Hi @GillSie,
I went through a similar issue some time ago and turns out it was a case of non-target amplicons which I am convinced is a lot more common than people expect in intestinal tissues (compared to say fecal samples). If your situation is the same, and there is reason to think it is, I gather that link can provide some guidance, in short, get rid of those reads...you can use a positive filter similar to what deblur uses by default.
The fact that this issue is occurring only in certain samples might be a biological clue, is there anything similar to those samples? Perhaps the way their DNA was extracted, maybe you had very low biomass or DNA yields? They went through extra PCR cycles etc. It could just be bad luck too with contaminants taking over.
Lastly, what is the coverage and % identity values when you are blasting these? Uncultured bacterium is unfortunately not very reliable in BLAST and I personally would exclude these from my analysis.
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