How can we populate from different index using reference id stored in main index as in Mongodb

I think it would help if you recreate a minimal example which can be run from Kibana Dev Console as described in About the Elasticsearch category. It will help to better understand what you are doing. Please, try to keep the example as simple as possible.

A full reproduction script is something anyone can copy and paste in Kibana dev console, click on the run button to reproduce your use case. It will help readers to understand, reproduce and if needed fix your problem. It will also most likely help to get a faster answer.