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Nielsen, Google, Amazon, Smashwords, Apple, Barnes & Noble, Ingram, 24bookprint, Kobo etc all have separate databases.
There isn't actually a single database for paper books using ISBNs, though you can figure who issued the ISBN block to a publisher, or there may be a record with a wholesaler, then the publisher can be discovered. But the publisher isn't absolutely obliged to tell anyone what ISBNs have been issued or update any of the free databases run by Agencies that issue ISBNs.
A "free" ISBN for ebook or paper from a retailer or self publishing support company such as Amazon/CreateSpace, Smashwords, 24bookprint will show them as being the publisher as they bought the original big block of ISBNs.
They can cost £100 each or pennies if you buy a block of 100,000 ISBNs.
Ebooks don't need ISBNs.
Paper books aren't obliged to have ISBNs, but it's tricky for a physical bookshop or a customer to order the correct edition without an ISBN. Books can have the same title and be unrelated. Authors exist with the same names.
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