Sometimes resetting a device isn’t as easy as expected. After some research i figured out, that opening a serial connection with a special baud rate would to the job for our Arduino Micro (and similiar like Leonardo):

#!/usr/bin/env python


import serial
port='/dev/ttyACM0' #adjust this in case your device differs
ser = serial.Serial() #open serial connection
ser.port=port #setting the port accordingly

#in case your usual baudrate isn't 9600 reset will not work, therefore we will open a resetable connection
#thanks to mattvenn.net for suggesting to add this step!
ser.baudrate=9600
ser.open(); ser.close()

ser.baudrate=1200 # set the reset baudrate
ser.open(); ser.close()
#don't forget to sleep some reset time

Run the script as root. It might need required to change your port according to your serial controller status.