Cultivated Escherichia coli diversity in intestinal microbiota of Crohn's disease patients and healthy individuals: Whole genome data

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.

Role of adherent invasive Escherichia coli in pathogenesis of inflammatory bowel disease

Gut microbiota imbalances play an important role in inflammatory bowel disease (IBD), but no single pathogenic microorganism critical to IBD that is specific to the IBD terminal ileum mucosa or can invade intestinal epithelial cells has been found. Invasive Escherichia coli (E. coli) adhesion to macrophages is considered to be closely related to the pathogenesis of inflammatory bowel disease. Further study of the specific biological characteristics of adherent invasive E. coli (AIEC) may contribute to a further understanding of IBD pathogenesis. This review explores the relationship between AIEC and the intestinal immune system, discusses the prevalence and relevance of AIEC in Crohn's disease and ulcerative colitis patients, and describes the relationship between AIEC and the disease site, activity, and postoperative recurrence. Finally, we highlight potential therapeutic strategies to attenuate AIEC colonization in the intestinal mucosa, including the use of phage therapy, antibiotics, and anti-adhesion molecules. These strategies may open up new avenues for the prevention and treatment of IBD in the future.

Age and the aging process significantly alter the small bowel microbiome

Gut microbial diversity decreases with aging, but existing studies have used stool samples, which do not represent the entire gut. We analyzed the duodenal microbiome in 251 subjects aged 18-35 (n = 32), 36-50 (n = 41), 51-65 (n = 96), and 66-80 (n = 82). Decreased duodenal microbial diversity in older subjects is associated with combinations of chronological age, number of concomitant diseases, and number of medications used, and also correlated with increasing coliform numbers (p < 0.0001). Relative abundance (RA) of phylum Proteobacteria increases in older subjects, with increased RA of family Enterobacteriaceae and coliform genera Escherichia and Klebsiella, and is associated with alterations in the RA of other duodenal microbial taxa and decreased microbial diversity. Increased RA of specific genera are associated with chronological age only (Escherichia, Lactobacillus, and Enterococcus), number of medications only (Klebsiella), or number of concomitant diseases only (Clostridium and Bilophila). These findings indicate the small intestinal microbiome changes significantly with age and the aging process.

Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals

Crohn's disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenome-assembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage.

Myricetin and M10, a myricetin-3-O-β-d-lactose sodium salt, modify composition of gut microbiota in mice with ulcerative colitis

Our previous studies found that M10, a myricetin-3-O-β-d-lactose sodium salt, possessed higher effects of ameliorating ulcerative colitis (UC) than Myricetin in mice. Here, we aim to investigate whether the inhibition of UC is the consequence of the effects of M10 that leads to the changed microbiota. Mice model of UC was induced by dextran sulfate sodium (DSS) treatment. M10 and Myricetin were orally administrated for 12 weeks. We performed 16S rDNA sequencing assay to analyze the composition of gut microbiota isolated from ileocecum. Both M10 and Myricetin normalized the composition of Firmicutes and Actinobacteria as healthy mice had. At genus level, the effects of M10 and Myricetin on colitis were associated to the increase of probiotics, such as Akkermansia, and the inhibition of pathogenic microorganisms, such as Ruminococcus and Parabacteroides. M10 had stronger activity than Myricetin in the improvement of biosynthesis and degradation activities, resulting to increasing metabolism of sulfur, pyruvate, steroid biosynthesis and unsaturated fatty acid biosynthesis in gut. Furthermore, M10 normalized the proportion of Firmicutes and Actinobacteria in gut microbiota. It suggests that the improvements in UC are the consequence of the effect of M10 that leads to the changed intestinal microbiota. Conclusion: M10 contributed the pharmacological effects on UC by modification of the intestinal microbiota.

Review article: impact of cigarette smoking on intestinal inflammation-direct and indirect mechanisms

BACKGROUND

The inflammatory bowel diseases, Crohn's disease and ulcerative colitis are related multifactorial diseases. Their pathogenesis is influenced by each individual's immune system, the environmental factors within exposome and genetic predisposition. Smoking habit is the single best-established environmental factor that influences disease phenotype, behaviour and response to therapy.

AIM

To assess current epidemiological, experimental and clinical evidence that may explain how smoking impacts on the pathogenesis of inflammatory bowel disease.

METHODS

A Medline search for 'cigarette smoking', in combination with terms including 'passive', 'second-hand', 'intestinal inflammation', 'Crohn's disease', 'ulcerative colitis', 'colitis'; 'intestinal epithelium', 'immune system', 'intestinal microbiota', 'tight junctions', 'mucus', 'goblet cells', 'Paneth cells', 'autophagy'; 'epigenetics', 'genes', 'DNA methylation', 'histones', 'short noncoding/long noncoding RNAs'; 'carbon monoxide/CO' and 'nitric oxide/NO' was performed.

RESULTS

Studies found evidence of direct and indirect effects of smoking on various parameters, including oxidative damage, impairment of intestinal barrier and immune cell function, epigenetic and microbiota composition changes, that contribute to the pathogenesis of inflammatory bowel disease.

CONCLUSIONS

Cigarette smoking promotes intestinal inflammation by affecting the function and interactions among intestinal epithelium, immune system and microbiota/microbiome.

Inflammatory Bowel Diseases: Host-Microbial-Environmental Interactions in Dysbiosis

Crohn's Disease (CD) and Ulcerative Colitis (UC) are world-wide health problems in which intestinal dysbiosis or adverse functional changes in the microbiome are causative or exacerbating factors. The reduced abundance and diversity of the microbiome may be a result of a lack of exposure to vital commensal microbes or overexposure to competitive pathobionts during early life. Alternatively, many commensal bacteria may not find a suitable intestinal niche or fail to proliferate or function in a protective/competitive manner if they do colonize. Bacteria express a range of factors, such as fimbriae, flagella, and secretory compounds that enable them to attach to the gut, modulate metabolism, and outcompete other species. However, the host also releases factors, such as secretory IgA, antimicrobial factors, hormones, and mucins, which can prevent or regulate bacterial interactions with the gut or disable the bacterium. The delicate balance between these competing host and bacteria factors dictates whether a bacterium can colonize, proliferate or function in the intestine. Impaired functioning of NOD2 in Paneth cells and disrupted colonic mucus production are exacerbating features of CD and UC, respectively, that contribute to dysbiosis. This review evaluates the roles of these and other the host, bacterial and environmental factors in inflammatory bowel diseases.