Is your wife taking a probiotic supplement? This is recommended to help counter the risk of C. Diff. bacteria in the large intestine (common symptom is diarrhea), and to help reduce the risk of yeast overgrowth in the body.
Also, your wife may need to do some detoxing to help get rid of the die-off toxins created when the antibiotics kill the Lyme bacteria. There are some suggestions in the thread at the top of the Lyme forum titled, "New to Lyme?.......Start here!"
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 weaning off TPN.
Meds: Pulmicort, IV Doxycycline, Heparin (to flush PICC line), Claritin, Singulair, Domperidone, Colloidal Silver (topically & nasally), probiotics, Liver support herbs, Ailanthus, digestive enzymes, homeopathy.