The vagus nerve does control a lot of things in the body: It slows down the heartbeat (if left to its own devices, our heart wants to beat very, very rapidly, and the vagus nerve slows this it down - i.e., vagus nerve damage results in heart palpitations), it has a role in swallowing, and (perhaps important for PATM) it seems to regulate gut motility.
Before I developed PATM, I experienced difficulty sleeping and swallowing, which I thought might be an issue with the vagus nerve, but my doctors chalked it up to stress and anxiety. Personally, I wouldn't rule out the vagus nerve as having some kind of role in gut issues as well as (potentially) in PATM (albeit indirectly), and I'm intrigued that someone else might have issues with it.
Just a note on the biology of the vagus nerve: It surely wouldn't create bacteria or carry acid or anything like that. It's a nerve, so it only carries electro-chemical nerve impulses. If it's claimed to have a role in regulating gut bacteria, it's through its influence on gut motility. It probably also has a role in the tonic contraction of muscles like the esophageal sphincter, which means acid reflux could become a problem if the vagus nerve were damaged.