Hi spooler,
have you been told to take probiotics (lactic acid bacteria/bifidobacteria) while you are on the antimicrobial treatment? I'd strongly recommend those, they could help balance the microbial flora into a more healthy one. Especially now as the antibiotic kills them nonselectively. What about increasing the amount of vegetables and fibre in your diet, especially if you yourself feel that could be increased? You might wish to ask your doctor about this.
I'm not familiar at all with SIBO, but I've yet to come across evidence that probiotic products would be harmful to anyone.
All the best,
T