Bacterial Community and Antibiotic Resistance Gene Profiles of Fish Gut Contents and Their Aquaculture Environment in Tianjin, China

Abstract

The continuous expansion of freshwater fish culture is confronted with environmental problems owing to their high antibiotic inputs and antibiotic-resistant bacteria. This study explored the antibiotic resistance gene (ARG) profiles of water and fish gut contents from three fishponds in Tianjin using a metagenomics approach. Proteobacteria, Bacteroidetes, and Actinobacteria were the most abundant phyla in all water samples. However, the microbial composition of the fish guts was distinctly different among the three aquaculture farms. Cetobacterium, Bacillus, Weissella, and Fusobacterium were the dominant genera in the gut contents of all fish. More than 20 unique ARGs with relatively high abundances were detected in both water and fish gut content samples. The dominant genes and pathways of antibiotic resistance mechanisms detected in all samples were antibiotic efflux, antibiotic inactivation, antibiotic target alteration, antibiotic target protection, antibiotic target replacement, and reduced permeability to antibiotics. In addition, our results indicate that antibiotics, such as florfenicol, and heavy metals, such as Zn and Cu, could have a significant correlation with some common ARGs, indicating that antibiotic-resistant bacteria could co-occur with heavy metals. Our study provides a research basis for the development of a strategy for practical antibiotic application and heavy metal monitoring in aquaculture.