Changes of the Concentration of Short-Chain Fatty Acids in the Intestines of Mice with Different Types of Obesity

We studied the production of short-chain fatty acids (SCFA) by the intestinal microbiota in mice with obesity caused by a diet and a genetic defect in the leptin receptor gene. In mice, intestinal contents were examined and SCFA were quantitatively assayed by gas chromatography. SCFA concentration in the intestinal contents of mice with alimentary obesity model was significantly lower in the first phase of the experiment (day 14), and the change in their production in dynamics was fundamentally different from this process in the control group (standard diet). The dynamics of the concentration of these metabolites in the model of genetic obesity was similar to that in the control, but the production of SCFA was significantly reduced in mice with leptin resistance in the middle phase (day 60) of the experiment. These findings indicate that the production of SCFA is more influenced by the diet than by leptin resistance.

Adipokines and myokines as indicators of obese phenotypes and their association with the gut microbiome diversity indices

Today, metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO) are distinguished. Adipose and muscle tissues can determine the obese phenotype due to adipokine and myokine production. Gut microbial community is also involved in MHO. The study was aimed to reveal the features of adipokine and myokine levels and their association with the gut microbiome alpha diversity in patients with MHO and MUO. A total of 265 subjects were divided into two groups: healthy individuals and obese patients. The latter were divided into two subgroups: patients with MHO and patients with MUO. Body mass index, waist circumference, HOMA-IR, adipokine and myokine levels, gut microbiome taxonomic composition, alpha diversity indices were defined in all the surveyed individuals, lipid and carbohydrate metabolism was also assessed. Significant differences in the adipokine and myokine levels and their association with the gut microbiome diversity indicators were revealed in patients with different obese phenotypes. Patients with MHO and MUO showed significantly lower adiponectin levels (р < 0.05) and significantly higher leptin and asprosin levels (р < 0.05) than healthy individuals. Patients with MUO had lower adiponectin and leptin levels (p < 0.05) than patients with MHO. Significantly higher FGF21 levels were observed in patients with MUO. Large-scale correlation analysis revealed the relationship between the glucose levels and the gut microbiome diversity indices that was missing in patients with MUO. This indicated the loss of the microbiota diversity effects on the blood glucose control in individuals with MUO, as well as different regulatory roles in the gut microbiome‒liver‒muscle/adipose tissue axes of individuals with MHO and MUO played by gut microbiota. The findings show the relationship between the gut microbiome diversity and the obese phenotype.

Competitive ability of <i>Escherichia coli</i> strains in the intestinal microbiota of patients with Crohn's disease and healthy volunteers: physiological, biochemical and genetic characteristics

Introduction. Crohn's disease (CD) is a chronic inflammation of various parts of the gastrointestinal tract with an increased proportion of Escherichia coli. However, the role of E. coli in disease remains unclear. This study aims to evaluate the competitive abilities of E. coli strains from CD patients and healthy volunteers, and to identify the biochemical and genetic determinants underlying these features. Materials and methods. The antagonistic activity was assessed by co-cultivation of 11 clinical E. coli strains inhibiting the growth of the K-12, with Enterobacter cloacae, Klebsiella pneumonia and Salmonella enterica. To elucidate the mechanism of antagonistic activity, the evaluation of biochemical properties and a comparative genomic analysis were used. Results and discussion. Genes of bacteriocin production systems were identified in genomes of 11 strains from CD patients and healthy volunteers active against the E. coli K-12 strain. Three strains from healthy individuals demonstrated activity against several Enterobacteriaceae bacteria. The strains biochemical properties were typical of representatives of E. coli. Strains 1_34_12, active against E. cloacae, and 1_45_11, inhibiting all tested enterobacteria, are phylogenetically related to the laboratory strain K-12. Strain 1_39_1, active against K. pneumonia and S. enterica, is phylogenetically close to the Nissle1917, contains the genes for colibactin biosynthesis and a variant of the fimH gene that increases the adhesive ability of bacteria. Conclusion. The identified E. coli strains are able to displace Enterobacteriaceae bacteria and can be used to study the bacteria-bacteria and host-bacteria interactions, to understand their role in gut homeostasis and intestinal inflammation.

Markers of dysbiosis in patients with ulcerative colitis and Crohn's disease

AIM

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

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.

Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses

Background

Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.

Methods

We performed a metagenomic study investigating the gut microbiota of patients with Crohn’s disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.

Results

The abnormal shifts in the microbial community structures in Crohn’s disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.

Conclusions

The genomic diversity of Crohn’s disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn’s disease and the development of new strategies for the prevention and treatment of this disease.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5306-5) contains supplementary material, which is available to authorized users.

[MOLECULAR-GENETIC ANALYSIS OF MICROORGANISMS WITH INTRAEPITHELIAL INVASION ISOLATED FROM PATIENTS WITH COLORECTAL CANCER]

The facultative aerobic bacteria isolated from the mucosa of rectum in patients with colorectal cancer in the zone of malignant tumor and neighboring normal mucosa was studied using molecular-genetic methods. The species attribution of bacteria was implemented using the cultural-morphological analysis and sequencing of the 16S rRNA locus. The microorganisms with the intraepithelial invasion to rectal mucosa isolated were identified as representatives of the adherent-invasive (AIEC) subgroup of Escherichia coli and species Klebsiella pneumonia. The molecular analysis by genetic determinants controlling adhesive, hemolytic, and toxigenic activity revealed that some bacterial isolates were able to produce toxins with potential cancerogenic activity (e.g., colibactin and cytotoxic necrotic factor I). Certain bacterial species isolated from malignant and normal rectum epithelium of the same patient demonstrated no difference between analyzed factors of toxigenicity.