Pathogen identification and epidemiological assessment in Recirculation Aquaculture System based on Illumina sequencing technology

  • Sugachenko O. 1
  • Sukhanova L. 1
  • Sidorova T. 1
  • Andrianov V. 2
  • Garan’ A. 2
  • Dmitrieva A. 3
  • Sapozhnikova Y. 1
  • Glyzina O. 1
  • Yakhnenko V. 1
  • Tyagun M. 1
  • Belkova N. 4
  • 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk, 664033, Russia
    2 Research and production company Irkutskaya Forel (Irkutsk Trout), LLC
    3 Irkutsk State University, Karl Marx Str. 1, Irkutsk 664003, Russia
    4 Scientific Сentre for Family Health and Human Reproduction Problems, Timiryazeva Str., 16, Irkutsk 664003, Russia
Keywords: Recirculation Aquaculture System, epidemiological assessment, pathogen identification, amplicon metasequencing, Illumina sequencing technology


Microbial polymorphism in water, on the skin, and internal organs of juvenile trout, reared in Recirculation Aquaculture System (RAS) of a trout farm, was analyzed by 16S rDNA amplicon Meta Sequencing (Illumina sequencing technology). The microbiome pattern of water from different locations indicated the perfect work of RAS. Flavobacterium was identified as the only pathogen in the ulcers and internal organs of the diseased fish larvae. We proposed that pathogenic Flavobacterium sp. entered a trout farm through contaminated eggs. Metagenomic analysis of the microbial community is a sensitive and informative indicator of the epidemiological situation in RAS. In terms of amplicon metasequencing, modern NGS technologies become a powerful instrument for microbial monitoring in fish aquaculture.