I have always come across ''Changes in bacterial composition were determined using high-throughput sequencing of the V3/V4-region of the 16S rRNA encoding gene''. Could anyone explain to me why V3/V4 region is normally used in this case? Why not other V regions?
Thank you.
The choice of certain variable regions in the 16S rRNA gene to be studied stems from the aim of trying to classify bacterial communities present in the analyzed samples.
The classical approach was to look at the V3/V4 regions and estimate diversity based on the discrepancies and similarities of bacterial gDNA sequences that get aligned to be compared to one another.
Recently, there have been advances in sequencing technologies and high throughput data analysis that enable us to actually compare the choice of variable regions in the 16S rRNA gene and improve our choice of target sites based on the sequencing technology used and the ultimate aim of a study.
https://www.nature.com/articles/sdata20197
The 16S rRNA gene is approximately 1600 base pairs long and includes nine hypervariable regions of varying conservation (V1-V9). More conservative regions are useful for determining the higher-ranking taxa, whereas more quickly evolving ones can help identify genus or species. The main reason for using V3/V4 region in majority of the cases that these regions contain the maximum nucleotide heterogeneity and displays the maximum discriminatory power. However, it should be noted that no single region can differentiate among all bacteria. I do agree with the comments given by Balig Panossian and also recommend you to read the paper entitled “The effect of 16S rRNA region choice on bacterial community metabarcoding results” (https://www.nature.com/articles/sdata20197) for more details.
Simon Dingsdag
Thank you very much for this explanation, much appreciated!
I have started bioinformatics analysis of my 16s metagenomics data.SILVA_138.1_SSURef_NR99_tax_silva.fasta.gz should I use this data set as my reference
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