There are ready methods for some popular alterations:
If you need a custom alteration then use the query() and resetDdlCache() methods of the \Magento\Framework\DB\Adapter\AdapterInterface:
An example from the core:
By default the \Magento\Framework\DB\Adapter\AdapterInterface interface is implemented by the \Magento\Framework\DB\Adapter\Pdo\Mysql class:
When you have a \Magento\Framework\DB\Adapter\Pdo\Mysql instance you can also use rawQuery() method instead of query() (rawQuery() method is absent in the \Magento\Framework\DB\Adapter\AdapterInterface):