I believe there's been some modestly successful research done on faecal transplants, particularly people who have been on long term antibiotics (also interestingly as a potential treatment for allergies), that's really the only way you'll get gut bacteria up there, sadly not through drinking a little yoghurt via the top end.
Any course of antibiotics will generally do a number on your guts, mostly I suspect the microbiome mostly recovers eventually. It's exceedingly complex, they've only recently through metagenomics really started to understand a little of the complexity and how it varies along the gut, changes over time, and depends on diet and other factors. What that means to health remains mostly undefined. There's far more bacteria in us and on us than there are actual cells.