Effects of probiotic and antibiotic on gut microbiome and antibiotic resistance genes in black tiger shrimp (Penaeus monodon) in Bangladesh

Black tiger shrimp (Penaeus monodon) is the major brackish-water aquaculture species in Bangladesh and other parts of the world. The use of antibiotics and probiotics in shrimp cultivation could potentially impact the gut microbiome, leading to the emergence of antibiotic resistance genes (ARGs) in aquaculture environments. This research investigated the dynamics of shrimp gut microbial community structure and the prevalence of ARGs over a 28-day period. Four treatments were included: control, probiotics ( Bacillus ), antibiotics (oxytetracycline), and a combination of probiotics and antibiotics. The microbiome was determined using the 16S rRNA metabarcoding analysis, and 19 ARGs were detected using PCR. The microbiome analysis revealed that Bacillus and Acinetobacter were initially abundant in the groups, and changes in the genus composition were observed over the treatment period. The temporal changes in community structure in the antibiotic treatment group suggested that while antibiotics may initially impact on the bacterial community, the community may eventually recover and become similar to the other treatment groups. The combined treatment of antibiotics and probiotics resulted in an initial equilibrium between Firmicutes and Proteobacteria on day 8, followed by a subsequent transition toward Firmicutes dominance, probably because of the continued presence of the probiotic bacteria. The antibiotic treatment revealed the highest number of ARGs ( tetA, tetC, sul1, bacA, and ere(A) ), followed by the control group (tetA, tetC, ere(A), and bacA ). Three ARGs ( tetA, tetC, and bacA ) and two ( tetA and dfrA1 ) were detected in the probiotic and mixed treatment groups, respectively. No ARGs were detected from the mixed treatment group at the end of the treatment. These findings suggest that the simultaneous use of antibiotics and probiotics may potentially reduce the emergence of ARGs in shrimp farming. The findings may contribute to the development of strategies for using probiotics and antibiotics in shrimp farming and addressing the issue of antibiotic resistance in the aquaculture sector. • Proteobacteria (52.04 %) and Firmicutes (47.06 %) dominated the gut microbiota of shrimp. • Bacillus spp. addition was not dominant in the probiotic group. • Six antibiotic-resistant genes (ARGs) were detected in the gut of the shrimp. • Antibiotic-treated shrimp showed the highest ARGs tetA, tetC, sul1, bacA, and ere(A). • Co-treated group (probiotic-antibiotic) reduced the abundance of ARGs.