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No there is not. There has been lots of discussion wether it should be part of the JRE or not and there have been some attempts (like jUSB) but there is nothing that works well on all operating systems. If you're going to write an application that communicates with USB devices I would recommend a language that's closer to the OS than Java.
Well these micro-controller devices very often open a serial (COM) port over the USB connection. If this is the case (it probably will be), you can use this serial port to communicate with the microcontroller. You're limited to a serial port of course (this means slow speeds, typically around 9600bps (that's bits per second)), but if it's just to exchange some commands and/or control information, this will be enough. You can use the rxtx library (http://users.frii.com/jarvi/rxtx/) with Java.
If on the other hand you need full usb support you'll best use a language that's closer to the OS, like C++. The big disadvantage is you loose cross-platform support. If you decide to go down this path, you could also consider using C#, which is closer to Java in syntax and supports USB trough native calls (see http://www.developerfusion.com/article/84338/making-usb-c-friendly/ for an example).