Haven't our digestive system co-evolved with a ton of bacteria? Wouldn't we be pretty boned if we just kicked them to the crub?

Sterile environments are actually bad. So what'll probably be astonishing is our lack of knowledge about how these viruses and bacteria shape our lives for good and bad.

More likely, they will be astonished that we managed to survive so long while still perceiving the natural world in a reductionist manner instead of noticing the symbiosis and holism that characterize and sustain it.

Many of the bacteria are certainly necessary. Healthy gut flora is very important. The viruses probably not.

I occasionally imagine what it would be like to wake up after being cryogenically preserved, be told that they'd fixed your <top ten cause of death>, and then being given a list of everything else that was wrong with you that you didn't even know was a thing.

Well, our bodies don't work without a ton of bacteria. Its fundamental to who we are. Clearly some are not beneficial, but getting rid of bacteria in general would be catastrophic.

There’s probably quite a few specific viruses and bacteria people 100 years from now will be astonished we just lived with in our bodies, but it seems unlikely that having a lot of bacteria and viruses in general will be seen that way. I guess it’s possible that we will develop non-bacterial alternatives to the beneficial bacteria and viruses that exist, but it’s not clear what the advantage would be.

until then, I will enjoy my yogurt

There are about as many bacterial cells in your body as human cells, so they could just as easily say the inverse.