The choice of variable regions (V3–V4 vs. V4–V5) depends on study goals. V3–V4 is widely used for its balance between resolution and amplicon length, while V4–V5 may provide better coverage for certain taxa, including archaea. In silico validation is essential tools like PrimerEvalPy and Primer-BLAST (NCBI) help assess specificity and efficiency. Common pitfalls include primer dimer formation (avoid complementarity at 3’ ends), mismatches in conserved regions, and non-specific amplification, which should be checked before experimental validation. For step-by-step guidance, Illumina’s "16S Metagenomic Sequencing Library Preparation" and Thermo Fisher’s "16S rRNA Gene Sequencing" video are useful resources.

you can ask for advise of the company which are selling consumables for PCR

Go to github and run V-Xtractor works perfectly well used it to distinctly differentiate between S aureus and S epidermidis, for verifying primers etc use blast, for dimer et al use IDT, and for the Tm maybe use the Tm calculator for the company whose polymerase you will use