The Starfield aceles or microbe choice happens during the final mission of the UC Vanguard faction questline. There's a Terrormorph problem, and it's up to you to pick the best solution to fix it, but that's easier said than done when you don't know the consequences of whatever you choose.
You'll need to decide at the end of A Legacy Forged. Saving just before you make your choice can eliminate any immediate consequences, but what about the effects on the story overall? With that in mind, here's what happens when you choose aceles or microbe in Starfield.
Should you choose aceles or microbe?
While the decision you need to make at the end of the UC Vanguard questline might seem like a big deal, in reality, it really has very little consequence to the rest of the story. The biggest impact is on your companion, as they will react to whichever choice you make—either favourably or unfavourably, depending on the individual you have with you at the time. If you have the Empath trait, you'll also receive a self-esteem buff or debuff, too, so plan ahead.
While it may seem like there's a "good" and "bad" choice, your companion might surprise you with their reaction, so your best bet is to save before making any decision, then you can try both options before continuing.
Microbe feels like the more sinister and risky option for dealing with the Terrormorphs as it involves releasing a kind of virus to kill them quickly. Sounds great, except it's essentially a bio-weapon. That said, Sarah is likely to like this option, presumably because it's science-y.
Aceles, on the other hand, sees the reintroduction of a specific type of creature to deal with the Terrormorphs in a more "natural" way.
In short, do whatever feels right for your character as the outcome of the quest is identical, whichever you choose.
As for the rest of the story, there really is little impact. Aside from the fact that you might spot the aceles creatures when you're out exploring planets, the aceles or microbe choice doesn't have any lasting consequences for your playthough.