Survey of the Intestinal Bacterial Compositions of Three Sympatric Passeriformes Species

Aims: The gut microbiota of avian species, especially wild birds, is studied less than that of mammals. Moreover, due to ethical concerns, a vast majority of microbiota studies have been limited to their feces. In this study, we investigated the microbial composition in the upper intestinal tract of sympatric, heterospecific bird species.

Study Design: We obtained samples from three wild bird species belonging in the same Order Passeriformes: Cedar Waxwing (Bombycilla cedrorum), American Robin (Turdus migratorius) and Dark-eyed Junco (Junco hyemalis). The samples were obtained from wild birds soon after they died due to physical injury. Microbial diversity was analyzed via high-throughput sequencing of 16S rRNA gene fragments.

Place and Duration of Study: Indiana University Kokomo campus, Indiana. United States, between October 2019 and December 2020.

Methodology: Illumina Miseq sequencing of V3-V4 region of the 16S rRNA gene was employed to determine microbial composition. The α and β diversity were determined by Shannon’s diversity index and principal coordinate analysis, respectively. Pair-wise comparison of Bray-Curtis dissimilarity between birds of same species, different species, collection dates and years were analyzed.

Results: The proteobacterial sequences were predominant in all samples. However, the comparison at the level of bacterial class revealed a significant intraspecies variation in both α and β diversity. Additionally, some microbiota exhibited higher interspecies similarity than intraspecies similarity, despite these birds not sharing the same foraging guilds.

Conclusion: Our study revealed high variability in the microbial compositions within the upper part of the digestive tract of closely related Passeriform birds in their natural environment.