whether possible for a microcontroller (in a separate pcb) to read from pen drive?

NOTE: The first part of this response talks about an approach with SD cards.

It all depends on what the microcontroller is and what the database is.

If the uC has quite a bit of program memory and ram, you may be able to use something to read FAT files. From there, if the file is stored with a simple structure, the uC should be able to parse it (the less parsing the better).

Alternatively, you can write to the card as a raw device, imposing your own data structure on it. This will reduce the complexity to the uC, but make it a lot harder to access from another device (maybe you can have another uC that provides that interface via USB?)

Oh, pen drive... I was thinking SD card. Different USB sticks tend to have different drivers under windows, so they may have to be handled differently at a low level. That may be a burden for the uC. Also you now need a host port, and I have no experience with them (in a uC environment)

If you can get by with an SD card in an SD to USB enclosure, then you can talk directly to the SD card from the uC (which is relatively easy) and via USB (by placing it in the adapter) to talk to a PC.

Sorry if this isn't a lot of help.