our mission is to understand tropical biodiversity and its importance to human welfare, to train students to conduct research in the tropics and to promote conservation by increasing public awareness of the beauty and importance of tropical ecosystems. Watch our video , and visit our website , Facebook , X and Instagram for updates.
