Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease

Abstract

Background & AimsMicrobial dysbiosis and aberrant host–microbe interactions in the gut are believed to contribute to the development and progression of Crohn’s disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine.MethodsParaffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease–free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer. Diseased and healthy-appearing ileum was identified using microscopy, and paraffin blocks were macrodissected using a core needle to specifically isolate DNA. Illumina Whole Genome Sequencing was used for microbial sequence identification and subsequent taxonomic classification using the PathSeq tool.ResultsWe observed significant differences between the microbiome of CD samples vs inflammatory bowel disease–free controls, including depletion of Bacteroidetes and Clostridia. Notably, microbial composition at the phyla level did not differ markedly between healthy and diseased areas of CD patients. However, we observed enrichment of potentially pathogenic organisms at the species level.ConclusionsOur study showed dysbiosis within deeper layers of the ileum of CD patients, specifically enrichment of enterotoxigenic Staphylococcus aureus and an environmental Mycobacterium species not described previously. Future studies with larger cohort sizes are warranted to confirm these findings. Studies would benefit from effective microbial DNA extraction methods from paraffin sections and host nucleic acid depletion approaches to increase microbial read coverage.

Microbial network disturbances in relapsing refractory Crohn’s disease

“…There is strong evidence indicating that the intestinal microbiota is responsible for triggering inflammatory bowel disease (IBD): animal models of chronic intestinal inflammation are almost all mitigated when re-derived to germ-free status 1,2 ; humans with IBD have altered reactivity to their intestinal microbes 3 ; the genetic loci for human susceptibility to Crohn's disease (CD) and/or ulcerative colitis (UC) mainly encode proteins required for innate or adaptive mucosal immune defense mechanisms and overlap with genes known to cause microbiota-sensitive intestinal inflammation in animal models 4 . Whilst no persistent pathogen has been consistently identified as being responsible for IBD, strategies reducing microbiota exposure such as surgical fecal stream diversion 5 , elemental diets or antibiotic treatment can have beneficial effects in particular IBD cases [6][7][8] .…”

PRWHMDA: Human Microbe-Disease Association Prediction by Random Walk on the Heterogeneous Network with PSO

“…Research showed that dysbiosis within deeper layers of the ileum of CD patients, there were specifically enrichment of enterotoxigenic Staphylococcus aureus . Staphylococcus (5th in the prediction list) was thus validated 36 .…”

Stress responses, M2 macrophages, and a distinct microbial signature in fatal intestinal acute graft-versus-host disease

“…We then used PathSeq as a mapping and taxonomic classification algorithm to estimate abundance of candidate microbes using read counts assigned to each organism (13). This approach has previously been used to assess mucosal dysbiosis in Crohn's disease (55). The raw data for both RNA-Seq and PathSeq are available at the Gene Expression Omnibus (accession GSE134662).…”