SwiftKey's keyboards have long had a good reputation thanks to their prediction algorithm, which is both smarter than most and optionally taps into your own email and social networks for help. Microsoft could use that to boost its Word Flow keyboard. However, SwiftKey's prediction recently got much smarter: the company has been trying out neural network technology to better understand what you want to write. For Microsoft, acquiring SwiftKey could help implement artificial intelligence (currently all the rage among rivals) into its products.
This may not be very reassuring if you like SwiftKey, though. Microsoft tends not to discontinue acquired products right away, but their long-term fates vary. Acompli's email app eventually became Outlook Mobile, but Sunrise Calendar? That's being discontinued as Microsoft folds its features into Outlook. It's easy to see SwiftKey surviving due to sheer popularity, but don't be shocked if you eventually have to look at Swype or other alternatives.
Update (2/3): Sure enough, Microsoft has confirmed the acquisition. SwiftKey's technology will eventually integrate into Microsoft's Word Flow keyboard, which is thankfully coming to other platforms soon.