I dont know where else to ask this. I am from a marine background, now studying soil bacteria. We have run a bunch of marine and soil samples in one channel of a HiSeq run. I am analysing the soil samples, and cant help but notice a bunch of classified sequences that are (supposedly) strictly marine bacteria. In fact, a particular family/genera I isolated from seaweeds during in my phd thesis, that I was hoping would pop up in my 454 sequencing datasets and did not, is now occurring in my soil samples!! WTF… They are in relatively low abundance about 10-40 in some samples (with 55000 quality filtered sequences/sample)
Has anyone else come across this? It might not be so apparent if all your samples are from similar environments. Has anyone sequenced completely different mock communities in the same channel before?