Specific taxonomic abundance level check

[sooni]

Hello.
When creating a taxonomy barplot, is it possible to also check the abundance of species that do not appear in the barplot?
For example, in my taxonomy barplot, there is no E. coli abundance. But, I want to check E. coli abundance per samples. If the taxonomy barplot doesn't have E. coli, is there any way to check the abundance of E. coli?

I am curious about this topic. Please let me know. Thank you.

[Nicholas_Bokulich]

Hi @sooni ,

The taxonomy barplot made by the q2-taxa plugin shows everything that was detected in the sample. If E. coli does not exist anywhere in the barplot, it was not detected. Most likely:

1. you did not get species-level classification. This is common for Enterobacteraceae, due to the high similarity of 16S within this group.
2. depending on the database that you are using, it might not be called Escherichia. Some databases, e.g., group Escherichia and Shigella as a single genus, reflecting the complicated taxonomy.
3. it was not present in the sample

I hope that helps!

[sooni]

I use shot-gun metagenomics data. Is this data the same as what you answered?

[Nicholas_Bokulich]

Thanks for clarifying. Yes, points 2 and 3 still hold. Point 1 is more specific to 16S sequencing, but could still apply for shotgun, depending on the conditions. The barplot works the same in either case: all taxa that were detected are shown, unless if the data were filtered to specifically exclude taxa.