Non-lethal sampling of passerine gut microbiome

As our understanding of the development and function of the gut microbiome grows, so too does the range of taxa being investigated. Bird gut microbiota are recently gaining more attention, and provide an interesting class of organisms to study for many reasons; including their myriad digestive physiologies and dietary strategies, conservation concern, and agricultural relevance. Many studies have used fecal samples and cloacal swabs to study avian gut bacteria without sacrificing the host bird, but none have yet evaluated how reflective these samples are of gut bacterial communities in passerines. This limits our ability to interpret results based on fecal samples and cloacal swabs. Our study compared five sample types from Zebra Finches Taeniopygia guttata: feces, cloacal swabs, large intestine, small intestine, and proventriculus.