On mice colon mucosal mirobiome study, treat mice with DSS to induce colitis, then collect the mucosal microorganism to analyze mirobiome change, but colon has four different parts, so which part of colon I should use to collect the mucosal microorganism and can reflect the mirobiome change under colitis?
Dss will cause different changes in different regions of the colon. You should define the inflammatory insult in your model using histology and possibly measure cytokine production also. This allows you then know which regions are inflammed and which are not. It also depends on your hypothesis.
In order to reflect the comprehensive difference in colon mucosal microbiome in different mice model, DSS could induce colitis throughout the large intestine, so I think it’s better to collect the whole large intestine mucosal microorganism, although it may has much more samples to collect. Someone may say that just collect the colon site where colitis occur, but I think colitis is a chronic inflammation and I do not know where the next colitis site is.
You should remember though that the amount of bacteria will vary in different regions also.
I think it depends on your hypothesis. A better experiment may be a pilot where you look at various places throughout the colon, then for future experiments focus in on the area(s) where you saw the most DSS-induced change. I know that isn't an ideal answer and it will take a lot more work, but I also see it as a potential reviewer question in the future once you try to publish. This would kill two birds with one stone, so to speak
Dear Xin Wang
if you are doing the DSS induced induce colitis study for first time then you should go for pilot study, it will help you to explore the actual or main area where the DSS can make the ulcertion at that particular site, again you go for main study, and focus, then it will not only give you the exact idea to which part should be taken, but also improve your result and it will save your time
And manbe you should compare the acute DSS colitis with the chronic DSS colitis. Because the short-term treatment in the acute colitis models might not show a significant change in the microbial distribution.
@Xinyun Qiu.. Can you please share any Literature related that you mention as there is no significant change in microbial diversity in acute colitis.?