When I ran the distance matrix ordination using bray curtis and Unweighted Unifrac, I found that samples from both the run formed distinct groups. See below:
After merging, I created a rooted-tree based on the merged table. Since we normally outsource our samples for sequencing, I am unsure if this group could be due to difference in sequencing parameter. I usually do 100000 reads/sample. I am not sure what is causing this. Please advise.
looks like you have the same or similar issue (i.e., runs from different primers, or even slightly different lengths, etc).
You can check out the q2-fragment-insertion plugin to see if that fixes your issue. Otherwise scan this forum for lots of previous troubleshooting of similar issues.