PCR-screening of bacterial strains isolated from the microbiome of the Lubomirskia baicalensis sponge for the presence of secondary metabolite synthesis genes


  • Kaluzhnaya, O. V. 1
  • Lipko, I. A. 1 ID
  • Itskovich, V. B. 1 ID
  • 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, Irkutsk, 664033, Russia




The microbial communities of sponges (Porifera) are often a source of natural bioactive metabolites. From the microbiome of the endemic Lubomirskia baicalensis sponge, 35 bacterial strains were isolated and identified using molecular methods. The strains belonged to the phyla Actinobacteria, Firmicutes, and Proteobacteria (classes Alpha- and Betapriteobacteria). To analyze the strains for the presence of genes in the synthesis of secondary metabolites, polyketide synthases (PKS), PCR screening was applied using degenerate primers. Overall, 15 out of 35 strains contained PCR products corresponding in size to a fragment of the ketosynthase domain of the PKS gene cluster. Thus, the proposed method is applicable for rapid screening of the potential ability of microorganisms of different taxonomic groups to produce secondary metabolites. The work contributes to the study of the taxonomic diversity of cultured microorganisms, potential producers of biologically active substances, isolated from the microbiomes of Baikal sponges.