Temporal dynamics of the chicken mycobiome

Authors: Davies, Cary; Summers, Katie; ARFKEN, ANN - Oak Ridge Institute For Science And Education (ORISE); DARWISH, NADIA - US Department Of Agriculture (USDA); CHAUDHARIL, ATUL - US Department Of Agriculture (USDA); Foster Frey, Juli; Schreier, Lori; Proszkowiec-Weglarz, Monika

Submitted to: Frontiers in Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2022
Publication Date: 12/15/2022
Citation: Davies, C.L., Summers, K.L., Arfken, A., Darwish, N., Chaudharil, A., Foster Frey, J.A., Schreier, L.L., Proszkowiec-Wegla, M.K. 2022. Temporal dynamics of the chicken mycobiome. Frontiers in Physiology. 13:1057810. https://doi.org/10.3389/fphys.2022.1057810.
DOI: https://doi.org/10.3389/fphys.2022.1057810

Interpretive Summary: It is well established that bacterial members of the gut microbiome play an integral role in host health. Yet recent studies indicate that lowly abundant organisms such as fungi also play a critical role in gut homeostasis and disease. Here, we examine the fungal communities, or mycobiomes, in the small and large intestine of broiler chicks from birth through 14 days of age. We also assess the effects of posthatch delays in access to feed on mycobiome composition. In commercial production, newly hatched chicks do not have access to feed for the first few days following birth due to variable hatch times, sexing and sorting, vaccination, and transport from the hatchery to farms. This delay results in numerous negative health repercussions. We did not find that posthatch delays in food access altered the long term composition of the mycobiome. However, we did find significant trends in mycobiome composition across development and among different sites in the gastrointestinal tract. These data advance our understanding of intestinal function in the chicken and provide a foundation for the development of therapeutics which target the gut to improve chicken health and productivity.

Technical Abstract: The microbiome is an integral part of chicken health and can affect immunity, nutrient utilization, and performance. The role of bacterial microbiota members in host health is relatively well established, but less attention has been paid to fungal members of the gastrointestinal tract (GIT) community. Yet human studies indicate that fungi play a critical role in health. Here, we describe fungal communities, or mycobiomes, in both the lumen and mucosa of the chicken ileum and cecum from birth through 14 days of age. We also assess the effects of delayed access to feed immediately post-hatch on mycobiome composition, as post-hatch feed delay is commonly associated with poor health performance. Chicken mycobiomes in each of the populations are distinct and changed over time. All mycobiomes were dominated by Giberella, but Aspergillus, Cladosporium, Sarocladium, Meyerozyma, and Penicillium were also abundant. Relative abundances of some taxa differed significantly over time. In the cecal and ileal lumens, Penicillium was present in extremely low quantities or absent during days one and two and then increased over time. Meyerozyma and Wickerhamomyces also increased over time in luminal sites. In contrast, several highly abundant unclassified fungi decreased after days one and two, highlighting the need for improved understanding of fungal gut biology. Mycobiomes from chicks fed during the first two days post birth versus those not fed during the first two days did not significantly differ, except during days one and two. Similarities observed among mycobiomes of fed and unfed chicks at later timepoints suggests that delays in post-hatch feeding do not have long lasting effects on chicken mycobiome composition. Together, these results provide a foundation for future mycobiome studies, and suggest that negative health and production impacts of delayed feeding are not likely related to development of fungal populations in the GIT.