Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota

Michael Edward Michael, John M. Ngunjiri, Kara J.M. Taylor, Hana Ji, Amir Ghorbani, Mahesh Kc, Mohamed Elaish, Hyesun Jang, Bonnie Weber, Timothy J. Johnson, Chang Won Lee

Research output: Contribution to journalArticlepeer-review

Abstract

Although poultry microbiome discoveries are increasing due to the potential impact on poultry performance, studies examining the poultry respiratory microbiome are challenging because of the low microbial biomass and uniqueness of the avian respiratory tract, making it difficult to sample enough material for microbial analysis. Invasive sampling techniques requiring euthanasia are currently used to increase microbial mass for the analysis, thus making it impossible to sample individual birds longitudinally. In this study, we compared invasive (nasal wash, upper tracheal wash, lower tracheal wash, and lower respiratory lavage) and noninvasive (tracheal and choanal swabs) respiratory sampling techniques in two independent experiments by using 4-wk-old chickens. We first established the experimental baseline of respiratory microbiota by using invasive techniques to enable reasonable comparisons between sampling methods and between experiments. Although noninvasive sampling (live-bird swabs) resulted in lower 16S ribosomal RNA gene copy numbers compared with invasive sampling, live swabs were able to detect the dominant microbes captured by invasive techniques. Nevertheless, swabs from euthanatized birds were more reflective of the microbiota captured through invasive methods than live swab. Furthermore, from two separate experiments, we also demonstrated that respiratory microbiota sampling is highly reproducible, especially in the trachea and lower respiratory tract. Our study provides new insights and perspectives on decision making when sampling and studying poultry respiratory microbiota.

Original languageEnglish (US)
Pages (from-to)277-285
Number of pages9
JournalAvian diseases
Volume64
Issue number3
DOIs
StatePublished - Sep 1 2020

Bibliographical note

Funding Information:
The authors thank Dr. Juliette Hanson and Megan Strother for assistance with animal care. Sequence processing and analysis were performed by 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 2015-68004-23131 from the U.S. Department of Agriculture, National Institute of Food and Agriculture (to C.-W. L. and T. J. J.).

Publisher Copyright:
© 2020 American Association of Avian Pathologists. All rights reserved.

Keywords

  • invasive sampling
  • microbiota
  • noninvasive sampling
  • poultry respiratory microbiome

PubMed: MeSH publication types

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

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