There is within the Watson Discovery API an api call that will search multiple collections similar to the single collection api call. This particular call will take multiple collection id's and search these. The api call is similar to the single collection api call, and thus is a simple change to the cloud function. I have used it myself. Your only consideration now is if the different collections return different JSON payloads, and thus how you manage these. In my case I created a default standard JSON payload that then gets returned to Watson Assistant, and merge the different results into this standard payload.