gastro-jРоссийский журнал гастроэнтерологии, гепатологии, колопроктологииRussian Journal of Gastroenterology, Hepatology, Coloproctology1382-43762658-6673«Gastro» LLC10.22416/1382-4376-2022-32-2-19-34gastro-j-632Research ArticleОБЗОРЫREVIEWSПрямые и косвенные методы изучения микробиоты человекаDirect and Indirect Methods for Studying Human Gut Microbiotahttps://orcid.org/0000-0002-6815-6015ИвашкинВ. Т.IvashkinV. T.

Ивашкин Владимир Трофимович — доктор медицинских наук, профессор, академик РАН, заведующий кафедрой пропедевтики внутренних болезней, гастроэнтерологии и гепатологии 

119435, г. Москва, ул. Погодинская, д. 1, стр. 1

Vladimir T. Ivashkin — Dr. Sci. (Med.), Prof., Full Member of the Russian Academy of Sciences, Head of the Chair of Internal Disease Propaedeutics, Gastroenterology and Hepatology

119435, Moscow, Pogodinskaya str., 1, bld. 1

ivashkin_v_t@staff.sechenov.ruhttps://orcid.org/0000-0001-8942-4851МедведевО. С.MedvedevO. S.

Медведев Олег Стефанович — доктор медицинских наук, профессор, заведующий кафедрой фармакологии факультета фундаментальной медицины 

119991, г. Москва, Ломоносовский просп. д. 27, корп. 1

Oleg S. Medvedev — Dr. Sci. (Med.), Prof., Head of the Chair of Pharmacology, Faculty of Fundamental Medicine; Head of the Laboratory of Experimental Pharmacology

119991, Moscow, Lomonosovskiy Ave., 27, bld. 1

medvedev@fbm.msu.ruПолуэктоваЕ. А.PoluektovaE. A.

Полуэктова Елена Александровна — доктор медицинских наук, профессор кафедры пропедевтики внутренних болезней, гастроэнтерологии и гепатологии

119435, г. Москва, ул. Погодинская, д. 1, стр. 1

Elena A. Poluektova — Dr. Sci. (Med.), Prof., Chair of Internal Disease Propaedeutics, Gastroenterology and Hepatology

119435, Moscow, Pogodinskaya str., 1, bld. 1

poluektova3_e_a@staff.sechenov.ruhttps://orcid.org/0000-0002-3722-8207КудряцеваА. В.KudryavtsevaA. V.

Кудрявцева Анна Викторовна — кандидат биологических наук, заведующая лабораторией постгеномных исследований, заместитель директора по научной работе 

119334, г. Москва, ул. Вавилова, 32, стр. 1

Anna V. Kudryavtseva — Cand. Sci. (Biol.), Head of the Laboratory of Postgenomic Research; Deputy Director for Science

119334, Moscow, Vavilova str., 32, bld. 1

rhizamoeba@mail.ruhttps://orcid.org/0000-0003-0937-313XБахтогаримовИ. Р.BakhtogarimovI. R.

Бахтогаримов Ильдар Рамилевич — аспирант, старший лаборант лаборатории постгеномных исследований

119334, г. Москва, ул. Вавилова, 32, стр. 1

Ildar R. Bakhtogarimov — Postgraduate Student, Senior Laboratory Assistant, Laboratory of Postgenomic Research

119334, Moscow, Vavilova str., 32, bld. 1

bakhtogarimov@gmail.comhttps://orcid.org/0000-0001-6647-0572КарчевскаяА. Е.KarchevskayaA. E.

Карчевская Анна Евгеньевна — младший научный сотрудник лаборатории общей и клинической нейрофизиологии; медицинский психолог; студентка 

119048, Москва, Трубецкая ул., 8, стр. 2

Anna E. Karchevskaya — Junior Researcher, Laboratory of General and Clinical Neurophysiology; Physician (medical psychology); Graduate Student

119048, Moscow, Trubetskaya str., 8, bld. 2

ankar1998@yandex.ruФГАОУ ВО «Первый Московский государственный медицинский университет им. И.М. Сеченова» (Сеченовский университет) Министерства здравоохранения Российской ФедерацииI.M. Sechenov First Moscow State Medical University (Sechenov University)ФГБОУ ВО «Московский государственный университет имени М.В. Ломоносова»; ФГБУ «Национальный медицинский исследовательский центр кардиологии имени академика Е.И. Чазова» Министерства здравоохранения Российской ФедерацииM.V. Lomonosov Moscow State University; National Medical Research Center of CardiologyФГБУН «Институт молекулярной биологии им. В. А. Энгельгардта Российской академии наук»V.A. Engelgardt Institute of Molecular BiologyФГАОУ ВО «Первый Московский государственный медицинский университет им. И.М. Сеченова» (Сеченовский университет) Министерства здравоохранения Российской Федерации; ФГАУ «Национальный медицинский исследовательский центр нейрохирургии им. академика Н.Н. Бурденко» Министерства здравоохранения Российской Федерации; ФГБУН «Институт высшей нервной деятельности и нейрофизиологии» Российской академии наукРоссияI.M. Sechenov First Moscow State Medical University (Sechenov University); N.N. Burdenko National Medical Research Center of Neurosurgery; Institute of Higher Nervous Activity and NeurophysiologyRussian Federation2022150520223221934Copyright © Ивашкин В.Т., Медведев О.С., Полуэктова Е.А., Кудряцева А.В., Бахтогаримов И.Р., Карчевская А.Е., 20222022Ивашкин В.Т., Медведев О.С., Полуэктова Е.А., Кудряцева А.В., Бахтогаримов И.Р., Карчевская А.Е.Ivashkin V.T., Medvedev O.S., Poluektova E.A., Kudryavtseva A.V., Bakhtogarimov I.R., Karchevskaya A.E.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://www.gastro-j.ru/jour/article/view/632Цель публикации

Цель публикации: рассмотреть основные методы исследования микробиоты желудочно-кишечного тракта.

Основные положения

Основные положения. В настоящее время молекулярно-генетические методы используются преимущественно для фундаментальных исследований и не имеют единого «протокола» анализа данных, что затрудняет их внедрение в клиническую практику. Исследование короткоцепочечных жирных кислот (КЦЖК) в плазме крови может служить косвенным маркером микробного состава толстой кишки, однако на сегодня нельзя с уверенностью связать количество и соотношение определяемых КЦЖК с определенной нозологической формой; изучение уровня ТМАО в плазме крови и моче также может отражать наличие в составе кишечной микробиоты особых кластеров бактерий, несущих гены Cut, CntA/CntB и YeaW/YeaX. Однако необходимы дальнейшие исследования по выявлению корреляционных связей между определенными заболеваниями, микробным составом ЖКТ, рационом и уровнем ТМАО. Газовые биомаркеры (водород, метан и сероводород) гораздо лучше изучены по сравнению с другими типами биомаркеров функции и состава микробиоты. Преимуществом газовых биомаркеров является возможность их неинвазивного, многократного измерения, что позволяет получать информацию о соотношении гидрогенных и гидрогенотрофных микроорганизмов.

Выводы

Выводы. Объединение информации, полученной при исследованиях кишечной микробиоты на уровнях генома, транскриптома и метаболома, позволит произвести более глубокий анализ состава и функционирования микробиоты человека. Такой подход имеет несомненный потенциал для понимания патогенеза различных заболеваний и открывает возможности для разработки новых стратегий профилактики и лечения. 

Aim

Aim: To review the main methods of intestinal microbiota studying.

Key points

Key points. Currently, molecular genetic methods are used mainly for basic research and do not have a unified protocol for data analysis, which makes it difficult to implement them in clinical practice. Measurement of short chain fatty acids (SCFA) concentrations in plasma provides the data, which can serve as an indirect biomarker of the colonic microbiota composition. However, currently available evidence is insufficient to relate the obtained values (SCFA levels and ratio) to a particular disease with a high degree of certainty. Trimethylamine N-oxide (TMAO) levels in the blood plasma and urine can also reflect the presence of specific bacterial clusters containing genes Cut, CntA/CntB and YeaW/YeaX. Therefore, further studies are required to reveal possible correlations between certain disorders and such parameters as the composition of gut microbiota, dietary patterns and TMAO concentration. Gas biomarkers, i.e. hydrogen, methane and hydrogen sulphide, have been studied in more detail and are better understood as compared to other biomarkers of the gut microbiome composition and functionality. The main advantage of gas biomarkers is that they can be measured multiple times using non-invasive techniques. These measurements provide information on the relative proportion of hydrogenic (i.e. hydrogen producing) and hydrogenotrophic (i.e. methanogenic and sulfate-reducing) microorganisms. In its turn, this opens up the possibility of developing new approaches to correction of individual microbiota components.

Conclusions

Conclusions. Integration of the data obtained by gut microbiota studies at the genome, transcriptome and metabolome levels would allow a comprehensive analysis of microbial community function and its interaction with the human organism. This approach may increase our understanding of the pathogenesis of various diseases as well open up new opportunities for prevention and treatment.

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The authors declare that there are no conflicts of interest present.