Prion diseases are not as simple as coming into contact with a protein composed of D-amino acids.

While it's still not fully known, it's generally one specific type of protein PrP^C that gets transformed by PrP^Sc, converting the C to Sc, and so on.

D-amino acids also occur naturally on earth.

As for B vitamins, none include proteins as far as I remember, they're all small(ish) molecules like biotin and folate. Also having a difference in stereochemistry with most of these vitamins, wouldn't cause toxicity.

Obviously there are some cases of small stereochemical changes being toxic (thalidomide). But generally small changes won't automatically make something toxic.

Prions wouldn't work like that. They would have to be very similar, and the same chirality, as our own proteins, or else the misfold would not self-replicate like prion diseases do.

Obligatory "that Venn diagram is basically a circle."

Yeah, it is probably going to be one of the top 5 reasons to join a starship crew, so life will probably, ah, find a way. For all we know, NASA might even have a focus group working on this already.

BUT that doesn't mean it won't lead to the extinction of one or both species involved.

Read "scientities"

That's the result of a balance between different microbes and their own defensive measures. Entirely novel microbes and biological functions could overwhelm all of that. Hell, if they have just evolved a next level ATP, they could have access to an order of magnitude more energy than our microbes and bodies can use, in which case we'd probably have no chance unless it doesn't recognize us as food.

It's not guaranteed to happen, but with 0 data about alternate evolution trees, any reasoning about the odds is speculation (including my use of "decent chance").

Edit: This would be the case for viruses. Unless they work very differently or our biochemistry has some convergent evolutions, alien viruses should be harmless to us and vice versa. Just like the hundreds of viruses we are exposed to with every breath, most don't react to our cells any differently from how they'd react to wet rocks.

I guess it's possible to have safe alien sex with a full body latex suit and respirator. Though maybe think twice if the alien has sharp spike features.

Oxygen is reactive enough that free O2 doesn't tend to stay that way. Even to us, too much oxygen is toxic because it starts reacting with things we don't want it to inside our bodies (which is why antioxidants are beneficial). The presence of oxygen in an atmosphere implies there's life producing it (or maybe some other process we aren't yet aware of). It can also imply that there's also life using it to keep it in a balance that doesn't freeze the planet or allow it to destroy any life because oxygen producers keep pumping more of it into the atmosphere.

And the danger part comes from a combination of alien life maybe having microbes our immune systems can't defend against and the possibly of picking one of those up and bringing it back to other human settlements before the carriers realize they have a fatal infection.

That second part is what makes it more dangerous than a ship accidentally flying into a star or trying to land on a gas giant, which would probably be fatal to all aboard the ship but not dangerous to humanity as a whole. Even just entering an oxygen atmosphere with a ship that never lands could be bad if that ship must later return home.