UNIVERSITY PARK, Pa. —The bacteria living on frogs’ skin could serve a vital role in protecting the animal from a deadly fungal disease. A team of researchers led by Penn State scientists found that frogs’ natural skin bacteria can help them fight disease and improve their chances of survival.
The study, recently published in the journal Animal Microbiome , draws a causal relationship between the natural bacteria inhabiting the frog’s skin, called the skin microbiome, and the frog’s ability to survive a deadly fungal pathogen — a major threat to wild frogs and other amphibious animals throughout the world.
“This is one of the clearest demonstrations that a host's natural skin bacteria can be a frontline defense against a pathogen that has devastated amphibian populations globally,” said Gui Becker, associate professor of biology in the Penn State Eberly College of Science and senior author of the paper. “One of the key messages from this study is that it's not simply the diversity of these bacteria — referred to as the skin microbiome — that matters, but the protective function of these bacteria.”
The pathogen is called a chytrid fungus (Batrachochytrium dendrobatidis or Bd); it causes skin damage in amphibians and eventually heart failure. To test how skin-associated bacterial communities can protect tropical frog species against disease, the research team conducted a lab experiment in Brazil focusing on two frog species: Haddadus binotatus and Ischnocnema henselii. The experimental design allowed them to understand the effect of microbiome suppression on disease risk in these amphibians. Throughout the study, researchers used DNA sequencing to identify the bacteria living on each frog's skin and compare how these bacterial communities predict host health.
The team found that one frog species, H. binotatus , naturally tolerated the fungus when its healthy skin microbiome could help protect it from infection. When that protective community of bacteria was suppressed with antibiotics, the frogs became more likely to develop signs of disease. In contrast, the second frog species, I. henselii , remained highly susceptible to the fungus regardless of skin microbiome suppression, indicating that different frog species rely on different strategies to defend themselves against this fungal disease.
“We see this striking contrast: one species has one of the highest prevalences of the fungus, while the other has no infections in the wild. That made them a perfect pair to understand what role the microbiome might be playing,” said Laura Schuck, doctoral student in the Intercollege Graduate Degree Program in Ecology at Penn State and lead author of the study. “For years we knew that the tropical frog H. binotatus rarely became infected with the fungus in the wild, but we didn't know why. Now we know. This study moved us from correlation to experimental evidence that the microbiome really is important against this disease.”
Developing an understanding of specific protective bacterial mechanisms was painstaking work, the researchers said. Schuck cultured roughly 700 strains of bacteria from the frogs’ skin, grew each one in culture, and exposed the chytrid fungus to the bacteria’s chemical byproducts, tracking fungal growth over a week.
The team then sequenced each culture, building a custom reference database that linked bacterial identity to how strongly it inhibited the fungus, so they could map exactly which protective bacteria were present on each frog and when. The database allowed the researchers to identify disease-inhibiting bacteria that helped certain frogs survive infection.
“We designed the experiment at two levels,” Becker said. “First, a simple yes-or-no test to see if the microbiome was contributing a defense against disease, then we dug deeper into the function of every bacterium, building a reference database. Those two checks together allowed us to test the specific defense mechanisms of the microbiome.”
The next step, the researchers said, is to look even closer into how frogs recruit their protective skin microbiomes from the natural environment with the goal of safeguarding habitats that supporting the beneficial microbes.
“If we understand how this frog recruits and maintains beneficial bacteria, we can begin to understand how the microbiome works as a natural defense and what we need to protect in the environment to keep those bacteria available to amphibians and other endangered vertebrates,” Schuck said.
Other authors on the study are Shannon Buttimer, postdoctoral scholar at Penn State who recently earned a doctorate in ecology from the University; Julia R. Ernetti and Luís Felipe Toledo of the University of Campinas; Ananda B. de Assis and Renato A. Martins of São Paulo State University; Mariana Pontes and Maria B. Tosta of University of São Paulo; and Ana C. Zanatta of the University of São Paulo–Ribeirão Preto.
This research was funded by the U.S. National Science Foundation under award numbers DBI-2120084 and DEB-2413542; the Sao Paulo Research Foundation under award numbers (FAPESP #2022/11096-8, #2020/02994-7 and #2022/07125-2; and the National Council for Scientific and Technological Development under award numbers CNPq #302834/2020-6 and #152052/2024-0 This content is solely the responsibility of the authors and does not necessarily represent the views of the funders.
At Penn State, researchers are solving real problems that impact the health, safety and quality of life of people across the commonwealth, the nation and around the world.
For decades, federal support for research has fueled innovation that makes our country safer, our industries more competitive and our economy stronger. Recent federal funding cuts threaten this progress.
Learn more about the implications of federal funding cuts to our future at Research or Regress .
Animal Microbiome
Experimental study
Animals
Differential skin-bacteriome-mediated defense against chytridiomycosis in two neotropical frog species
4-Aug-2026