Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease

Abstract

Inflammatory bowel diseases (IBD), which include ulcerative colitis (UC) and Crohn’s disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBD have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of the IBD and the dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identify a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward toward understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBD.

The role of gut microbiome in inflammatory bowel disease diagnosis and prognosis

“…In a study of 2045 non‐IBD and IBD patients from four European countries, an algorithm based on eight selected genera from stool samples ( Faecalibacterium , an unknown Peptostreptococcaceae , Anaerostipes , Methanobrevibacter , an unknown Christensenellaceae , Collinsella and Fusobacterium , Escherichia ) performed well in discriminating CD from UC, irritable bowel syndrome, anorexia, and healthy control 57 . By assessing 20 bacteria markers in mucosal samples from Chilean and Spanish patients with IBD, Chamorro et al 58 . were able to discriminate dysbiosis and eubiosis in IBD patients, with an AUC ranging from 0.96 to 0.99.…”

“…identified 117 differential bacterial taxa from stool samples for discriminating CD with UC which showed excellent performance (AUC >0.90). Using only 11 mucosal bacteria, Chamorro et al 58 . could differentiate UC from CD with an AUC of 0.83.…”

The role of cholesterol and mitochondrial bioenergetics in activation of the inflammasome in IBD

“…IBD patients present different microbiota compositions; some having eubiotic (homeostatic) or dysbiotic (imbalanced) microbiota. Increased facultative anaerobes and aerobic bacteria is seen in dysbiotic IBD patients compared to healthy control and eubiotic IBD patients (characterized by high obligate anaerobe abundance) (136). This evidence is consistent with the hemoglobin (oxygen carrier) and ROS release to the intestinal lumen, increasing oxygen levels to overgrown facultative anaerobes and aerobic bacteria (137).…”

Enteropathy and gut dysbiosis as obstacles to achieve immune recovery in undetectable people with HIV: a clinical view of evidence, successes, and projections

“…Among these, abundance of Faecalibacterium prausnitzii has been highlighted as a healthy bacteriome composition marker [28]. On the other hand, enrichment of Proteobacteria, for example, is typically found in pro-inflammatory bacteriomes, such as those from patients with IBD [60,61].…”