I'm completely new to the field, and am hoping to start a project soon examining the oral, airway, and gut microbiome of TB patients.
I'm seeking advice on which primers (targeting specific regions of the 16S RNA gene - V1, V2, V4 etc.) to use. There doesn't seem to be a good consensus in the literature.
I am aware that different primers offer different levels of discriminatory power and, if the amplicon is too long, it is difficult to get good quality sequence from a single read near the end of the strand (and discriminatory power is subsequently lost). Is this accurate?
We plan on using an Illumina HighSeq instrument, but also have a MiSeq available. Which machine would be better for this purpose?