Cyanobacterial OTUs have been taxonomically identifed as streptophyta, chlorophyta, stramenopiles

[suran nambisan]

Hi everyone

I am working on plant root-associated microflora. We did 16S rDNA sequencing of V3 region (Illumina MiSeq 2x150 base reads) to profile root-associated microflora.

After running QIIME pipeline, nearly 80% of the OTUs observed under Cyanobacteria phylum are classified as Chloroplast (class) under which I see (orders) Streptophyta, Chlorophyta, Stramenopiles and Rhodophyta which come under algae. The QIIME version is 1.9.0 and GreenGenes database version is gg_13_5.

pick_otus.py was used to pick OTUs and cut-off was kept at 0.97 for OTU picking.

Is there a way to resolve this? Root doesn't have much of chloroplast, so is it likely these are reads belonging to Cyanobacteria?

Thank you for your help

regards

Suran

[zech xu]

Hi Suran,

I don't know much about plant biology, but is it true your plant root don't have chloroplast? I mean plastids that contain its own chromosome (and 16S), more accurately. I would just blast a read of those OTUs against NCBI to double check if it truly matches to cynanobactiera or chloroplast.