Found three OTUs/ASV that are highly abundant in my sample. How likely are they to be true OTUs/ASVs?

I found three OTUs that are highly abundant in my sample. I have eight unique stool samples from eight laboratory mice. We want to look microbiome dynamics from three timepoints (three sequencing preparation batches of these mice).

We got results from second batch not long ago, and found above-mentioned three highly abundant OTUs in the second batch. We observe very small number of them in the previous first batch.
I noticed we used different thermal cycler between batches for PCR. We suspect that the second batch thermal cycler is in a very questionable condition, how likely are these OTUs to be a true results and not an artifact caused by faulty PCR process?


  1. We measure V3-V4 16s region.
  2. The OTUs taxa is d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Morganellaceae;g__Proteus;__
  3. This is the frequency according to table.qzv,

Thank you very much.