Grigoryeva, T. V. | Search bioRxiv

bioRxiv2024

Bacteroides vesicles promote functional alterations in gut microbiota composition

Inflammatory bowel diseases are characterized by chronic intestinal inflammation and alterations of gut microbiota composition. Bacteroides fragilis, which secretes outer membrane vesicles (OMVs) with polysaccharide A (PSA), can moderate inflammatory response and possibly alter microbiota composition. In this research, we created a murine model of chronic DSS- induced intestinal colitis and treated it with Bacteroides fragilis OMVs. We monitored the efficiency of OMVs therapy by determining the disease activity index (DAI) and histological examination (HE) of the intestine before and after vesicles exposure. We also analyzed the microbiota composition using 16S rRNA gene sequencing. Finally, we evaluated the volatile compounds composition in animals stools by HS-GC/MS to assess the functional activity of the microbiota. As a result, we observed a more effective intestine repair after OMVs treatment according to DAI and HE. The metabolomic study also indicated the microbiota functional activity change, showing a predominance of phenol and pentanoic acid in the control group compared to the group treated with DSS (DSS) and the group treated with OMVs (DSS OMV). We also observed a positive correlation of these metabolites with Saccharibacteria and Hungatei Clostridium in the control group, whereas in the DSS group there was a negative correlation of phenol and pentanoic acid with Lactococcus and Romboutsia. According to metabolome and sequencing data, the microbiota composition of the DSS OMV group was intermediate between the control and DSS groups. It can be concluded that OMVs not only have an anti-inflammatory effect, but also contribute to the recovery of the microbiota composition.

microbiology↗

bioRxiv2018

Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy

The human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. Here we report a whole genome sequencing metagenomic study of the intestinal microbiota changes caused by Helicobacter pylori eradication therapy. We have found the decrease in taxonomic alpha-diversity due to the therapy. The changes observed were more extensive for patients with duodenal ulcer and female ones. As well across the patients under the therapy we have detected the shifts in the metabolic potential and resistome. Seven KEGG pathways associated with quorum sensing, genetic Information processing and environmental Information processing were increased, while metabolic pathways related with metabolism of cofactors and vitamins and glycan biosynthesis and metabolism decreased. Changes in the resistome profile have also been identified. We observed perturbations in intraspecies structures, which were higher in group of patients under the therapy than in control group of people without treatment. The Eubacterium rectale pangenome extracted from metagenomic data were changed. We also isolated and sequenced Enterococcus faecium strains from two patients before and after eradication therapy. After the therapy this bacterium increased as the antibiotic resistance in vitro, as well the number of ARGs to macrolides and tetracyclines and metagenomic relative abundance in comparison with strains before therapy. In summary, microbial community demonstrated shift to reduce metabolic potential and to increased mechanisms, which mediate more survival condition through intraspecies perturbations.\n\nImportanceThe human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. H. pylori eradication therapy causes multiple shifts and alterations (including intraspecies changes) of the intestinal microbiota structure and leads to the accumulation of genes which determine resistance to macrolides. Since these changes are not the same for patients with various diseases, patients with duodenal ulcer may be further paid special attention for reducing side effects, such as antibiotic-induced dysbiosis. Also, study of antibiotic treatment in terms of its impact upon the human gut microbiota allows shedding light on of the complex processes that cause accumulation and spread of antibiotic resistance. An identification and understanding of these complicated processes may help to constrain antibiotic resistance spread, which is of great importance for human health care.

microbiology↗