In Becky Chambers’ Wayfarer series, there is a species who actually breathes methane. The focus though is less on how that actually happens and more on how they navigate as the only species for whom oxygen is toxic. It’s a great series, btw. It’s a not-quite-as-optimistic as star trek future, but still optimistic and with a vast range of species who are all intermingling as learning how to get along.