Chicken intestinal mycobiome: Initial characterization and its response to bacitracin methylene disalicylate

Kelsy Robinson, Yingping Xiao, Timothy J. Johnson, Binlong Chen, Qing Yang, Wentao Lyu, Jing Wang, Nicole Fansler, Sage Becker, Jing Liu, Hua Yang, Guolong Zhang

Research output: Contribution to journalArticlepeer-review


The gastrointestinal (GI) tract harbors a diverse population of microorganisms. While much work has been focused on the characterization of the 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 of the mycobiota along the GI tract of day 28 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. Out of 124 samples sequenced, we identified a total of 468 unique fungal features that belong to four phyla and 125 genera in the GI tract. Ascomycota and Basidiomycota represented 90% to 99% of the intestinal mycobiota, with three genera, i.e., Microascus, Trichosporon, and Aspergillus, accounting for over 80% of the total fungal population in most GI segments. Furthermore, these fungal genera were dominated by Scopulariopsis brevicaulis (Scopulariopsis is the anamorph form of Microascus), Trichosporon asahii, and two Aspergillus species. We also revealed that the mycobiota are more diverse in the upper than lower GI tract. The cecal mycobiota transitioned from being S. brevicaulis dominant on day 14 to T. asahii dominant on day 28. Furthermore, 2-week feeding of 55 mg/kg BMD tended to reduce the cecal mycobiota α-diversity. Taken together, we provided a comprehensive biogeographic view and succession pattern of the chicken intestinal mycobiota and its influence by BMD. A better understanding of intestinal mycobiota may lead to the development of novel strategies to improve animal health and productivity.

Original languageEnglish (US)
Article numbere00322-20
JournalApplied and environmental microbiology
Issue number13
StatePublished - Jul 1 2020

Bibliographical note

Funding Information:
We thank Jiangchao Zhao at the University of Arkansas for his encouragement in using the Deblur program in QIIME 2. We also appreciate Elizabeth Miller at the University of Minnesota for her guidance on the cumulative sum scaling (CSS) normalization. This work was supported by the USDA National Institute of Food and Agriculture (grant no. 2018-68003-27462), the Ralph F. and Leila W. Boulware Endowment Fund, and the Oklahoma Agricultural Experiment Station Project H-3025. K.R. was supported by a USDA-National Institute of Food and Agriculture (NIFA) predoctoral fellowship grant (2018-67011-28041), while S.B. was supported by the Wentz undergraduate research scholarship at Oklahoma State University.

Publisher Copyright:
© 2020 American Society for Microbiology.


  • Bacitracin methylene disalicylate
  • Chickens
  • Microbiome
  • Microbiota
  • Mycobiome
  • Mycobiota
  • Poultry

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.


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