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It might be a case of one extreme or another. Bacteria and viruses on Earth have evolved to infect particular species and use them to breed and spread to others. It might be the case that you could no more catch alien flu than you can catch fowl pest from a chicken. Or: if somehow they were able to infect you, your body would have no defence whatsoever against a new disease and the result would be a repeat of what happened to the Aztecs when they caught measles from the Conquistadors, a disease hitherto unknown in the Americas.
Food from other planets might also prove to be indegistible. Not toxic, perhaps, but your gut flora might not be able to break down unfamiliar cells and compounds. It might be like trying to eat wood. It wouldn't poison you, but you would get very little nutrition from it.
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