I enjoyed reading this! Sci-fi with a bit of a horror kick I guess. It sort of reminds me of Philip K. Dick's early short stories.

Science-wise, I think something like The Good Gut might've been a better source or inspiration, in the sense that there's a bunch of foodstuff that are good for our guts, but mostly it's plants, rather than the probiotics made popular by the media (not much money to be made in plants, whereas probiotics can be packaged and sold at a premium). Having said that, it's good that you went for the almond milk kefir, since people who haven't been exposed to kefir before might show an initial reaction (in the form of gas) when they're first introduced to the real-milk-based version.

Anywayz, good story, upvoted!