The current state of molecular genetic research on the taxonomic diversity of the enteric microbiota of Siberian fish

Abstract

This paper presents the current state of research on the intestinal microbiota of fish of different ecological groups from water bodies of West and East Siberia. The present study focused on the gut bacterial diversity of 16 species/forms of fish (due to intricate taxonomical position of whitefish from Teletskoye Lake) inhabiting Chany Lake (Novosibirsk oblast), Teletskoye Lake (Altai Republic), Baikal Lake and other water bodies of East Siberia using molecular genetic methods. The analysis of the conducted studies shows the main features of gut bacterial communities in the digestive tract of fish and to better understand the features of the functioning of aquatic ecosystems in Siberia. In all studied fish (except for Lena grayling and Baikal omul), regardless of their habitat, taxonomy, digestive system structure (presence or absence of stomach and pyloric caeca) and feeding habits, bacteria of all four phyla (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were found among the dominants. Such differences can also be explained by sample preparation techniques before sequencing that researchers may apply. Also, the uncultivated microbiota such as Pseudoalteromonadaceae (Lake Chany), Comamonadaceae and Bacillaceae (whitefish from Lake Teletskoye) and Rhodobacteraceae (Baikal omul and whitefish) were often found among the dominant bacterial taxa in the digestive tract of the most studied fish. Moreover, the data focused on the structure of gut bacterial community of fish will be useful for the development of aquaculture industry in the region, since the information makes it possible to identify pathogenic, opportunistic, and probiotic bacteria in aquatic ecosystems.