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

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.

Keywords

• butyrate
• butyric acid
• crohn's disease
• gut dysbiosis
• gut microbiota
• inflammatory bowel disease
• metabiotics
• metabolome
• microbiome
• ulcerative colitis