Comparison of sampling methods in assessing the microbiome from patients with ulcerative colitis

Abstract

Background Dysbiosis of ulcerative colitis (UC) has been frequently investigated using readily accessible stool samples. However, stool samples might insufficiently represent the mucosa-associated microbiome status. We hypothesized that luminal contents including loosely adherent luminal bacteria after bowel preparation may be suitable for diagnosing the dysbiosis of UC. Methods This study included 16 patients with UC (9 men and 7 women, mean age: 52.13 ± 14.09 years) and 15 sex- and age-matched healthy individuals (8 men and 7 women, mean age: 50.93 ± 14.11 years). They donated stool samples before colonoscopy and underwent luminal content aspiration and endoscopic biopsy during the colonoscopy. Then, the composition of each microbiome sample was analyzed by 16S rRNA-based next-generation sequencing. Results The microbiome between stool, luminal contents, and biopsy was significantly different in alpha and beta diversities. However, a correlation existed between stool and luminal contents in the Procrustes test (p = 0.001) and Mantel test (p = 0.0001). The stool microbiome was different between patients with UC and the healthy controls. Conversely, no difference was found in the microbiome of luminal content and biopsy samples between the two subject groups. The microbiome of stool and lavage predicted UC, with AUC values of 0.85 and 0.81, respectively. Conclusion The microbiome of stool, luminal contents, and biopsy was significantly different. However, the microbiome of luminal contents during colonoscopy can predict UC, with AUC values of 0.81. Colonoscopic luminal content aspiration analysis could determine microbiome differences between patients with UC and the healthy control, thereby beneficial in screening dysbiosis via endoscopy. Trial registration: This trial was registered at http://cris.nih.go.kr. Registration No.: KCT0003352), Date: 2018–11-13.

Evidence for translocation of oral Parvimonas micra from the subgingival sulcus of the human oral cavity to the colorectal adenocarcinoma

“…Most microbiome and GI cancer studies have focused on the microbiome analysis in fecal samples [1,29], which is a convenient and non-invasive approximation of the patient intestinal microbial biodiversity. However, it is well known that fecal samples do not represent the microbial communities of colon tissues [30,31]. In addition, last year's works support the correlation between oral and tumor microbiota [3,26,27,29,32], underlining that further microbiome analyses of oral uids and colon mucosa tissues in CRC patients are needed in order to study the potential role of anaerobe oral pathobionts in initiation and/or aggravation of CRC.…”

Bioinformatic evaluation of the potential oral-gut translocation of periodontal pathogens in patients with colorectal polyps

“…2B ). It is commonly observed that LAM and MAM exhibit differences in their composition 14,35,36 . For instance, Miyauchi et al 14 conducted a comparative analysis between LAM derived from feces and MAM samples collected by swabbing the mucosa in healthy volunteers.…”

The microbiome in adolescents with irritable bowel syndrome and changes with percutaneous electrical nerve field stimulation

“…While we used fecal calprotectin as a measure of intestinal inflammation, evaluating histological markers that are elevated in IBS patients such as mast cells would allow for a more accurate measure of inflammation including by location in the GI tract and types of inflammation 48 . Similarly, given potential differences in the microbiome between direct luminal sampling and stool samples, direct sampling during endoscopy may provide a better representation of the relationship between our IBS measures and the microbiome 49,50 . Other future directions could include investigating the potential link between metabolic pathways with the gut–brain axis and neuromodulation and the inclusion of metabolomic analysis.…”