Gastrointestinal Microbiome

Emerging research in mammals supports relationships between an animal’s health, including the stress response and cognition, and its gut microbiome. Most of what is known about this “microbiota-gut-brain-HPA axis” stems from captive mammalian research, while these relationships are largely untested in wild, non-mammalian populations. To test this in avian taxa, I conducted a series of studies with captive Zebra Finches (Taeniopygia guttata) and a wild population of Northern Cardinals (Cardinalis cardinalis). First, I quantified performance by Zebra Finches on cognitive tasks measuring learning and memory for comparison to alpha and beta diversity of the gut microbiome sampled via cloacal swab. Performance on cognitive tasks related to beta diversity but not alpha diversity, providing some of the first evidence of an avian microbiota-gut-brain axis. Next, testing for relationships between host fitness and the microbiome, I sought baseline relationships between free-living cardinals’ microbiomes and their sexual ornamentation, stress response, and body condition index. Bacterial diversity related to individual variation in body condition and several sexual ornaments, but not glucocorticoid concentrations. Finally, in an empirical test that an acute stress response can cause microbiome dysbiosis, I captured wild cardinals to sample their gut microbiome, stress response, body condition, and beak ornamentation, then recaptured and resampled individuals after ~11 days. Between captures, I administered one of two challenges to each cardinal: a temporary hold of an additional hour in a cage post-capture, repeated simulated territorial intrusions (STIs), or no challenge (as a control). Challenge type had no effect on change in alpha diversity between sample timepoints, but it had a significant impact on microbiome dissimilarity assessed by beta diversity between timepoints. Overall, the birds that showed the largest beta diversity and greatest decrease in alpha diversity between samples experienced the greatest increase in CORT scope; there were mixed results supporting a link between a reduction in beak ornamentation and microbiome dysbiosis. This is some of the first evidence of a proximate effect of a fitness challenge on the microbiome of an adult free-living songbird, with concurrent data on shifts in glucocorticoids, body condition, and ornamentation.