Gut microbiome of juvenile coregonid fishes: comparison of sympatric species and their F1 hybrids

Gut prokaryotic communities of coregonid fishes reared in the aquaria of the Baikal Museum (Listvyanka sttl., Lake Baikal, Russia) for two years were identified using next generation sequencing of 16 S rDNA. We compared pelagic planctophage Baikal omul, Coregonus migratorius Georgi, bathypelagic bentophage lacustrine Baikal whitefish, Coregonus baicalensis Dyb. and their first generation hybrid crosses (female omul x male whitefish and vice versa). The closest prokaryotic communities were determined in the omul and female omul x male whitefish hybrid, which differ from whitefish and the female whitefish x male omul hybrid. Most of the bacteria were Proteobacteria, Bacteroidetes, Firmicutes or Actinobacteria. The number of bacterial operational taxonomic units (OTUs) was 624 and declined from the omul to hybrids and to whitefish. The dominant bacterial OTU in all examined fish was closely related to the genus Serratia of the Enterobacteriaceae family. In total, 34 OTUs were detected in all studied fishes, consisting of 91.4 % of the total number of sequences. The highest diversity of microorganisms was found in omul, where 197 unique OTUs were detected belonging to Chlamydiae, Chloroflexi, Deinococcus-Thermus, Fusobacteria, Spirochaetes, Synergistetes, Verrucomicrobia and Candidatus Saccharibacteria. The effect of respective ecotypes on the gut microbiome diversity is discussed.