Every time I've had to take antibiotics, I've eaten probiotic yogurt for breakfast for a bit afterwards to rebalance my biome, but I haven't tried actual probiotic pills, which are a lot stronger.

(Side note, our gut biomes are mildly contagious! If you live with somebody for a long time, you catch each other's gut bacteria and end up with similar ones. This probably helps people who wander into a different environment with different food adapt faster by snagging gut flora from other individuals).