Could you brief about what medium and procedure you are following for isolation?

There are selective primers for methanogenic bacteria, you could confirm the isolates using those primers.

Isolation technique is the best. But use correct favourable conditions and environmental parameters which simulate the source sample and most important use manifold dilutions. Methanogens are interdependable on each other and they give a consortium effect

I am working in a liquid state and with mixed culture generated from cow dung.