Probiotic-driven microbiota shifts confer the resistance to infectious bronchitis virus infection in poultry

Infectious bronchitis virus (IBV) is an economically significant viral infection in commercial broilers. Despite vaccination, outbreaks are still reported due to the emergence of new IBV variants. Probiotics, particularly strains of Lactobacillus, have been shown to help mitigate various disease outbreaks and exhibit strong immunomodulatory effects, especially in the respiratory tract. A study was conducted to understand the effect of a cocktail of Lactobacillus and a commercial probiotic on respiratory and gastrointestinal microbiome shifts in 6, 9 and 15 days post-infection (dpi) following IBV infection in commercial broilers. In general the virus-challenged group without any probiotics showed significantly higher (p = 0.0488) histopathological lesion scores compared to both probiotics treated groups prior to the IBV challenge. Cecum alpha diversity in Lactobacillus supplemented group prior to infection showed significantly higher (p < 0.05) diversity and evenness compared to the group supplemented with Lactobacillus only in all the considered time points, whereas the group supplemented with commercial probiotics prior to viral challenge showed significantly lower (p < 0.05) diversity compared to commercial probiotics only group at 15 dpi. Beta diversity analysis in cecum indicated both Lactobacillus supplemented and commercial probiotics supplemented prior to infection developed a significantly different (p < 0.05) and distinct microbial composition compared to all the other groups. According to differential abundance analysis, IBV infection was shown to favor the abundance of Lactobacillus in cecum. Commercial probiotics supplemented prior to the infection showed despite initial dysbiosis, dominant bacteria were able to get restored at 15 dpi in both cecum and trachea. Functional analysis in the cecum and trachea depicted that although Lactobacillus supplemented prior to infection showed more stress and proliferation in the initial time point, all the groups have more similar pathways at the later stage in the cecum but in the trachea, the group supplemented with Lactobacillus prior to infection was still showing transition to more colonization focused state. The study outcome adds to the understanding of respiratory and gastrointestinal microbiome shifts in a lengthier time period in probiotics supplemented broilers prior to IBV infection.