Algal vs bacterial 16s chloroplast

Question

[khp35]

Hello,

I'm new to sequencing and this field in general. I recently did a 16s sequencing of V4 region of a community that had unknown bacteria and Chlamydomonas reinhardtii.

The sequencing results, analyzed using DADA2, show some reads that are classified as Phylum Cyanobacteria, Class Chloroplast and Family Not assigned.

I want to know if these reads came from the Chlamydomonas reinhardtii or if there was some cyanobacteria present in the community. Please let me know if there's a way to do this?

On searching I only find ways where all chloroplast reads are discarded or there are suggestions to avoid algal chloroplast contamination during DNA extraction.

I was wondering if just discarding all chloroplast reads is the right approach if I want to know the bacterial composition? If some of the chloroplast reads came from cyanobacteria, and I discard all such reads, will I not miss the presence of cyanobacteria? What's the best way to tell if the reads are form cyanobacteria or algae?

Thanks and best regards,

K.

Answer 1

[Lille My]

Are you using qiime2? if you are, you can view the sequences using qiime2 viewer (rep-seqs.qzv if you follow the tutorial). from there you can press the link of the relevant sequence and it opens a blast window. If you are not sure which sequence it is, you can look it up in taxonomy.qzv.

Answer 2

[Chris Fields]

This depends on how different the 16S from Chlamydomonas is from cyanos (and whether you can detect this from the V4 region alone). Do you see any other cyano sequences popping up beside the one ASV with the chloroplast assignment?