The scientific revolution in microbiology and its importance for practice
https://doi.org/10.32634/0869-8155-2020-341-9-37-42
Abstract
The accumulation of knowledge in the process of scientific and technological development does not occur linearly, but in leaps and bounds: periods of relative stagnation are replaced by scientific revolutions. The scientific revolution is the change of explanatory paradigms by the scientific community. A few years ago, the establishment of the taxonomic affiliation of microorganisms by cultivation and counting by methods of classical microbiology was fraught with a number of insurmountable difficulties. The complex composition of the media, the presence of an excess of inhibiting compounds in the composition of the nutrient media, the need to maintain extreme temperatures, the composition of gases and pressure for cultivation, the susceptibility of the culture to the effects of oxygen excluded uncultured microorganisms from the field of view of the researcher. The emergence of molecular genetic methods made it possible to study the diversity of microorganisms, bypassing the previously obligatory stage of cultivation, isolation of a pure culture and comparison with a reference sample. Through the prism of scientific revolutions and changes in scientific paradigms, the differences between the methods of classical microbiology and molecular genetic methods are revealed. The experience of BIOTROF LLC in the application of molecular genetic methods for the identification of microorganisms in livestock and poultry farming is summarized. Based on the use of 16S metagenomics, it was possible to show for the first time that health disorders of farm animals and birds, a decrease in productivity and the duration of economic use in many cases are associated with dysbiotic phenomena in the gastrointestinal tract. Thus, in cows culled due to lactic acidosis, in comparison with clinically healthy animals, inhibition of the growth of bacteria synthesizing cellulases and microorganisms of the order Selenomonadales, capable of fermenting lactic acid to volatile fatty acids, was observed. Based on the calculation of Pearson's correlations, it was shown that an increase in the content of lactobacilli of the family Lactobacillaceae in the intestines of poultry was associated with an increase in meat productivity, and an increase in staphylococci, with a decrease.
About the Authors
D. G. Tyurina
BIOTROF LLC
Russian Federation
Ph.D. Sci., Deputy Director
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
Russian Federation
Ph.D. Sci., Deputy Director
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
G. Yu. Laptev
BIOTROF LLC
Russian Federation
Doctor of Biological Sciences, Director
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
Russian Federation
Doctor of Biological Sciences, Director
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
N. I. Novikova
BIOTROF LLC
Russian Federation
Russian Federation
candidate of biological sciences, deputy director
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
E. A. Yildirim
BIOTROF LLC
Russian Federation
Russian Federation
Doctor of Biological Sciences biotechnologist of the molecular genetic laboratory
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
L. A. Ilyina
BIOTROF LLC
Russian Federation
Russian Federation
Candidate of Biological Sciences, Head of the Molecular Genetic Laboratory
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
N. V. Tarlavin
BIOTROF LLC
Russian Federation
Russian Federation
biotechnologist of the molecular genetic laboratory
Russian Federation, St. Petersburg, Kolpino, Izhora Plant, 45, letter DV
References
1. Zavarzin GA Does evolution make up the meaning of biology? Bulletin of the Russian Academy of Sciences, 2006, 76 (6): 522–533 (In Russ.)
2. Kiyashchenko L. P. Ethos of post-nonclassical science (to the formulation of the problem) — Philosophy of Science, 2005, v. 11, No. 1, pp. 29–53 (In Russ.)
3. Malakhov VV Revolution in zoology: new ideas about the system and phylogeny of multicellular animals — Bulletin of the Russian Academy of Sciences, 2013, v. 83, no. p. 210–215 (In Russ.)
4. Yu. Odum. Fundamentals of ecology — M., Mir, 1975, p. 613 (In Russ.)
5. Bergey's guide to bacteria. In 2 volumes.Vol. 1: Per. from English / Ed. J.Hoult, N.Krieg, P.Sneet, J.Steley, S. Williams — M., Mir, 1997, pp.10–11 (In Russ.)
6. Sokolenko A.V. Morphology, ultrastructure, metabolism of uncultivated forms of Vibrio cholerae. Abstract of thesis ... Cand. biol. sciences. 2000. Rostov-on-Don. — 21 p. (In Russ.)
7. Stepin V.S. Scientific knowledge and values of technogenic civilization — Questions of Philosophy, 1989, no. 10, p. 3–18 (In Russ.)
8. Stepin V.S. Philosophy of Science. Common problems. M .: Gardariki, 2006 — p. 267– 27 (In Russ.)
9. Butkevich N.V., Butkevich aVS Multiplication of sea bacteria depending on the composition of the medium and on temperature. Microbiology (Moscow). — 1936. — V.5 — P. 322–342.
10. Ekweozor C.C., Nwoguh C.E., Barer M.R. Transient increases in colony counts observed in declining populations of Campylobacter jejuni held at low temperature // FEMS Microbiol. Lett. — 1998. — V. 158 (2). — P. 267–72.
11. Alexander E., Pham D., Steck T.R. The viable- butnonculturable condition is induced by copper in Agrobacterium tumefaciens and Rhizobium leguminosarum // Appl. Environ. Microbiol. — 1999. — V. 65(8). — P. 3754–3756
12. Achtman M, Wagner M. 2008. Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 6: 431–440
13. Bik EM, et al. 2010. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 4: 962–974
14. Bomar L, Maltz M, Colston S, Graf J. 2011. Directed culturing of microorganisms using metatranscriptomics. mBio 2(2): e00012–11 doi:10.1128/mBio.00012–11
15. Dinis JM, et al. 2011. In search of an uncultured humanassociated TM7 bacterium in the environment. PLoS One 6: e21280 doi:10.1371/journal.pone.0021280
16. Hardoim CCP, et al. 2009. Diversity of bacteria in the marine sponge Aplysina fulva in Brazilian coastal waters. Appl. Environ. Microbiol. 75: 3331–3343
17. Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67: 411–419
18. Goodman AL, et al. 2011. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl. Acad. Sci. U. S. A. 108: 6252–6257
19. Davis DJ. 1921. The accessory factors in bacterial growth. IV. The “satellite” or symbiosis phenomenon of Pfeiffer's Bacillus (B. influenzae). J. Infect. Dis. 29: 178–186
20. D'Onofrio A, et al. 2010. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem. Biol. 17: 254–264
21. Keller M, Zengler K. 2004. Tapping into microbial diversity. Nat. Rev. Microbiol. 2: 141–150
22. Rappe MS, Giovannoni SJ. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57: 369–394
23. Rheims H, Rainey FA, Stackebrandt E. 1996. A molecular approach to search for diversity among bacteria in the environment. J. Ind. Microbiol. 17: 159–169
24. Rosello-Mora R., Amman R. The species concept for prokaryotes. FEMS Microbiology Reviews, Volume 25, Issue 1, January 2001, p. 39–67.
25. Sejrsen K., Hvelplund T., Nielsen M.O. Ruminant physiology. Digestion, metabolism and impact of nutrition on gene expression, immunology and stress. Wageningen Academic Publishers, 2008, p.22
26. Vartoukian SR, Palmer RM, Wade WG. 2010. Cultivation of a Synergistetes strain representing a previously uncultivated lineage. Environ. Microbiol. 12: 916–928
27. Woese CR. 1987. Bacterial evolution. Microbiol. Rev. 51: 221–271
28. Stiverson J, Morrison M, Yu Z. Populations of select cultured and uncultured bacteria in the rumen of sheep and the effect of diets and ruminal fractions. Int J Microbiol. 2011;2011:750613. doi:10.1155/2011/750613
29. Rhoads Daniel D., . Wolcott Randall D, Yan Sun, Scot E. Dowd. Comparison of Culture and Molecular Identification of Bacteria in Chronic Wounds // Int. J. Mol. Sci. 2012, 13, 2535–2550; doi:10.3390/ijms13032535
30. Mackie R.I., White B.A. Recent advances in rumen microbial ecology and metabolism: potential impact on nutrient output // J Dairy Sci. -1990. — V. 73(10). — P. 2971–95.
Review
For citations:
Tyurina D.G., Laptev G.Yu., Novikova N.I., Yildirim E.A., Ilyina L.A., Tarlavin N.V. The scientific revolution in microbiology and its importance for practice. Agrarian science. 2020;(9):37-42. (In Russ.) https://doi.org/10.32634/0869-8155-2020-341-9-37-42
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