Background Several studies have highlighted the role of host–microbiome interactions in the pathogenesis of inflammatory bowel disease (IBD), resulting in an increasing amount of data mainly focusing on Western patients. Because of the increasing prevalence of IBD in newly industrialized countries such as those in Asia, the Middle East, and South America, there is mounting interest in elucidating the gut microbiota of these populations. We present a comprehensive analysis of several IBD-related biomarkers and gut microbiota profiles and functions of a unique population of patients with IBD and healthy patients from Kazan (Republic of Tatarstan, Russia). Methods Blood and fecal IBD biomarkers, serum cytokines, and fecal short-chain fatty acid (SCFA) content were profiled. Finally, fecal microbiota composition was analyzed by 16S and whole-genome shotgun sequencing. Results Fecal microbiota whole-genome sequencing confirmed the presence of classic IBD dysbiotic features at the phylum level, with increased abundance of Proteobacteria, Actinobacteria, and Fusobacteria and decreased abundance of Firmicutes, Bacteroidetes, and Verrucomicrobia. At the genus level, the abundance of both fermentative (SCFA-producing and hydrogen (H2)-releasing) and hydrogenotrophic (H2-consuming) microbes was affected in patients with IBD. This imbalance was confirmed by the decreased abundance of SCFA species in the feces of patients with IBD and the change in anaerobic index, which mirrors the redox status of the intestine. Conclusions Our analyses highlighted how IBD-related dysbiotic microbiota—which are generally mainly linked to SCFA imbalance—may affect other important metabolic pathways, such as H2 metabolism, that are critical for host physiology and disease development.
The results of recent studies indicate a significant role of gut microbiota in the pathogenesis of inflammatory bowel diseases (IBD). The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. Materials and methods. Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. Results and discussion. Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. Conclusion: the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.
Low patient compliance due to the development of adverse events in the form of antibiotic-associated diarrhea (AAD) is considered as the main reason for the failure of the eradication of optimized anti-Helicobacter therapy regimens. A key mechanism for the development of AAD is to reduce the number and species diversity of bacteria that form butyric acid. Aim. The purpose of this study was to study the comparative effect on the clinical effectiveness of eradication therapy (ET) of Helicobacter pylori infection and metabolic changes in the colon microbiota of additional inclusion in the optimized treatment regimen of the combined prebiotic Zakofalk (inulin + butyrate) with probiotics (lacto- and bifidobacteria in an amount of at least 1017 СFU). Materials and methods. 120 patients with chronic gastroduodenal diseases and infected H. pylori were еxamined. A comparative analysis of the effect of a combined prebiotic and lacto-bifid-containing probiotics on improving the effectiveness of the optimized ET scheme and improving its tolerability, as well as on the quantitative and qualitative content of short-chain fatty acids (SFA) in feces. The success of eradication was controlled by a 13C urease breath test. Results. According to the results of the study in randomized groups of patients, an excellent percentage of eradication (95%) was achieved in patients who performed ET with the addition of the prebiotic Zakofalk. In the same group of patients, there was an increase in the absolute content of SFA and a significant increase in the concentration of butyric acid. In the group of patients who received ET with the addition of probiotics, an acceptable level of eradication was achieved (85.7%), but no changes in SFA were found indicating an increase in the number or activity of the butyrate-producing flora. Patients who performed ET without the addition of pre-probiotics did not achieve the target percentage of successful eradication (83.3%), and a significant quantitative decrease in SFA was found with a significant decrease in the proportion of butyric acid. Conclusion. The inclusion of Zakofalk in the ET scheme, in comparison with probiotics, significantly increases the probability of successful eradication, more effectively restores the metabolic potential of the microbiota, and prevents the development of AAD.
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