Search on two groups of indices

I have two groups of indices. What I want to do is perform search sometimes on one group of indices, and sometimes search on joint groups of indices. How can I do it? Should I create different nodes or shards to enable it? I noticed that if I put all indices of two groups together in one cluster, it behaves unstably, which seems it relates to some limitation of disk usage.

Any idea is appreciated.!

It's pretty simple -

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