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The study focused on identifying autochthonous bacteria from the indigenous catfish intestine and evaluating their impacts on survival, growth and against Aeromonas veronii infection in Clarias batrachus and Heteropneustes fossilis under laboratory conditions. Candidate bacteria were isolated using Nutrient Agar (NA) and de Man, Rogosa and Sharpe (MRS) agar in duplicate. An immersion technique was employed to determine the biosafety of these isolates in both catfish species at a dose of 107 CFU/mL. Three experimental diets: D1 (basal diet + putative Bacillus sp., 108–109 CFU/g), D2 (basal diet + 3% BioFav Aqua) and D3 (basal diet + putative Lactobacillus sp., 108–109 CFU/g) were prepared to conduct a 4‐week long feeding trial, whereas the control diet received no probiotic supplementation. The probiotic performance was analysed by comparing the growth performance and survival of C. batrachus and H. fossilis. Resistance against Aeromonas veronii infection was determined by a challenge test of catfish. Initially, 16 autochthonous isolates were collected, and among them, an isolate from C. batrachus intestine and another from the gut of H. fossilis were selected for further studies. A series of biochemical analyses identified that the putative bacteria were Bacillus sp. and Lactobacillus sp., respectively. The biosafety test showed no clinical signs of infection or mortality among experimental catfishes. All probiotic‐treated fish showed higher growth increments than control. Incorporation of Bacillus sp. and Lactobacillus sp. in the basal diet significantly (p < 0.05) improved growth and survival in both catfish, where Bacillus sp. showed the best effects in C. batrachus, and Lactobacillus sp. in H. fossilis. Intramuscular (IM) injection with A. veronii revealed that probiotic‐treated fish had better survival rates. The study demonstrated the potentiality of autochthonous bacteria to enhance growth, survival, feed efficiency and immunity and hence recommended as a better health management approach in catfish aquaculture.

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