An integrated method for taxonomic identif ication of microorganisms
Yu. E. Uvarova,
A. V. Bryanskaya,
A. S. Rozanov,
V. N. Shlyakhtun,
E. A. Demidov,
K. V. Starostin,
T. N. Goryachkovskaya, 
S. V. Shekhovtsov,
N. M. Slynko,
S. E. Peltek
S. V. Shekhovtsov,
N. M. Slynko,
S. E. Peltek https://doi.org/10.18699/VJ20.630
Abstract
For accurate species-level identification of microorganisms, researchers today increasingly use a combination of standard microbiological cultivation and visual observation methods with molecular biological and genetic techniques that help distinguish between species and strains of microorganisms at the level of DNA or RNA molecules. The aim of this work was to identify microorganisms from the ICG SB RAS Collection using an integrated approach that involves a combination of various phenotypic and genotypic characteristics. Key molecular-genetic and phenotypic characteristics were determined for 93 microbial strains from the ICG SB RAS Collection. The strains were characterized by means of morphological, physiological, moleculargenetic, and mass-spectrometric parameters. Specific features of the growth of the strains on different media were determined, and cell morphology was evaluated. The strains were tested for the ability to utilize various substrates. The strains studied were found to significantly differ in their biochemical characteristics. Physiological characteristics of the strains from the collection were identified too, e. g., the relationship with oxygen, type of nutrition, suitable temperature and pH ranges, and NaCl tolerance. In this work, the microorganisms analyzed were combined into separate groups based on the similarities of their phenotypic characteristics. This categorization, after further refinement and expansion of the spectrum of taxa and their metabolic maps, may serve as the basis for the creation of an “artificial” classification that can be used as a key for simplified and quicker identification and recognition of microorganisms within both the ICG SB RAS Collection and other collections.
Keywords
identification of microorganisms,
biochemical characteristics of bacteria,
chemosystematics,
mass spectrometric analysis
Supporting agencies: This work was done within the framework of State Assignment Kurchatov Genomic Center of ICG SB RAS (075-15-2019-1662). The English language was corrected and certified by shevchuk-editing.com.
About the Authors
Yu. E. Uvarova
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
A. V. Bryanskaya
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
A. S. Rozanov
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
V. N. Shlyakhtun
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
E. A. Demidov
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
K. V. Starostin
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
T. N. Goryachkovskaya
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
S. V. Shekhovtsov
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
N. M. Slynko
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
S. E. Peltek
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
Russian Federation
Novosibirsk
Russian Federation
Novosibirsk
References
1. Church D.L. Biochemical tests for the identification of aerobic bacteria. In: Leber A. (Ed.). Clinical Microbiology Procedures Handbook. Fourth Edn. AMS Press, Washington, 2016;3.17.1.1-3.17.48.3. DOI 10.1128/9781555818814.ch3.17.
2. DasSarma P., Capes M.D., DasSarma S. Comparative genomics of Halobacterium strains from diverse locations. In: Das S., Dash H.R. (Eds.). Microbial Diversity in the Genomic Era. Acad. Press, 2019; 285-322. DOI 10.1016/B978-0-12-814849-5.00017-4.
3. Gaudreau A.M., Labrie J., Goetz C., Dufour S., Jacques M. Evaluation of MALDI-TOF mass spectrometry for the identification of bacteria growing as biofilms. J. Microbiol. Methods. 2018;145:79-81. DOI 10.1016/j.mimet.2018.01.003.
4. Hammer O., Harper D.A., Ryan P.D. PAST: paleontological statistics software package for education and data analysis. Palaeontol. Electronica. 2001;4(1):9.
5. Jenkins R.E., Tanner M.J.A. The structure of the major protein of the human erythrocyte membrane. Characterization of the intact protein and major fragments. Biochem. J. 1977;161(1):139-147. DOI 10.1042/bj1610139.
6. Kardymon O.L., Kudryavtseva A.V. Molecular genetic methods for intestinal microbiome investigation. Rossiiskiy Zhurnal Gastroenterologii, Gepatologii, Koloproktologii = Russian Journal of Gastroenterology, Hepatology, Coloproctology. 2016;26(4):4-13. DOI 10.22416/1382-4376-2016-26-4-4-13. (in Russian)
7. Logan N.A., De Vos P. Genus I. Bacillus. In: Bergey’s Manual of Systematic Bacteriology. Vol. 3. The Firmicutes. Springer, 2009;21-128.
8. Maniatis T., Fritsch E., Sambrook J. Molecular Cloning. Cold Spring Harbor lab., 1982. (Russ. ed. Maniatis T., Frich E., Sembruk D. Metody Geneticheskoy Inzhenerii. Molekulyarnoe Klonirovanie. Moscow: Mir Publ., 1984. (in Russian)
9. Netrusov A.I., Egorova M.A., Zakharchuk L.M. Workshop on Microbiology. Moscow: Academy Publ., 2005. (in Russian)
10. Reyes A.T. Morpho-biochemical aided identification of bacterial isolates from Philippine native pig. Adv. Pharmacol. Clin. Trials. 2018; 3(5):000148. DOI 10.23880/apct-16000148.
11. Schäffer C., Wugeditsch T., Kählig H., Scheberl A., Zayni S., Messner P. The surface layer (S-layer) glycoprotein of Geobacillus stearothermophilus NRS 2004/3a: analysis of its glycosylation. J. Biol. Chem. 2002;277(8):6230-6239. DOI 10.1074/jbc.M108873200.
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