Calculating GC Content of Bacteria?

General Discussion
1

Hello,

I am learning about PCR bias associated with the GC content of amplified bacterial DNA. It seems that the more GC content a target has the less it will be amplified in PCR. I was wondering how I might know the GC content of each bacterial group before beginning the PCR. Is there a way to calculate the GC content of V4 regions using QIIME2 and reference databases?

Some PCR master mixes supply GC enhancers to increase the representation of high GC targets. It could be useful to know the relative amount of high GC bacteria before I begin PCR so as to add the right about of the GC enhancer.

I'd be appreciative of anyone's thoughts on this :).

2

Hello Stephan,

Not out of the box. However, you could use qiime feature-classifier extract-reads to cut out a region from a database, export that fasta file, then count letter frequencies with a linux script.

It's an interesting idea, but I'm not sure how much it's needed. Differences in primer design or region sequenced will also have very large effect on observed composition, which is why it's common to see sample-to-sample comparisons and not assertions about the 'true' composition of the microbial community.

But if you are missing important tax you expect to find due to a low GC content, this may be worth a short!

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