Question
Dear Gene, my lab is working on a soil microbial community characterization project, but what is the difference between traditional 16S using the V3/V4 region and full length 16S using the V1/V9 region? Will this increase the taxonomic resolution of my study?
Answer
This is a great question! Historically, 16S sequencing methods have targeted the V3/V4 region due to read length limitations of traditional methods on Illumina instruments. While the V3/V4 region has been the traditional target, the region encompasses a small portion of the 16S rRNA gene and presents notable limitations on taxonomic resolution due to target length. This shorter target can reliably identify taxa at genus level and sometimes species level, but strain or subtype level resolution is rarely differentiated, especially in high diversity sample types like soil and stool. In these sample types, better resolution in species or strain level identification can alter the landscape of a study. That is where full length 16S sequencing can help!
What does this mean for your research?
Starting at $45 per sample, you can target the entire V1/V9 16S region in full length 16S sequence on the PacBio platform. This captures all available 16S nucleotide information, allowing for better resolved taxonomic grouping and biologically meaningful differentiation at a level that is impossible to capture with the V3/V4 region alone. Key benefits of full length 16S sequencing are:
- Amplifying the entire 16S rRNA gene
- Producing sequencing read accuracy that rivals and even exceeds that of short read platforms
The result? More precise taxonomic resolution without any sacrifice to the quality of your data. Worried about cost? Our PacBio full length 16S sequencing service has the same per-sample cost as our Illumina V3/V4 sequencing pipeline for equivalent amounts of data and includes a complimentary bioinformatic analysis via QIIME2.
Not sure if full length 16S sequencing is right for your project? We can help, just reach out!
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