Almanac of Clinical MedicineAlmanac of Clinical MedicineАльманах клинической медицины2072-05052587-9294Moscow Regional Research and Clinical Institute (MONIKI)87810.18786/2072-0505-2018-46-5-396-425REVIEW ARTICLEОБЗОРMicrobiome, gut dysbiosis and inflammatory bowel disease: That moment when the function is more important than taxonomyМикробиом, дисбиоз толстой кишки и воспалительные заболевания кишечника: когда функция важнее таксономииSitkinS. I.СиткинС. И.
Russian Federation

Stanislav I. Sitkin – MD, PhD, Leading Research Fellow, Laboratory of Microbiology, State Research Institute of Highly Pure Biopreparations; Associate Professor, Chair of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University named after I.I. Mechnikov.

7 Pudozhskaya ul., Saint Petersburg, 197110; 47 Piskarevsky prospekt, Saint Petersburg, 195067.

Tel.: +7 (812) 498 48 56.

Ситкин Станислав Игоревич – кандидат медицинских наук, ведущий научный сотрудник лаборатории микробиологии ФГУП «Гос.НИИ ОЧБ» ФМБА России, доцент кафедры пропедевтики внутренних болезней, гастроэнтерологии и диетологии ФГБОУ ВО СЗГМУ им. И.И. Мечникова МЗ России.

197110, Санкт-Петербург, ул. Пудожская, 7; 195067, Санкт-Петербург, Пискаревский пр., 47.

Тел.: +7 (812) 498 48 56. 

drsitkin@gmail.comVakhitovT. Ya.ВахитовТ. Я.
Russian Federation

Timur Ya. Vakhitov – ScD in Biology, Head of the Laboratory of Microbiology.

7 Pudozhskaya ul., Saint Petersburg, 197110.

Вахитов Тимур Яшэрович – доктор биологических наук, начальник лаборатории микробиологии.

197110, Санкт-Петербург, ул. Пудожская, 7.

DemyanovaE. V.ДемьяноваЕ. В.
Russian Federation

Elena V. Demyanova – PharmD, PhD, Deputy Head of the Laboratory of Microbiology.

7 Pudozhskaya ul., Saint Petersburg, 197110.

Демьянова Елена Валерьевна – кандидат фармацевтических наук, заместитель начальника лаборатории микробиологии.

197110, Санкт-Петербург, ул. Пудожская, 7.

State Research Institute of Highly Pure BiopreparationsФГУП «Государственный научно-исследовательский институт особо чистых биопрепаратов» ФМБА РоссииNorth-Western State Medical University named after I.I. MechnikovФГБОУ ВО «Северо-Западный государственный медицинский университет имени И.И. Мечникова» Минздрава России1911201846539642516112018Copyright ©; 2018, Sitkin S.I., Vakhitov T.Y., Demyanova E.V.Copyright ©; 2018, Ситкин С.И., Вахитов Т.Я., Демьянова Е.В.2018Sitkin S.I., Vakhitov T.Y., Demyanova E.V.Ситкин С.И., Вахитов Т.Я., Демьянова Е.В.https://creativecommons.org/licenses/by/4.0https://almclinmed.ru/jour/article/view/878

The altered gut microbiome (dysbiosis) is involved in the  pathogenesis of most  non-infectious  gastrointestinal diseases, such as inflammatory bowel disease (IBD), irritable bowel syndrome, colorectal cancer, celiac disease, hepatic encephalopathy, non-alcoholic  fatty  liver disease,  alcoholic  liver disease, cholelithiasis and  others. The molecular aspects  of the interaction  between dysbiotic microbiota and host immune system are considered in the context of IBD pathogenesis. The authors do provide  original interpretations  of the  concepts of taxonomic (microbiological) and metabolic (functional) dysbiosis. Special attention is paid to the hypothesis  that gut dysbiosis is caused not so much by structural changes  in the microbiome as by alterations  in microbial metabolism. Thus, the metabolome is a greater  predictor  of dysbiosis, than  the  taxonomic  composition  of the  microbiome. It is important to consider dysbiotic changes in the  gut  microbiota  in patients  with ulcerative colitis and  Crohn's  disease,  since  they  may  significantly affect the course and prognosis  of IBD. Factors  hampering  the   microbiota   assessment in  clinical practice  are  discussed  in  detail,  and advanced  dysbiosis tests, including  the  GA-map Dysbiosis  Test  (GA-test) and  the   Colonoflor-16 Test, are described. By means of clinical studies it is demonstrated that  a reduction  in the  genetic capacity of the  microbiome  for butyrate  synthesis, together with an increase in pathobionts and a decrease  in microbial diversity, is an important and necessary feature of dysbiosis in IBD patients. Thus, the butyryl-CoA:acetate CoA-transferase (BCoAT) gene  level can be considered  as a valuable biomarker to assess gut microbiota  function in clinical practice.  In  conclusion,  approaches to correct gut dysbiosis using probiotics, prebiotics, metabiotics  and fecal microbiota  transplantation as an addition to conventional treatment in IBD are critically discussed.

Измененный микробиом кишечника (дисбиоз) вовлечен в патогенез большинства неинфекционных заболеваний органов  пищеварения  – воспалительные  заболевания кишечника (ВЗК), синдром  раздраженного кишечника, колоректальный рак, целиакия, печеночная  энцефалопатия, неалкогольная  жировая болезнь печени, алкогольные поражения  печени, желчнокаменная болезнь и другие. В статье рассматриваются молекулярно-биологические аспекты взаимодействия дисбиотической микробиоты с иммунной  системой  человека  в контексте  развития ВЗК. Авторами даются оригинальные  трактовки понятий таксономического (микробиологического) и метаболического  (функционального) дисбиоза. Особое внимание уделяется гипотезе о том, что дисбиотические состояния микробиоценоза  кишечника обусловлены не столько изменениями  структуры микробиома, сколько нарушениями его метаболизма, а метаболом является  бóльшим предиктором  дисбиоза, нежели таксономический состав микробиома. Отмечается важность учета дисбиотических изменений   микробиоты   кишечника   у  пациентов  с язвенным  колитом и болезнью  Крона, поскольку  они  могут существенно  влиять  на течение и прогноз ВЗК. Подробно обсуждаются факторы,   затрудняющие   оценку  микробиоты в клинической практике, и описываются современные  тесты на дисбиоз, включая GA-map Dysbiosis Test  (GA-тест) и  отечественный  тест «Колонофлор-16».   На  основании   результатов клинических исследований, в том числе собственных, демонстрируется, что снижение генетической бутират-продуцирующей способности микробиома, наряду с увеличением численности патобионтов и снижением микробного разнообразия, – важная и неотъемлемая характеристика  дисбиоза  у пациентов  с ВЗК, а уровень гена бутирил-КоA:ацетат-КоA-трансферазы (BcoAT) может рассматриваться как потенциальный биомаркер  для оценки функциональных возможностей микробиоты кишечника в клинической  практике. В  заключение  критически обсуждаются  подходы  к коррекции   дисбиоза кишечника с использованием пробиотиков, пребиотиков, метабиотиков  и трансплантации фекальной  микробиоты  в дополнение  к стандартной терапии ВЗК.

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