Chicken intestinal mycobiome: Biogeography, succession, and its response to bacitracin methylene disalicylate

The gastrointestinal (GI) tract harbors a diverse population of microbes consisting of not only bacteria, but also fungi, viruses, and protozoa. While much work has been focused on the characterization of intestinal bacterial community, very little is known about the fungal community, or mycobiota, in different animal species and chickens in particular. Here we characterized the biogeography and maturation of the mycobiota in the GI tract of broiler chicks and further examined its possible shift in response to bacitracin methylene disalicylate (BMD), a commonly used in-feed antibiotic, through Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes. We revealed an obvious biogeographic difference in the mycobiota composition along the GI tract, with the crop, gizzard, and duodenum being the most diverse than the jejunum, ileum, cecum, and colon. The intestinal mycobiome was dominated by Ascomycota and Basidiomycota, with 3 genera including Microascus, Trichosporon, and Aspergillus accounting for over 83% of the total fungal population in any given segment, except for the duodenum, which harbored the most diverse fungal community. We also observed an obvious age-dependent shift of the cecal mycobiota. Dietary supplementation of BMD at a subtherapeutic level of 55 mg/kg resulted in a significant decrease in the cecal fungal diversity. Taken together, we provided a comprehensive biogeographic view and maturation of the chicken intestinal mycobiota and its influence by an in-feed antibiotic. A better understanding of intestinal mycobiota may lead to development of novel strategies to improve poultry health and productivity.

Key Words: mycobiome, microbiome, gut health, poultry.