I have an article on line about this, Candida, will be expanding it later, but the jist, yes---the colon is the home of a large amount of friendly bacteria, the ones that make your B12, critical if you are a vegan like me, and digest everything your GI tract can't before expelling the waste, any you need. They are vital for good health, but usually ignored by the medical profession.
Antibiotics do kill this flora, particularily the broad spectrum ones like amomocillin, but don't take this as personal advice. I don't prescribe prescription drugs or recommend what to do with them to individuals. But, I do take them when needed, ie a course of penicillin this summer for a tooth extraction, followed by lower right quadrant problems (cecum) and leg pain, which I relate to the damage to flora in my cecum. But better than getting rheumatic fever again, so I use them.
The enemas, it's not the enemas that are likely the problem, it's the colon. If you are still on the antibiotics, check the PDR and see for yourself when the antibiotics are active. Usually you take the pills, an hour or so later the effect is the strongest then it tapers off, and you have a few hours before the next pill. If you take acidophilus it will be killed, but if you time it, it may have a few hours of it working before the next antibiotic pills. You can always do this by enema injection, retain it, and get the most benefit.
Then after you are done with the antibiotics eat all the fresh, lightly washed, without chlorox etc, veggies you can get. Acidophilus (good bacteria) is on uncooked veggies as they come from the garden, this makes it through the stomach and goes on to set up house keeping in the colon. If you have a garden this is simple. If you don't, two problems, are you sure the unwashed greens are bad bacteria free, and how to they process them. They may sterilize them before sale. Also you may want to take a range of good supplements of live bacteria for the colon from the health food store to restore the balence.
And an accurate diagnosis is important. A cause of severe throat pain may be candida. If the antibiotics fixed it, it's not candida. If they make it worse. Likely it is. For that you need to go on a regime to treat the candida, and yes, colon problems like you are describing would go with this. Most antibiotics kill normal healthful flora, but don't bother candida---the usual cause of candidiasis is antibiotics, either taken via prescription, or eaten in animal products (vegans don't get this). So if the throat and colon are worse with the antibiotics look in to candida. I've never had a case of that not improve with the proper care, but it is the opposite of antibiotic care. Instead of killing bad bacteria, you work to get good flora back into your colon and all the other symptoms fade.