I'm studying the gut microbiota of chickens. I have jejunal contents/digesta and also mucosal scrapings. See attached/below the taxonomic assignments (using SILVA) for the taxa in each of my treatment groups! (AGP is antibiotic-supplemented).
My question is... there's a lot of "Cyanobacteria" here, which, if you look at the genus level assignments, turn out to be mostly (99.1%) chloroplasts. BUT... I'm suspicious of this because of the high relative abundance of them in the mucosal scrapings in particular. Surely if you were expecting chloroplasts (presumably from the chicken feed), you'd get them in the gut digesta. And you do get some, but the mucosa have a much high level, which you wouldn't really expect. Those scrapings DO, however, inevitably contain a lot of chicken DNA from scaping the gut. Those samples contained a very high concentration of DNA but were difficult to amplify with my 16S primers and I suspected that was because a lot (most?) of the DNA was chicken rather than bacterial.
I know the mitochondria and chloroplasts are both closely related to bacteria and I've already eliminated them from my table before diversity analysis etc. I'll be manually taking them out of this graph too, but I was just wondering if it seems likely that the "chloroplasts" in this case are actually mitochondrial sequences and how I might go about confirming that?
Thanks so much!