What is your mongo version ? There is a very good tool keyhole, it will help you collects information about your instance, also you can use keyhole to analyze your mongod log file - The logs keep a history of the server operations over time. Keyhole, with the -loginfo option, reads mongo logs and prints a summary of slow operations grouped by query patterns.
Is MongoDB only one instance that is running on your machine or there is also some other server? Is the CPU consumption high all the time or only from time to time ?
in the beginning, during high CPU usage, can you provide the output of:
top
iostat
ps -eo pcpu,pid,user,args | sort -k 1 -r | head -10
db.currentOp({"secs_running": {$gte: 3}})
db.serverStatus().wiredTiger.concurrentTransactions
db.serverStatus().globalLock