Probiotics have been considered a powerful tool to improve nutrition and health by inhibiting the proliferation of pathogenic microorganisms, biosynthesizing vitamins, and promoting nutrient digestion and uptake for several farmed aquatic species. However, most probiotics were originally isolated from the environment or other host species, which may not present the best candidate taxa for all species due to poor adaptation to the target host and possibly an environmental pollution hazard. In the present study, 3,000 hybrid catfish (~70 g) were distributed equally in three 0.1 ha ponds and fed a commercial feed for three months. Each pond was partially seined (~25% of the population), and a total of 45 individuals underperforming and 45 overperforming were hand selected, euthanized, and their intestinal contents sampled. The DNA from the digesta was extracted for each of these samples and amplified microbial DNA (V4 - 16S rRNA) subjected to microbiota profiling via next-generation sequencing (Illumina MiSeq). Differences in the intestinal microbiota profile was assessed in fish overperforming against the fish with stunted growth. Although diversity metrics were not significantly different between under- and overperforming fish, significant differences in relative abundance were observed.
A total of 40 probiotic candidates were isolated from the digesta of overperforming farmed catfish using Lactobacillus selective medium and non-selective medium under both aerobic and anaerobic conditions. To verify the functional potential of the isolates, lipolytic and proteolytic abilities were measured. The selected candidates were further investigated using a biochemical panel, to better understand their nutrient utilization. In the bacterial inhibition assay, pathogenic bacteria that afflict the catfish industry (e.g., Edwardsiella ictaluri, E. piscicida, and Aeromonas hydrophila) were co-cultured with the selected isolates. In this assay, 26 candidates inhibited the growth of these pathogenic bacteria. The hemolytic ability and antibiotic susceptibility were evaluated on the selected isolates to ensure host safety. In summary, a total of 20 samples were identified as potential hybrid catfish autochthonous probiotics with lipolytic and proteolytic ability, which may promote better nutrition absorption for the catfish. In addition, these bacteria inhibited the proliferation of pathogens in vitro, and did not present hemolytic activity, which can be a virulence factor.