National Science Centre, SONATA 17 “Mutual microbiota-virus interactions during avian coronavirus infection” November 15, 2022 – November 14, 2025

Project Leader: Joanna Ewa Sajewicz-Krukowska, PhD

Financial resources: PLN 539,800.00

Project description: The community of microorganisms that colonize the gastrointestinal tract of chickens is referred to as the microbiota. The main component of this community is bacteria. The intestinal microbiota is considered a unique ecosystem that has a significant impact on the functioning of the entire organism. The local microflora plays a key role in preventing and treating microbial infections and is often referred to as the “forgotten organ.” Not only does the host influence the composition of its microbiota, but the microbiota also positively affects the host, including its metabolism, nutrition, development, and modulation of immunity and response to infections. The microbiota is currently recognized as a regulator of many physiological functions of the host and extends far beyond its role in digestion. During disease, major changes occur in the composition of the microbiota. Such a disruption of balance is called dysbiosis or dysbacteriosis. It is associated with many diseases. Intestinal dysbacteriosis induced by viruses may promote viral replication and transmission in organisms. Infectious bronchitis virus (IBV), a coronavirus causing infectious bronchitis (IB) in chickens, causes one of the greatest economic losses in poultry farming in Poland and worldwide. Along with highly pathogenic avian influenza (HPAI) and Newcastle disease (ND), IB is the most economically important viral respiratory disease affecting the poultry industry worldwide. There are many genotypes/variants of IBV that differ genetically and also infect different tissues/organs/systems. However, it should be remembered that the main route of entry for all IB viruses is the respiratory system. Therefore, the project includes an assessment of both intestinal and respiratory microbiota following IBV infection in chickens. Using lung tissue and small intestine samples and modern molecular biology methods, we plan to conduct detailed microbiota studies regarding the qualitative and quantitative composition of bacteria in virus-infected chickens compared to healthy chickens. In the experiment, we will use two strains representing different genotypes. The project also includes induced changes in the quantitative composition and qualitative structure of the microbiota. We intend to achieve this through the use of broad-spectrum antibiotic therapy. We assume that such changes will affect the chickens’ response to infection, which in turn will alter the course of the disease. Antibiotic therapy will serve as a model of dysbiosis (disturbances in the structure and composition of the microbiota) in early life. In practice, this may occur as a result of improper nutrition, antibiotic therapy, or infection. Such thorough analysis will be possible through the use of state-of-the-art molecular biology methods. To determine the type and number of bacteria, we will use next-generation sequencing (NGS) in a “metagenomic” approach, i.e., analysis of DNA isolated directly from microorganisms present in a given environment. Until recently, this was performed primarily using culture methods. However, these have many limitations: they cannot be used for bacteria that do not grow in cell culture, and they are selective for bacteria that readily multiply in cultures. Ultimately, the obtained nucleotide sequences will be subjected to bioinformatic analysis, which will allow each bacterium to be classified into a specific taxonomic group. The planned studies will also allow us to demonstrate differences in the interactions of the virus on the microbiota and the microbiota on the virus induced by two different genotypes. The project results will enable understanding of the role of the microbiome during IBV infection. They will provide answers as to whether and how microbiome modification (depletion) affects the course of infection at its earliest stages. In addition to cognitive aspects, the obtained results will help understand the molecular mechanisms involved in host microbiota-virus interactions. This may in the future enable further improvement of vaccines or implementation of preventive measures to modify the gastrointestinal microbiota using probiotics or targeted antibiotic therapy, which in turn could mitigate disease symptoms or prevent its occurrence. Knowledge about the mechanisms involved in IBV pathogenesis is still insufficient, and their understanding is also crucial in the context of the current SARS-CoV-2 pandemic.