To use mongodump as an effective, easy-to-implement solution for backing up a database in a replica, the need to filter by database is required.
The requirements are:
* Use the --oplog option, so that it's more likely that the data backed up is consistent.
* Exclude one of the logical databases from the backup - or alternatively, only include a subset of the logical databases in the backup.
Unfortunately, the --oplog option only works with a full dump - i.e., it is incompatible with the -d option.
The best option would be one that allows to either include several databases OR exclude a database. And it would be important that the oplog dump filters out the operations on namespaces on databases that are excluded.