New question:
What about human obligate intracellular parasites? Here's a short of list of things that need humans to stay alive and reproduce:
viruses:
smallpox, polio, EBV, herpes simplex, VZV, CMV, RSV, rhinovirus, influenza, parainfluenza, rotavirus, hantavirus, coronavirus, enterovirus, echovirus, HPV, HAV, HBV, HCV, HDV, HEV, HFV, HGV, measles, mumps, rubella, norwalk.
some bacteria that need humans to reproduce:
chlamydia, rickettsia, mycobacterium leprae (leprosy)
I excluded any viruses or parasites that may have vectors or infect other hosts (ticks, fleas, other primates). But these would also have to be on the ark, but not necessarily in humans:
viruses:
west nile, SIV/HIV, ebola, yellow fever, dengue fever, marburg, rabies, EEEV, WEEV, VEEV, bornavirus
parasites:
malaria
Now we'd also have to have like some sort of stagnant pool of water for all of the other single-celled organisms to live in that don't need a host. The disruption in chemistry of the bodies of waters would not likely be ideal and would probably kill them. God only spared the fishes, so we'd have to have a nice bucket of water full of the microorganisms. But that's pretty easy.
But basically, Noah and his family would have to have all of the human diseases. They must have been really sick. They all would have had failing livers, the worst upper respiratory infections ever, and tons of diarrhea. Also, the leprosy would suck, and I bet they'd all catch it from each other anyway. Poor Noah's wife would be at risk for cervical cancer should either she or Noah be the unlucky one with HPV. Then again, with the amount of incest that occurred after landing the boat, they probably all got chlamydia, HPV, and herpes simplex.
I didn't even mention the rest of the viruses and bacteria that infect the myriad other animals. We've just talked about a few human diseases. Each animal would have to have all of the infectious diseases that require them as a host.
Doesn't the flood story make much more sense if you had no idea about the germ theory of disease?