Microbiome, gut dysbiosis and inflammatory bowel disease: That moment when the function is more important than taxonomy

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Abstract

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.

About the authors

S. I. Sitkin

State Research Institute of Highly Pure Biopreparations; North-Western State Medical University named after I.I. Mechnikov

Author for correspondence.
Email: drsitkin@gmail.com

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.

Russian Federation

T. Ya. Vakhitov

State Research Institute of Highly Pure Biopreparations

Email: fake@neicon.ru

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

7 Pudozhskaya ul., Saint Petersburg, 197110.

Russian Federation

E. V. Demyanova

State Research Institute of Highly Pure Biopreparations

Email: fake@neicon.ru

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

7 Pudozhskaya ul., Saint Petersburg, 197110.

Russian Federation

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