First, see a different specialist if this one is meeting your expectations. Second, most of the time if you say anything related to your stomach or digestion is problematic they just throw an anti acid med at you, its honestly ridiculous. If you do not suffer from reflux, then prilosec, nexium, etc isnt going to do anything.
Do you have H.pylori? If so, then yes you need an antibiotic. If not, then unless you know for sure that you have a bacterial infection, taking an antibiotic could end up causing more harm than good.
The trick to gastritis is finding out what is causing it. And to answer your question, yes, autoimmune disorders can be related to food allergies i.e. celiac disease.
What are your symptoms?