Get rid of it? You mean, if it did turn out to be a varicocele? If that's what you mean.. it's not necessarily something you need to get rid of. 15% or more of males have it and are symptom free. Some do have pain as a result and would like a remedy. The standard treatment is surgery, but there is another option of embolization which inserts a coil into the offending vein. I have a varicocele and it does cause pain, but I prefer to go natural routes. So I found some possible solutions with herbs that are traditionally used for varicose veins, after all that's what it is.
No reason to go into detail as you might not have one, but if you do I've written some info on this site and I'll link you to it if it comes down to it and you're interested. I can't vouch for their working however, as I didn't follow the regimen because I needed to concentrate on a bigger problem.
As for replacing your good bacteria...buying an enteric coated, multi-strain, high count probiotic supplement would be your best bet. Take that for a couple months and then just use maintenance dosage if you want indefinitely. Take it in higher doses after antibiotics. In terms of diet, reducing sugar, refined carbs, alcohol, etc. Eating plain organic yogurt may also help as it contains good bacteria. Plain, because the others contain sugar, you can flavor it if you want by making a fruit smoothie with it or adding a natural (no high sugar, processed, artificial stuff) jam.