SAN FRANCISCO—Microsoft on Thursday warned thousands of its cloud computing customers, including some of the world’s largest companies, that intruders could have the ability to read, change or even delete their main databases, according to a copy of the email and a cyber security researcher. The vulnerability is in Microsoft Azure’s flagship Cosmos DB database. A research team at security company Wiz discovered it was able to access keys that control access to databases held by thousands of companies. Wiz Chief Technology Officer Ami Luttwak is a former chief technology officer at Microsoft’s Cloud Security Group. Because Microsoft cannot change those keys by itself, it emailed the customers Thursday telling them to create new ones. Microsoft agreed to pay Wiz $40,000 for finding the flaw and reporting it, according to an email it sent to Wiz. “We fixed this issue immediately to keep our customers safe and protected. We thank …