If surviving humans lost 50% of their gut bacteria, that means that those snapped away left 50% of their gut bacteria behind.

That's not how it worked. He killed 50% of gut bacteria by killing 50% of the hosts.

or 100% of the 50% that are destroyed are the gut bacteria in the humans etc that got snapped

Fewer than 50% of the cells in "your body" contain your own DNA.

There are many more bacteria, since they are much much smaller than "your own" eukaryotic cells.

Where you end and your "gut flora" begin and end is not as clear as you might first believe.

In reality, since it was more random, some poor soul would have their whole biomes destroyed, and just be rekd.

The snap was always the dumbest part of the entire avenger series. Let's say for example, you have a bunch of deer that are eating the forest bare, so you let hunters kill half of them... Then what happens next? You have the exact same problem in a few years. The snap solves nothing.

Also if you can snap your fingers and do this, why can't you snap your fingers and make twice the food supply?

The snap is just stupid, even in a world made-up physics-defying superheroes.

Losing 50% of your gut bioma will be fixed in an hour or two.

he would have to snap his fingers infinitely many times to kill everyone so he is not that powerful

Yeah but I thought about this I realized that whenever somebody vanished from the snap it would leave behind a slurry of gut microbes and a (different looking) dust from all of the skin mites, microbes, and stuff that just live all over the human body. Meaning the aftermath would have been even messier.

It's bullshit space magic, it probably considers what Thanos thinks of as life. Why it snapped the birds is a different plot hole altogether, because it means he snapped away half the food, too.

So will bacteriophages and viruses be snapped as well? Does it mean that scientists can utilize the Thanos snap to determine for good whether viruses are alive?

The snap must take intention into account, like a genie, and not the literal wording of the wish, like a monkey's paw, because otherwise everyone in the universe would have just been cut in half.

But also: what if Thanos himself got snapped out, along with the power glove (because for some reason it turned their clothes into dust, too)? The heroes would have been fucked, right? It's been a minute since I saw the movies but IIRC, they used the time stone to go back in time. But what if the stone was gone because it was part of Thanos' attire? He himself used the stones to destroy the stones, so there is probably a timeline where he got snapped away with everyone else, destroying the stones in the process.