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Why do you use 16S rRNA sequencing and not the genome shotgun method?
We use the 16S rRNA sequencing method because it’s more cost effective and more accessible to buy.
Whole genome shotgun sequencing is a completely different approach and, compared to 16S rRNA sequencing, generates information about the entire genome, instead of just sequencing the 16S gene.
This means that whole genome sequencing can theoretically not only identify bacteria based on the 16S gene, but also all other bacterial genes too.
If all possibilities are used, this is potentially a better approach, but it's more expensive, more time-consuming and there are only one or two offshoots of elite US universities that offer it.
The bottom line is, when it comes to identifying bacteria, it's not necessarily superior to 16S rRNA and it has the same difficulties.