Bacteria come from other bacteria. As for where “new” bacteria come from, there are two answers to that:
One, we don’t have a catalog of every type of bacteria that exists. The number of different bacteria that we don’t have a record of probably outnumbers the ones that we do know about explicitly. So sometimes a new type of bacteria is discovered not because it came from anywhere, but because no one noticed it before.
Two, every time a bacterium reproduces, just like anything else, there is a chance the reproduction process will include errors. These errors are mutations, which can change the nature of the bacteria that result. Accumulate enough mutations, and you wind up with, effectively, a new bacteria.
Bacteria reproduce extremely quickly in comparison to most macroscopic life, so changes that would take millennia or longer to happen in most species can take place in a matter of a few years with bacteria.
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