Coinfections are those opportunistic infections that may come along for the ride with the Lyme (such as Babesia, Bartonella, Ehrlichia/Anaplasma, Mycoplasma, Rickettsia, Rocky Mountain Spotted Fever, etc.) and/or may take advantage of the lowered immune system after Lyme infection has already begun (viruses are common).
Here are what I would ask about if I were you: Ask the doctor to explain why he considers you to be resistant to antibiotics, and why he thinks you have Lyme. Ask more questions about what herbs he thinks might be helpful for you and why. Ask specifics of dosing, too. You may find you need to start out at small doses and slowly work up to the full recommended dose of a particular herb or supplement. Ask about nutritional supplements. Ask about other things you might need to do to support your body's healing (such as dietary modifications, etc.).
If you really do have Lyme (and it is very likely if you have labwork that suggests it), then it is very possible that is why your experience is different than the pathology suggests as far as the severity of your "UC." Lyme bacteria can penetrate into the wall of the GI tract where they can cause problems that cannot be seen on the typical biopsy or by the doctor during the colonoscopy.
Chronic Lyme Disease, Chronic Bartonella (clinical dx only), Gluten & Sulfite Sensitivity, Many Food/Inhalant/Medication/Chemical Allergies & Intolerances, Asthma, Gut issues (dysmotility, non-specific inflammation), UCTD ("Secondary Lupus-Like Syndrome"), Osteoporosis, chronic Lymphopenia, etc.; G-Tube; Currently trying to wean off TPN.
Meds: Pulmicort, IV Ceftazidime, Heparin (to flush PICC line), Claritin, Domperidone, Colloidal Silver (used topically), probiotics, Milk Thistle, Ailanthus, homeopathy.