Routine methods of laboratory studies of intestinal microbiota: role and place in clinical practice

Kornoukhova L.A.; Emanuel V.L.; Denisov N.L.

doi:https://doi.org/10.17116/dokgastro2021100415

Kornoukhova L.A.

N.I.Pirogov Clinic of High Medical Technologies of the Saint-Petersburg State University;
Pavlov First Saint Petersburg State Medical University

SPIN RSCI: 5617-7827
ORCID: 0000-0002-3840-1032

Emanuel V.L.

N.I.Pirogov Clinic of High Medical Technologies of the Saint-Petersburg State University;
Pavlov First Saint Petersburg State Medical University

SPIN RSCI: 1177-4802
Scopus AuthorID: 6603693075
ORCID: 0000-0002-2079-0439

Denisov N.L.

N.I.Pirogov Clinic of High Medical Technologies of the Saint-Petersburg State University

RSCI AuthorID: 310235
Scopus AuthorID: 7006103472

Routine methods of laboratory studies of intestinal microbiota: role and place in clinical practice

Authors:

Kornoukhova L.A., Emanuel V.L., Denisov N.L.

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Journal: Russian Journal of Evidence-Based Gastroenterology. 2021;10(4): 5‑11

DOI: 10.17116/dokgastro2021100415

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To cite this article:

Kornoukhova LA, Emanuel VL, Denisov NL. Routine methods of laboratory studies of intestinal microbiota: role and place in clinical practice. Russian Journal of Evidence-Based Gastroenterology. 2021;10(4):5‑11. (In Russ.)
https://doi.org/10.17116/dokgastro2021100415

Подписка 2026 Доказательная гастроэнтерология (Russian Journal of Evidence-Based Gastroenterology)

Использование инфографики авторами научных работ

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Abstract:

The intestinal microbiome studies received a powerful impetus associated with the development of laboratory technologies; however, the value of some diagnostic methods in clinical practice has not been established.

OBJECTIVE

Compare the results of two methods, the cultural and chromatographic.

MATERIAL AND METHODS

A comparative study of feces by chromatography-mass spectrometry of microbial metabolites/markers (MSMM) and bacteriological culture (BC) was carried out in 30 patients. Inclusion criteria: all studies were prescribed by a gastroenterologist; a one-time receipt of biomaterial for research. In BC, cultivation of facultatively anaerobic, obligate anaerobic microorganisms and fungi was performed. Microorganisms were identified by MALDI-TOF mass spectrometry. The MSMM study was carried out according to the author’s methodology of Prof. G.A. Osipov.

RESULTS

Intraspecies typing of anaerobes in BC allows to identify microecological changes in the intestine, assess bacterial properties and their changes, such as the acquisition of pathogenic factors. This is not available for MSMM, which determines 56 indicators represented by genera, species, and strains of microorganisms, complicating the assessment and interpretation of the results. The MSMM method lacks species differentiation of Lactobacillus spp. and Bifidobacterium spp., Enterobacteriaceae. The results of the methods do not correlate for Enterococcus spp. (77% of results), Enterobacteriaceae (60%), Staphylococcus spp. (67%), Lactobacillus spp. (30%), Bifidobacterium spp. and Bacteroides spp. — 17% of the results, respectively.

CONCLUSIONS

It is necessary to rank the informativeness of laboratory technologies and thoroughly prepare practitioners for using new laboratory methods in practice. At the moment, the chromatographic method MSMM can be used only for scientific purposes to determine microbial metabolites; for the quantitative assessment of microbial communities, validation and verification of the method is required.

Keywords:

fecal chromatography

mass spectrometry of microbial markers

Osipov method

intestinal dysbiosis

Authors:

Kornoukhova L.A.

N.I.Pirogov Clinic of High Medical Technologies of the Saint-Petersburg State University;
Pavlov First Saint Petersburg State Medical University

SPIN RSCI: 5617-7827
ORCID: 0000-0002-3840-1032

Emanuel V.L.

N.I.Pirogov Clinic of High Medical Technologies of the Saint-Petersburg State University;
Pavlov First Saint Petersburg State Medical University

SPIN RSCI: 1177-4802
Scopus AuthorID: 6603693075
ORCID: 0000-0002-2079-0439

Denisov N.L.

N.I.Pirogov Clinic of High Medical Technologies of the Saint-Petersburg State University

RSCI AuthorID: 310235
Scopus AuthorID: 7006103472

Received:

16.06.2021

Accepted:

21.10.2021

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References:

Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341(6150):1241214. https://doi.org/10.1126/science.1241214
Gupta H, Youn GS, Shin MJ, Suk KT. Role of Gut Microbiota in Hepatocarcinogenesis. Microorganisms. 2019;7(5):121. https://doi.org/10.3390/microorganisms7050121
Oinotkinova OSh, Nikonov EL, Gioeva IZ. The role of microbiota in pathogenesis of dyslipidemia and associated metabolic disorders. Dokazatel’naya gastroenterologiya. 2017;6(2):29-34. (In Russ.). https://doi.org/10.17116/dokgastro20176229-34
Bajaj JS. Alcohol, liver disease and the gut microbiota. Nature reviews. Gastroenterology&Hepatology. 2019;16:235–246. https://doi.org/10.1038/s41575-018-0099-1
Arslan N. Obesity, fatty liver disease and intestinal microbiota. World Journal of Gastroenterology. 2014;20(44):16452-16463. https://doi.org/10.3748/wjg.v20.i44.16452
Young VB. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ. 2017;356:j831. https://doi.org/10.1136/bmj.j831
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402):207-214. https://doi.org/10.1038/nature11234
Chan YK, Estaki M, Gibson DL. Clinical consequences of diet-induced dysbiosis. Annals of Nutrition and Metabolism. 2013;63(suppl 2):28-40. https://doi.org/10.1159/000354902
Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavyy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SR, Lyalyukova EA, Livzan MA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG, Govorun VM. Human gut microbiota community structures in urban and rural populations in Russia. Nature Communications. 2013;4:2469. https://doi.org/10.1038/ncomms3469
Sweeney TE, Morton JM. The human gut microbiome: a review of the effect of obesity and surgically induced weight loss. JAMA Surgery. 2013;148(6):563-569. https://doi.org/10.1001/jamasurg.2013.5
Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM, Rensen SS. Human intestinal microbiota composition is associated with local and systemic inflammation in obesity. Obesity. 2013;21(12):607-615. https://doi.org/10.1002/oby.20466
Mouzaki M, Comelli EM, Arendt BM, Bonengel J, Fung SK, Fischer SE, McGilvray ID, Allard JP. Intestinal microbiota in patients with nonalcoholic fatty liver disease. Hepatology. 2013;58(1):120-127. https://doi.org/10.1002/hep.26319
Kemppainen KM, Ardissone AN, Davis-Richardson AG, Fagen JR, Gano KA, León-Novelo LG, Vehik K, Casella G, Simell O, Ziegler A.G, Rewers M.J, Lernmark Å, Hagopian W, She JX, Krischer JP, Akolkar B, Schatz DA, Atkinson MA, Triplett EW. TEDDY Study Group. Early childhood gut microbiomes show strong geographic differences among subjects at high risk for type 1 diabetes. Diabetes Care. 2015;38(2):329-332. https://doi.org/10.2337/dc14-0850
Ardatskaja MD, Belmer SV, Dobriza VP, Zaharenko SM, Lazebnik LB, Minushkin ON, Oreshko LS, Sitkin SI, Tkachenko EI, Suvorov AN, Havkin AI, Shenderov BA. Intestinal dysbiosis: the current state of the problem, comprehensive diagnosis and treatment correction. Experementalnaja i clinicheskaya gastroenterologija. 2015;117(5):13-50. (In Russ.).
Osipov GA, Rodionov GG. Application of the method of mass spectrometry of microbial markers in clinical practice. Poliklinika. Specvypusk «Laboratoriya». 2013;1-3:68-73. (In Russ.).
Platonova AG, Osipov GA, Bojko NB, Kirillova NV, Rodionov GG. Chromato-mass spectrometric study of microbial fatty acids in human biological fluids and their clinical significance. Klinicheskaya Laboratornaya Diagnostika. 2015;60(12):46-55. (In Russ.).
Osipov GA, Parfenov AI, Bogomolov PO. Comparative gas chromatography-mass spectrometric study of the composition of chemical markers of microorganisms in the blood and biopsies of the intestinal mucosa. Accessed April 20, 2020. (In Russ.). https://www.rusmedserv.com/microbdiag/gastart.htm