Oral rapamycin preparation and use for stomatitis

The disclosure teaches counter-intuitive methods for treating stomatitis using oral mTOR inhibiting preparations such as preparations of microcapsules and nanoparticles including an inhibitor of the mammalian target of rapamycin. The methods, preparations and other teachings are useful in various respects, especially for assisting in the treatment, prevention and management of stomatitis in feline subjects and, most especially, the treatment and management of Feline Chronic Gingivo-Stomatitis (FCGS), with secondary applications also related to management of gingivitis and autoimmune mucosal disorders. Disclosed embodiments illustrate multi-week dosing regimens and also address needs for alternative preparations or manufacturing processes that ensure efficacy while improving other performance characteristics such as storage stability, biodistribution, dosage cost, etc.