Maria Jara Montibeller and Shan Thomas
The use of variable region V3-V4 in 16S rRNA gene is mostly preferred in microbial community analysis, however, the reasons supporting this region in the previous answer are not correct.
"..and have a vast database compared to other regions."
>> Not correct! Databases are not region-specific and it has nothing to do with variable regions. Reference databases are based on full 16S sequences.
"Also, the region does not have any effect on your sequencing technique."
>> Not correct! It is also not because of the sequencing technique or technology. However, is due to the target you want to capture.
"The selected region affects your post sequencing data analysis."
>> Not correct! Data processing or analysis has nothing to do with which region you are targetting.
Most of the pipelines support v3-v4 region and it allows you to assign accurate taxonomy for your sequences.
>> Not correct! Sequence analysis pipelines are region independent.
The main reason why most of the studies are based on V3-V4 region is because of the heterogeneity of the region and low evolution as compared to other hypervariable regions which can help in better identification of the organism (not always true, however). V3-V4 region also has its own limitations and can not always resolve the sequence identity at the species level, therefore generally used at genus level classifications.
Additionally, this region is not universal and it may be possible that it cannot target a community you might be interested in. In stool samples, surely a lot of organisms will not be targetted by V3-V4 specific primers. So, you have to use any other region or design your own primers which can use some other regions of 16S sequence, any from region 1-9.
And as the data processing and databases are independent of which sequence region you are using it would make no difference in your analysis. The reason why databases have a major proportion of 16S sequence submitted from V3-V4 region is just because they are produced by V3-V4 region primers (most commonly used primers in microbial community analysis), and not because of software, data-processing or database specificity.
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