Low pathogenic avian influenza virus infection retards colon microbiota diversification in two different chicken lines

Klaudia Chrzastek,Roberto La Ragione,Joy Leng,Holly Shelton,Dagmara Bialy,Mohammad Khalid Zakaria

doi:10.1186/s42523-021-00128-x

Abstract

BackgroundA commensal microbiota regulates and is in turn regulated by viruses during host infection which can influence virus infectivity. In this study, analysis of colon microbiota population changes following a low pathogenicity avian influenza virus (AIV) of the H9N2 subtype infection of two different chicken breeds was conducted.MethodsColon samples were taken from control and infected groups at various timepoints post infection. 16S rRNA sequencing on an Illumina MiSeq platform was performed on the samples and the data mapped to operational taxonomic units of bacterial using a QIIME based pipeline. Microbial community structure was then analysed in each sample by number of observed species and phylogenetic diversity of the population.ResultsWe found reduced microbiota alpha diversity in the acute period of AIV infection (day 2–3) in both Rhode Island Red and VALO chicken lines. From day 4 post infection a gradual increase in diversity of the colon microbiota was observed, but the diversity did not reach the same level as in uninfected chickens by day 10 post infection, suggesting that AIV infection retards the natural accumulation of colon microbiota diversity, which may further influence chicken health following recovery from infection. Beta diversity analysis indicated a bacterial species diversity difference between the chicken lines during and following acute influenza infection but at phylum and bacterial order level the colon microbiota dysbiosis was similar in the two different chicken breeds.ConclusionOur data suggest that H9N2 influenza A virus impacts the chicken colon microbiota in a predictable way that could be targeted via intervention to protect or mitigate disease.

Highlights

Avian influenza A viruses (AIV), belong to the Orthomyxoviridae family, have segmented, single-stranded, negative sense RNA genomes with enveloped virions [1]
VALO chickens shed H9N2 virus infection from the buccal cavity, a day longer than Rhode Island Red (RIR) chickens Buccal viral shedding was determined by testing oropharyngeal (OP) swabs at day two, day three, day four, day five and day six post-challenge by plaque assay on Madin-Darby Canine Kidney (MDCK) cells (Fig. 1)
In conclusion, we have shown the dysbiosis in healthy colon microbiota following avian influenza virus (AIV) of H9N2 subtype in two divergent chicken lines

Summary

Introduction

Avian influenza A viruses (AIV), belong to the Orthomyxoviridae family, have segmented, single-stranded, negative sense RNA genomes with enveloped virions [1]. The interplay between pathogens and host microbiota play an important role in health and disease in many vertebrates [25,26,27,28]. Compelling evidence has shown that the gut microbiota can play a role in pathogenesis of various human diseases including those with primary involvement outside of the gut, such as respiratory, renal, or neurologic [20,21,22]. Recent studies reveal that immune protection and severity of infection by gammaherpesvirus, which can cause severe vasculitis and lethal pneumonia or respiratory syncytial virus infection of the lungs, can be dependent on the profile of the human gut microbiota [23, 24]. Analysis of colon microbiota population changes following a low pathogenicity avian influenza virus (AIV) of the H9N2 subtype infection of two different chicken breeds was conducted

Methods

Results

Discussion

Conclusion