This repository contains:
- Counts files produced by processing the sequences, see folder:
data - Participants information collected, see folder:
metadata - Scripts to run the analysis component of the project, see folder:
scripts - Results of the analysis (figures and tables), see folder:
results
Title:
Microbial associations with Microscopic Colitis
Authors:
Shan Sun, Ivory Blakley, Anthony A. Fodor, Temitope O. Keku, John T. Woosley, Anne F. Peery, Robert S. Sandler
This article is a preprint and has not been peer-reviewed. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.
BACKGROUND AND AIMS:
Microscopic colitis is a relatively common cause of chronic diarrhea and may be linked to luminal factors. Given the essential role of the microbiome in human gut health, analysis of microbiome changes associated with microscopic colitis could provide insights into the development of the disease.
METHODS:
We enrolled patients who underwent colonoscopy for diarrhea. An experienced pathologist classified patients as having microscopic colitis (n=52) or non-microscopic colitis controls (n=153). Research biopsies were taken from the ascending and descending colon, and the microbiome was characterized with Illumina sequencing. We analyzed the associations between microscopic colitis and alpha diversity and individual taxa of the microbiome with a series of increasingly complex models adjusted for a range of demographic and health factors, proton pump inhibitor and antibiotic use.
RESULTS:
We found that alpha-diversity was significantly lower in microscopic colitis cases compared to controls in the descending colon microbiome. In the descending colon, a series of models that adjusted for an increasing number of co-variates all found some taxa significantly associated with microscopic colitis. The taxa enriched with the strongest signal were mostly Proteobacteria, while the taxa enriched in controls were mostly driven by genus Collinsella. While the alpha-diversity and taxa were not significantly associated with microscopic colitis in the ascending colon microbiome, the inference p-values based on ascending and descending microbiomes were highly correlated, indicating changes in the ascending microbiome that were similar to changes in the descending microbiome but with a smaller effect size.
CONCLUSION:
Our study demonstrates an altered microbiome in microscopic colitis cases compared to controls. Because both the cases and controls had diarrhea, we have identified candidate taxa that could be mechanistically responsible for the development of microscopic colitis independent of changes to the microbial community caused by diarrhea.
Funding: This research was supported by funding from the National Institute for Digestive Diseases and Kidney NIH NIDDK R01 DK 105114 and P30 DK 034987
Availability of data and material: The sequences analyzed in this study are available at NCBI with BioProject PRJNA768799.