Three suggestions:
1) Ask your doctor about the possibility of yeast overgrowth in your gut. If you do have a yeast problem, your doctor will probably tell you to cut back on sugars for a while and might prescribe something like Nystatin or fluconazole.
2) You could try more intense probiotic supplementation than you'll get from yogurt or kefir (which might cause problems if you do have a yeast issue because many yogurt products are sweetened and yeast loves sugar).
I've been through the antibiotics wringer due to Lyme disease, so I've tried many, many different probiotics. I would most highly recommend the following:
- HLC Intensive by Pharmax, available locally at Pharmaca (located in West Seattle, Wallingford, Madison Park, and Redmond)
- A high quality probiotic containing Saccharomyces boulardii. S. boulardii is different from other probiotics in that it's a beneficial yeast that lives in the gut. (So if you do end up taking anti-yeast meds, you'll want to take the S. boulardii apart from the anti-yeasties.) Florastor is the best-known brand, but there are many good brands out there.
- Natren Healthy Trinity. This stuff is crazy expensive compared to many other brands, but I have found that it works better and faster (for me, at least). I don't know where to find it locally. I've ordered it from iHerb.com, which typically has very competive prices on all kinds of supplements.
3) When I have digestive issues of any kind, I find that a combination of peppermint, ginger, and licorice can be a nice, gentle cushion. I always have Nausea Ease (Vitanica brand) on hand. It's sold as a morning sickness aid, but it's good for any sort of angry stomach. A couple capsules of Nausea Ease plus some licorice (ask for DGL, which stands for Deglycyrrhizinated Licorice). You should be able to find both of these at PCC, Whole Foods, Pharmaca, and even some branches of Fred Meyer.
I hope you find something that helps!