The bioBakery help forum

UC patients data

We are interested in the host transcriptome data and the bacterial data (both 16S and metagenomics) in the presence of inflammation. Our focus is the inflammatory state in UC patients undergoing total proctocolectomy and how inflamed pouches are compared to other IBD types. Therefore it is important for us to understand if the sample was taken from an active inflammation (determined by histology endoscopy).

The column “is inflamed?” in the supplementary data was determined by the dysbiosis rather than the endoscopic/ histologic appearance?

If so, you pretty much cleared it for me and the only question left is regarding the non-IBD patients - can I assume that they are not actively inflamed?

Thank you very much again!

Hi Tom,

We mostly had inflamed biopsies for disease subjects in the relevant locations. non-IBD was assumed non-inflamed.

This is the table of biopsies with inflammation status:


Dear Sagun,
I would like to follow up on Tom’s query:
We are interested in the data collected from biopsies, host transcriptome. First is it true that all biopsies were collected at basline?
second, how can we know what is the inflammation level of the biopsies? do you have a histology or endoscopic score rather than disease activity score which is not always an indication of inflammation location (e.g. CD inflammation can be located in the ileum or colon).
Thank you in advance, your clarification is very much appreciated.

Hi kerenrabinowitz,

Yes, it is accurate that all biopsies were collected at basline. Unfortunately, we do not have the histology or the endoscopic score as it was not in the protocol that was followed for the study.