...
Full length amplicon vs hypervariable regions
Typically The 16S rRNA gene is about 1,500 bases in length. Illumina reads are much shorter than this, therefore amplicon analysis typically involves sequencing 2-3 ‘hypervariable’ 16S regions.
https://nf-co.re/ampliseq/2.9.0/docs/usage#taxonomic-classificationwww.nature.com/articles/s41598-023-30764-z
...
Different groups of bacteria are better represented by specific regions.
With the development of 3rd generation long read sequencing, such as Nanopore and PacBio, the full 16S length can be sequenced. This reduces bias and improves taxonomic resolution.
https://www.nature.com/articles/s41598-020-80826-9
NOTE: For eukaryotic (e.g. fungi) metagenomic amplicon sequencing, ITS (Internal transcribed spacer) regions are used.
...
https://data.eresearchqut.net/paulw/public/mahsa_manuscript2/index.html
...