Abstract
BACKGROUND: Selective breeding for disease resistance is an effective strategy to control duck hepatitis A virus type 3 (DHAV-3) in waterfowl. However, the mechanism underlying resistance remains poorly understood, particularly those associated with antioxidant defense, intestinal development and host-microbiota interactions. METHOD: A total of 100 1-day-old Pekin ducklings were used in this study with 50 DHAV-3 susceptible and resistant ducks, respectively. Samples were collected at 7 days post-hatching (D7), D21 and D42, 10 birds per group. We compared DHAV-3 resistant and susceptible ducks during early development with respect to immune organ indices, antioxidant capacity, intestinal morphology, barrier-related gene expression and cecal microbiota. RESULT: Resistant ducks exhibited higher spleen indices and stronger antioxidant capacity, characterized by increased superoxide dismutase, reduced glutathione, and total antioxidant capacity, along with lower malondialdehyde levels at D7 and D21. In contrast, susceptible ducks showed compensatory thymus hypertrophy and delayed development of antioxidant defense and intestinal maturation. Ileal morphology revealed greater villus height and width with more regular arrangement in resistant ducks at D7, whereas these differences diminished at D21 and D42. Gene expression analysis demonstrated higher early expression of the tight junction proteins CLDN1 and CLDN3 in resistant ducks, while susceptible ducks displayed elevated MUC2 and OCLN, suggesting stress induced compensatory responses. Cecal microbiota analysis revealed distinct colonization patterns in early development. Resistant ducks were enriched with Firmicutes and beneficial genera such as Enterococcus and Lactobacillus, whereas susceptible ducks harbored higher abundances of Bacteroidota and potentially opportunistic taxa. Microbial diversity increased with age in both groups, but resistant ducks displayed more orderly succession and enrichment of SCFA producing genera, including Subdoligranulum and Phascolarctobacterium, which positively correlated with plasma antioxidant indices. CONCLUSION: DHAV-3 resistant ducks exhibit early advantages in antioxidant defense, intestinal barrier development and colonization by beneficial microbiota, which collectively contribute to enhanced disease resistance. These findings highlight the synergistic roles of host physiology and gut microbiota in shaping resistance. In the future, integrating genomic selection with microbiota modulation and antioxidant interventions may accelerate the breeding of highly resistant duck lines and provide scientific evidence and practical strategies for controlling duck viral hepatitis.