The best type of apple cider vinegar to use to treat Lyme disease is organic and unfiltered. The organic vinegar is made from organic apple juice so it contains no remnants of pesticides. During a time of immune suppression, adding pesticides to the body is not advised. Unfiltered apple cider vinegar is better than the filtered varieties because it contains more of the active ingredients that fight off the bacteria. The filtered cider vinegar will also be effective but may take longer to act.