Northern Cardinal microbiome pilot study 2020-2021

Animal populations can exhibit dramatic variation in individual fitness, and microbiota are emerging as a potentially understudied factor influencing host health. Bacterial diversity and community structure of the gut microbiome are associated with many aspects of fitness in animals, but relatively little is known about the generality of these relationships in wild populations and non-mammalian taxa. We studied the Northern Cardinal (Cardinalis cardinalis), a member of a taxon that is ecologically important but underrepresented in microbiome research: songbirds. To test for relationships between the microbiota and host fitness, we sampled the cloacal microbiomes of wild cardinals and measured body condition index, assessed the coloration of sexual ornaments (beak and plumage), and collected blood to estimate the glucocorticoid response to stress. Both alpha and beta bacterial diversity were related to individual variation in body condition and several sexual ornaments, but not glucocorticoid concentrations. Our results from a free-living songbird population add to a growing body of research linking avian host fitness to internal bacterial community characteristics. This study sets the stage for manipulative experiments to determine how challenges to fitness and microbiomes may upset these relationships.

Methods
These data come from a wild population of Northern Cardinals (Cardinalis cardinalis) captured in South Florida from 2020-2021. Birds were captured in Tree Tops Park, Davie, FL. Data herein from each bird include 1) fitness-related parameters: coloration values of several sexual ornaments, body condition and morphometrics, and corticosterone concentrations from three sample time points during capture and 2) microbiome diversity, calculated from samples of the birds' cloacal microbiomes. Coloration was processed and calculated by photography analysis or spectroscopy (depending on which ornament is being inspected), corticosterone concentrations were estimated from blood samples using commercial enzyme immunoassay kits, and microbiome samples were processed via DNA extraction, PCR, and subsequent DNA sequencing of the V4 region of the 16S rRNA gene.