Yes - Lyme and bart can cause GI dysfunction - there is a condition called "palsy of the gut", which can do this:tinyurl.com/y7vlyvxc
But you're right - the sequence of what causes what is very confusing. Is the bacteria affecting ANS, which then causes the SIBO or is there a direct cause from the bacteria, itself? The GI world is not very well understood in western medicine and you probably need to work with someone to figure out where to start if a low-carb diet doesn't help. A functional doc is your best bet.
Likely, your issues are caused by both the imbalance created from the abx AND ANS impact. I would start with a very detailed diary of your daily food/beverage/meds/supplement intake, and your symptoms and overview of how you're feeling.
Unfortunately, you will likely need to take a methodical approach. I would start experimenting with dietary changes, implementing the probiotics GH mentioned, multi-vitamin (although you need to be careful which one you choose - most of the cheaper versions are just that - cheap ingredients that won't do much and note that you could experience some complications with B vitamins so you might try to find one w/out B's).
I would incorporate a good GI binder, etc...
Do everything only one at a time, at least a few days apart and take close notes on your reactions. And then move on to the next component.
Post Edited (Pirouette) : 11/13/2017 5:45:16 PM (GMT-7)