Microbiome Dynamics in Broilers Infected with Infectious Bronchitis Virus and the Protective Role of Lactobacillus-Based Probiotics

Infectious bronchitis virus (IBV) is a corona virus, which has economic significance in broiler industry due to reduced weight gain and carcass condemnation following infection. Regardless of on-going vaccination, still outbreaks occur indicating the need to investigate novel approaches to reduce infection. In our study first, we evaluated the respiratory and gastrointestinal microbiome dysbiosis at 6, 9 and 15 days post-infection (dpi) in commercial broiler chickens following challenge with IBV DMV/1639 strain. Trachea and cecal tonsils of IBV challenged group showed significantly higher histopathological lesions score compared to control. Significantly higher alpha diversity indexes including observed Operational Taxonomic Units (OTUs) and Shannon was observed in IBV challenged group compared to control in cecum at 6 and 15 dpi, whereas tracheal microbiome of IBV challenged group showed significantly higher evenness and Shannon index compared to control in 6 and 9 dpi respectively. Beta diversity indicated a significant microbial composition shift in both cecum and trachea following infection. Secondly, we analyzed the effect of two Lactobacillus based probiotics in trachea and cecal microbiome at 6, 9 and 15 dpi in commercial broiler chickens infected with IBV DMV/1639 strain. Virus infected group showed significantly higher histopathological lesion scores compared to both probiotics treated groups advance to IBV challenge. Alpha diversity of cecum in Lactobacillus cocktail supplemented group in advance to infection showed significantly higher diversity and evenness compared to Lactobacillus cocktail supplemented only group at all the observed time points, whereas Lactobacillus based commercial probiotics supplemented prior to IBV challenge showed significantly lower diversity compared to Lactobacillus based commercial probiotics only group at 15 dpi. Beta diversity analysis indicated IBV challenged only and both the probiotic supplemented groups in advance to viral challenge developed a distinct microbial composition following infection. According to differential abundance analysis, IBV infection favored the growth of Lactobacillus in cecum, whereas Lactobacillus based commercial probiotic limited the flourish of opportunistic bacteria in cecum following infection. The findings from our study contribute to the understanding of respiratory and cecum microbiome shift following IBV challenge and the impact of Lactobacillus based probiotics in ameliorating the dysbiosis.

Name thesis:degree_name

Master of Science (MSc)

Discipline thesis:degree_discipline

Veterinary Medical Sciences

Grantor

Veterinary Medicine

Year dc:date.issued

2025

Author dc:creator

• Herath Mudiyanselage, Heshanthi

Advisor dc:contributor.advisor

• Abdul Careem, Mohamed Faizal

Committee members dc:contributor.committeemember

• Gomis, Susantha M.
• Niu, Dongyan Xu
• Ojha, Shivani

• Infectious bronchitis virus
• broiler chicken
• microbiome
• caecum
• trachea
• bacterial diversity
• probiotics
• Lactobacillus

Statement dc:rights

• Unless otherwise indicated, this material is protected by copyright and has been made available with authorization from the copyright owner. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.

Language dc:language.iso

en

DOI

https://dx.doi.org/10.11575/PRISM/50470

OAI identifier oai:identifier

oai:ucalgary.scholaris.ca:1880/122876