Which is the best target region for amplicon sequencing of bacteria 16S rRNA gene sequence ?

Tosin Yetunde Senbadejo @Tosin-Senbadejo

21 February 2020 1 795 Report

Hi all,

Please I will like to know the hypervariable region of bacteria gene that will reveal abundant taxonomic composition from metagenomic DNA.

Marcin Golebiewski

Dear Tosin,

The answer to your question depends on which sequencing technology you are going to use. For Illumina MiSeq 2 x 300 cycles kit, I would recommend V3-4 (e.g. B357f-B786r pair), for HiSeq 2 x 150 cycles, this would be V4 alone. For other technologies, such as PacBio or OxfordNanonpore whole 16S sequence could and should be used.

I can refer you to my review paper: Article Generating amplicon reads for microbial community assessment...

It's free access, so there shouldn't be any problems with download, but in case you can't download the paper, don't hesitate to request full text via RG.

Best regards,

Marcin

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