Microbiome Changes Reveal Hidden Stress Responses in Songbirds

Every animal carries a microscopic community of bacteria, fungi and other microbes that play a critical role in health. These gut microbes help regulate the immune system, support digestion, and even influence how animals respond to stress. In birds, stress triggers the hormone corticosterone, which helps individuals cope with challenges. But when stress is prolonged or repeated, it can disrupt the balance of microbes in the gut, potentially affecting health in ways that aren't immediately visible.

While scientists have studied these stress–microbiome links extensively in mammals and domestic birds, little is known about how they operate in wild songbirds.

To fill this gap, Florida Atlantic University researchers and their collaborators studied free-living Northern cardinals (Cardinalis cardinalis), a common territorial songbird, to examine how everyday challenges affect gut microbial communities. The team characterized the birds' microbiomes before and after an 11-day period during which the birds experienced one of three conditions: repeated simulated territorial interactions with other males; a brief holding period following routine capture; or no treatment at all. Alongside the microbiome, researchers recorded levels of corticosterone, body condition and beak coloration – a carotenoid-dependent trait that signals diet, health and fitness.

The results, published in Scientific Reports, revealed that even relatively mild challenges can leave a clear mark on the gut microbiome. Birds exposed to social or environmental stressors showed changes in the composition of their gut bacteria, while the total number of microbial types remained stable. Notably, birds briefly held after capture exhibited larger and more consistent shifts in microbial communities than those exposed only to simulated social interactions, highlighting how short departures from normal routines can have measurable biological effects.

Findings show that even subtle, everyday challenges can have profound effects on an animal's internal ecosystem. By revealing the hidden links between stress, microbial communities and indicators of health, the study offers a new perspective on how wild animals navigate the demands of their environment – and how their tiny microbial passengers reflect those experiences.

These microbial changes were not just abstract numbers. They were closely linked to visible signs of health. Birds whose gut microbes shifted the most also showed changes in beak color, stress hormone levels, and body condition. Stress doesn't affect all birds in the same way. Instead, the microbiome may serve as a sensitive indicator of how individual animals are responding to their environment."

Rindy Anderson, Ph.D., senior author and associate professor, Department of Biological Sciences, FAU's Charles E. Schmidt College of Science

The study also uncovered links between specific types of bacteria and measures of health. For instance, males whose beaks became more orange – a signal often tied to condition and diet – also tended to have the largest shifts in their gut microbiome. Birds exposed to brief captivity showed changes in bacterial groups associated with stress and potential pathogens, whereas increases in beneficial bacteria were associated with better physiological condition. Stress hormone patterns mirrored these microbial shifts: in challenged birds, changes in corticosterone levels were strongly correlated with changes in gut microbes, while untreated birds showed little connection.

"This study shows that the microbiome can act like a biological record of what an animal has experienced," said Morgan C. Slevin, Ph.D., first author and alumnus of the Integrative Biology Ph.D. Program in the FAU Department of Biological Sciences. "By working with birds in their natural environment, we can see how different challenges – whether social interactions, environmental changes or brief disruptions – translate into real physiological changes that matter for health and fitness. These microbial shifts give us a window into the hidden ways wild animals respond to the world around them, helping us understand their resilience and overall well-being in ways we couldn't see from behavior alone."

By combining microbiome analysis with physiological measures and visual indicators of condition, the study offers one of the first integrated looks at how stress, health and microbial communities interact in a free-living songbird. The findings underscore the importance of studying animals in their natural habitats, where behaviors and environmental conditions can shape biology in ways that captivity studies may miss.

"The gut microbiome could serve as a sensitive measure of how wild animals respond to environmental changes, urbanization or other stressors, with potential applications for conservation, wildlife rehabilitation and understanding population health," said Anderson.

Study co-authors are Jennifer L. Houtz, Ph.D., an assistant professor of ecology and evolutionary biology at Allegheny College; and Maren N. Vitousek, Ph.D., an associate professor, Department of Ecology and Evolutionary Biology, Cornell University.

This study was funded by FAU graduate scholarships awarded to Slevin, FAU's Office of Undergraduate Research and Inquiry awarded to Anderson, the National Science Foundation Graduate Research Fellowship awarded to Houtz, and a United States Department of Education STEM EngInE grant awarded to Miami-Dade College North campus through a sub-award awarded to Anderson.