Phylogenetic study of the gut microbiome of broad whitefish (Coregonus nasus)
https://doi.org/10.52419/issn2072-2419.2025.4.47
Abstract
The intestinal microbiota of vertebrates is a complex biological system that plays a key role in metabolism and the formation of immune defense. Microbial communities decompose complex organic compounds, synthesize vitamins and ensure the stability of the internal environment of the body, closely interacting with its physiological processes. Thus, the intestinal microbiota directly affects the health of the host organism. The study of evolutionary relationships in the intestinal microbiota of broad whitefish (Coregonus nasus) by amplicon sequencing of the 16S rRNA gene contributes to an understanding of their trophic and competitive interactions in the host organism. The following methods were used in the study: NGS sequencing of the 16S rRNA gene in the V3-V4 and V4-V5 regions on the Illumina MiSeq platform in PE mode, as well as processing the obtained data using Trimmomatic v0.39, VSEARCH v2.21.1, MAFFT v7.505, FastTree v2.1.11 software. All analyses were performed on Python 3.10.6 using scipy, statsmodels, and biopython packages. The resulting phylogenetic trees demonstrate a high level of taxonomic differentiation, reflecting both recent evolutionary divergences (characterized by short branches and high node support) and ancient divergences supported by significant branch lengths in certain clades. Such organization indicates multiple radiations within bacterial taxa due to adaptation to different ecological niches, which indicates the complexity and interconnectedness of microbial communities in the studied samples. The high phylogenetic diversity of the detected taxa, including the presence of OTUs classified as Candidatus or belonging to poorly studied groups, highlights the insufficient study of the freshwater fish microbiota in existing databases.
About the Authors
K. E. Voronov
St. Petersburg branch of the State Scientific Center of the Russian Federation
FGBNU “VNIRO” (“GosNIORH” named after L. S. Berg)
Russian Federation
Russian Federation
Genetics Lab Engineer
Yu. N. Lukina
Institute of Water Problems of the North KarRC RAS (FGBI "IVPS FRC KarRC RAS")
Russian Federation
Russian Federation
Doctor of Biological Sciences, Institute Director
O. V. Apalikova
St. Petersburg branch of the State Scientific Center of the Russian Federation
FGBNU “VNIRO” (“GosNIORH” named after L. S. Berg)
Russian Federation
Russian Federation
Candidate of Biological Sciences, Head of the Genetics Lab
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Review
For citations:
Voronov K.E., Lukina Yu.N., Apalikova O.V. Phylogenetic study of the gut microbiome of broad whitefish (Coregonus nasus). International Journal of Veterinary Medicine. 2025;(4):47-57. (In Russ.) https://doi.org/10.52419/issn2072-2419.2025.4.47
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