Respiratory and gut microbiota in commercial turkey flocks with disparate weight gain trajectories display differential compositional dynamics

Kara J.M. Taylor, John M. Ngunjiri, Michael C. Abundo, Hyesun Jang, Mohamed Elaish, Amir Ghorbani, K. C. Mahesh, Bonnie P. Weber, Timothy J. Johnson, Chang Won Lee

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus, that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium. Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome.

Original languageEnglish (US)
Article numbere00431-20
JournalApplied and environmental microbiology
Issue number12
StatePublished - Jun 1 2020

Bibliographical note

Funding Information:
We thank the management team of the commercial farm participating in this study for providing turkeys and giving us access to flock treatment and management data related to this study. The identity of the commercial farm referenced in this study will remain anonymous as a condition of their open sharing of rearing metadata and cooperation during sampling. We have no conflicts of interest to declare. Sequence processing and analysis were performed using the resources of the Molecular & Cellular Imaging Center, Ohio Agricultural Research and Development Center, The Ohio State University. This project was supported by Agriculture and Food Research Initiative competitive grant number 2015-68004-23131 from the USDA National Institute of Food and Agriculture (to C.-W.L. and T.J.J.). C.-W.L. and T.J.J. developed the broad concept of the study. C.-W.L., J.M.N., and M.C.A. designed and managed the study. J.M.N., M.C.A., H.J., M.E., M.K.C., and C.-W.L. collected the samples. J.M.N., M.C.A., and A.G. performed sample processing and DNA extraction. B.P.W. and T.J.J. managed the DNA sequencing. K.J.M.T. and J.M.N. performed bioinformatics analyses. K.J.M.T. and J.M.N. wrote the manuscript with input from all authors. C.-W.L. provided reagents and sampling resources. All authors read and approved the final manuscript.


  • Commercial turkey
  • Microbiome
  • Turkey gut microbiota
  • Turkey respiratory microbiota

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