I thought the transporter filtered out any free riding organic material. Seriously.

So are you just losing your entire gut microbiome each time you transport, like a really heavy does of antibiotics? If that’s the case then you’re gonna need that food replicator to make a big bowl of yogurt for everyone coming back from an away mission.

Have you heard the theory that transporters destroy the person in order to create an exact copy of them elsewhere? So every time someone transports, they're being killed, and an unwitting doppelganger is created. And there's no reason to replicate any stray on-world microorganisms in the process.

It does, but it's a big galaxy out there.