Culture-dependent and -independent analysis of bacterial diversity in biofloc-based aquaculture systems enriched with homemade formulation of probiotics

Biofloc fish farming emerges as a promising technology in global aquaculture, which improves water quality, generates microbial proteins, and outcompetes potential pathogens. Nowadays, exogenous probiotics have been added to biofloc systems to enhance its benefits. Thus, it is necessary to characterize probiotic strains, identify microbial communities, and assess antibiotic resistance of microorganisms in biofloc systems. Therefore, this study applied both culture-dependent and 16S rRNA metagenomics methods to compare the bacterial communities present in different probiotics, biofloc culture water, and the guts of Nile tilapia and Stinging catfish from pond as well as biofloc systems. The bacterial phyla Proteobacteria, Firmicutes, Fusobacteriota, Bacteroidota, Actinobacteria, and Chloroflexi were consistently the most prevalent in all samples. The microbial diversity and richness of biofloc culture water were higher than in other samples. Proteobacteria was the dominant bacteria in homemade probiotics, biofloc culture water, and biofloc cultured shing gut samples. In contrast, Firmicutes was abundant in commercial probiotics and guts of tilapia (both pond and biofloc-cultured), but Fusobacteriota was prevalent in pond cultured shing gut samples. The phylum Firmicutes, to which the genus Bacillus belongs, was high in commercial probiotics (98.54 %). At the genus level, dominant microbes in homemade probiotics was Acetobacter , while those in commercial probiotics were Lysinibacillus , Cohnella , Bacillus , and Brevibacillus . In addition, Bacillus was the most common genus in the gut samples of tilapia grown in both pond and biofloc system. In contrast, the genera Lactobacillus , Enterobacter , Burkholderia , Cavalleronia , and Bifidobacterium were prominent in the biofloc shing gut samples. However, probiotic potential genera (for example, Bacillus ) were found in the gut samples of tilapia and shing fish. Moreover, antibacterial susceptibility testing confirmed the presence of antibiotic resistant bacteria in the studied samples. These findings can significantly enhance our understanding of the diversity and abundance of microbiota in probiotics and biofloc-based aquaculture systems. • Microbial diversity and richness of biofloc culture water were higher than in other samples. • Dominant microbes in homemade probiotics was Acetobacter , while in commercial probiotics it was Bacillus. • Bacillus was the most common genus in the gut samples of tilapia grown in both pond and biofloc systems. • Biofloc fish and pond fish gut samples had substantially different microbial compositions. • Antibiotic susceptibility test confirmed the presence of antibiotic-resistant bacteria in the studied samples.