"ASV" vs "Ribotype"

Hi… I’m a beginner in 16S amplicon sequencing data.

I have a question about “ASV” vs “Ribotype”.

Although the ASVs were targeted by V## primers…
I think the main concept of the “ASV” and “Ribotype” is almost identical…(because they are from PCR. isn’t it?)

I hope to find a novel thing by using QIIME2 products (V3-V4 ASVs) with ribotyping idea.

What is the main difference between ASV and Ribotype?

Thank you for reading :slight_smile:

Hi @KKN, welcome to :qiime2:!

I think I can be of help here, as I used to do a decent amount of ribotyping for public health using a RiboPrinter.

Ribotyping and ASVs are very different. Historically speaking ribotyping, is a method by which you digest a bacterial genome with a set of restriction enzymes. Then a gel is run to separate these fragments by size (i.e. RFLP). Afterwards an rRNA-oligonucleotide probe is applied to these fragments via Southern Hybridization. Only those fragments that bind, in part or in whole, to the probe are visualized.

ASVs are derived from PCR amplification and sequencing (usually by 2nd generation seqeuncing technologies like 454, Illumina, etc.), through down stream processing, are quality-filtered and denoised, resulting in unique DNA sequences. Hence the term Exact Sequence Variants, i.e. you obtain single-base level resolution.

However, I can see how the term "ribotyping" may have inappropriately co-opted to mean something different, like DNA sequences. Read this article which better explains ESVs.

Hopefully this helps. :man_scientist:

-Mike

3 Likes

Oh, I completely understand how the two segments are different.
I’m very happy to know this, and give thanks to you :slight_smile:
Have a nice day!
:blush:

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.