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Corruption. In MySQL if a database (more likely a few tables) become corrupt, you can repair them individually. In MongoDB, you have to repair on a database level. There is a command to do this but it reads all the data and re-writes it to a new set of files.
Since then, MongoDB has been adopted as backend software by a number of major websites and services, including Craigslist, eBay, and Foursquare among others. As of July 2015, MongoDB is the fourth most popular type of database management system, and the most popular for document stores.