BACKGROUND: Feeding adult zebrafish a diet supplemented with quenching enzyme AiiO-AIO6 for 3 wk improved the growth performance and disease resistance. However, when the feeding period was extended to 8 wk, zebrafish's disease resistance to Aeromonas veronii decreased. OBJECTIVE: We investigated the mechanisms of the reduced disease resistance of zebrafish induced by feeding on AiiO-AIO6 supplemented diet for a long-term (8 wk), and assessed the effectiveness of feed additives in restoring the low disease resistance. METHODS: One-month-old (adult) zebrafish were fed with a basal diet and the basal diet supplemented with AiiO-AIO6 (10 U/g) for 8 wk (Expt. 1). Furthermore, zebrafish larvae model (Expt. 2) was developed and used to study the mechanisms how AiiO-AIO6 affected the disease resistance (Expt. 3). We also investigated the effectiveness of selected prebiotic tributyrin, β-glucan or mannan in activating gut microbiota-hif1α to restore the low disease resistance of adult zebrafish fed with AiiO-AIO6 for 8 wk (Expt. 4). Lastly, the effects of Bacillus subtilis in activating the gut microbiota-hif1α and improving the low disease resistance of zebrafish larvae induced by AiiO-AIO6 was examined (Expt. 5). RESULTS: Feeding adult zebrafish with AiiO-AIO6 for 8 wk promoted the growth but disordered the gut microbiota and reduced disease resistance. Zebrafish larvae model confirmed that feeding AiiO-AIO6 for 2 d increased disease resistance, while 7 d decreased the resistance by suppressing hif1α. Using a germ-free zebrafish larvae model, we also demonstrated that AiiO-AIO6-induced gut microbiota mediated inhibition of hif1α. Furthermore, zebrafish fed on the AiiO-AIO6 containing diet supplement with tributyrin, β-glucan, mannan, or B. subtilis activated the gut microbiota-hif1α axis to reverse the low resistance caused by AiiO-AIO6. CONCLUSION: Activating the gut microbiota-hif1α axis has vital role in improving intestinal health and restores the low resistance to A. veronii caused by improper administration of dietary AiiO-AIO6 in zebrafish.