Preliminary insight into the fish microbiota in a small lowland river affected by municipal wastewater effluent

Based on 16S rRNA sequencing, the microbiomes of gudgeon, perch, and stone loach were characterized and compared between a site affected by municipal sewage discharge and an unpolluted site. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Planctomycetes were dominant in fish from unpolluted water, with microbial diversity varying among fish species. Shifts in Proteobacteria and Bacteroidetes were observed in stone loach and gudgeon between two studied sites. Microbiota of fish from polluted water contained more Actinobacteria, while from unpolluted water had more Patescibacteria, Planctomycetes, Cyanobacteria and Verrucomicrobia. The difference in bacterial families between polluted and unpolluted sites, with some bacterial taxa gained or lost were recorded and discussed as potential bioindicators of sewage pollutions.