I have sent my soil sample for amplicon sequencing, the primers are targeted on bacteria V3-V5 region. However, the result that I obtained contains other things such as animalia, archae and plantae. Is this normal?
Your primer didn't target the V3-V5 region. 517F is not in the range of V3 region. Usually V3 region starts at 341F. It's all right if your results contain archae. And that's inevitable when using 517F/519F. It does look abnormal when you get the sequences from animal or plant, but it will happen when you dealing with environmental samples. If they are not abundant, you can feel ok with you results.
May I know how can I determine the primers that they used are suitable or not? Besides, why environmental samples always give this kind of result? I should include them in or try to filter them out?
Yes you always get the whole range (Bacteria, Archaea etc) from the environmental samples. But in further processing steps you should filter the data you are focusing on.