Table 1.

Comparison between commensal and pathogenic gut-microbiota mediated immune modulation in AIV, IBDV, MDV, and NDV infected chickens.

Virus	Control Group		Infected Group
	Commensals	Effector Molecules and Outcomes	Pathogens	Effector Molecules and Outcomes
AIV	Collinsella, Faecalibacterium, Oscillibacter, Holdemanella, Pseudoflavonifractor, Anaerotruncus, Butyricoccus, and Bifidobacterium	Increase IFN-α, IFN-β, and IL-22 and antimicrobial peptides such as MUC, TFF, ZO, and tight junction proteins comprised of claudins, occludin, and zona occludens mRNA expressions	Proteobacteria Clostridium cluster XI, Escherichia, Shigella, Salmonella, Vampirovibrio, Clostridium cluster XIVb, and genus Ruminococcus	Downregulate the IFN-α, IFN-β, and IL-22 secretion and antimicrobial peptides such as MUC, TFF, ZO, and tight junction proteins comprised of claudins, occludin, and zona occludens mRNA expressions also enhance the secretions of proinflammatory cytokines IFN-γ, IL-17A, IL-6, and IL-1B and produce inflammation
IBDV	Clostridium XlVa	Induce T regulatory cells to produce anti-inflammatory cytokines	Desulfovibrionaceae	Produce hydrogen sulfides and cause inflammation
	Faecalibacterium	Enhance butyrate shortchain fatty acids (SCFA) and suppress the inflammation	Campylobacter jejuni	Inhibit butyrate SCFA production cause inflammation of GIT
	Probiotics	Increase immunoglobulins, FCR body weight gain	Salmonella typhimurium and Campylobacter jejuni	Decreased IgG and IgA production
MDV	Firmicutes	Induce T regulatory cells to produce anti-inflammatory cytokines	Pathogenic Lactobacillus spp., Proteobacteria	Suppress the T regulatory cells stimulation produce inflammation
	Blautia spp. and Faecalibacterium spp.	Produce succinate and lactate and provide energy and reduce inflammation	Streptococcus spp.	Septicemia, peritonitis, and endocarditis
NDV	Paenibacillus and Enterococcus	Antimicrobial peptides	Rhodoplanes, Clostridium, and Epulopiscium	Cause local mucosal infection