Alteration of the Chicken Upper Respiratory Microbiota, Following H9N2 Avian Influenza Virus Infection

Tara Davis; Dagmara Bialy; Joy Leng; Roberto La Ragione; Holly Shelton; Klaudia Chrzastek

doi:10.3390/pathogens12091168

Alteration of the Chicken Upper Respiratory Microbiota, Following H9N2 Avian Influenza Virus Infection

Pathogens. 2023 Sep 16;12(9):1168. doi: 10.3390/pathogens12091168.

Authors

Tara Davis¹, Dagmara Bialy¹, Joy Leng^{2

3}, Roberto La Ragione^{2

4}, Holly Shelton¹, Klaudia Chrzastek^{1

5}

Affiliations

¹ The Pirbright Institute, Pirbright, Woking GU24 0NF, UK.
² School of Veterinary Medicine, University of Surrey, Guildford GU2 7XH, UK.
³ Institute of Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
⁴ School of Biosciences, University of Surrey, Guildford GU2 7XH, UK.
⁵ Animal and Plant Health Agency, Pathology and Animal Sciences, APHA, Addlestone KT15 3NB, UK.

Abstract

Several studies have highlighted the importance of the gut microbiota in developing immunity against viral infections in chickens. We have previously shown that H9N2 avian influenza A virus (AIV) infection retards the diversity of the natural colon-associated microbiota, which may further influence chicken health following recovery from infection. The effects of influenza infection on the upper respiratory tract (URT) microbiota are largely unknown. Here, we showed that H9N2 AIV infection lowers alpha diversity indices in the acute phase of infection in the URT, largely due to the family Lactobacillaceae being highly enriched during this time in the respiratory microbiota. Interestingly, microbiota diversity did not return to levels similar to control chickens in the recovery phase after viral shedding had ceased. Beta diversity followed a similar trend following the challenge. Lactobacillus associate statistically with the disturbed microbiota of infected chickens at the acute and recovery phases of infection. Additionally, we studied age-related changes in the respiratory microbiota during maturation in chickens. From 7 to 28 days of age, species richness and evenness were observed to advance over time as the microbial composition evolved. Maintaining microbiota homeostasis might be considered as a potential therapeutic target to prevent or aid recovery from H9N2 AIV infection.

Keywords: H9N2; chicken; influenza; microbiota; respiratory tract; sequencing.

Grants and funding

This work described herein was funded by the Pirbright Institute BBSRC ISP grants BBS/E/I/00007030, BBS/E/I/00007034, BBS/E/I/00007038 and BBS/E/I/00007039. The funders had no role in the design of the study, collection, analysis and interpretation of data and writing the manuscript.