Abstract: A method of treating a waste stream comprising feeding a waste stream into a reactor constructed and arranged for a fast start and maintained in a thermophilic temperature regime of between about 50° C. and 62° C. for a HRT of less than or equal to 48 hours, wherein the reactor contents are maintained at a pH less than or equal to 6.5; drawing a portion of the contents of the reactor and feeding the drawn contents into a second reactor which is maintained in a mesophilic temperature regime of between about 28° C. to 38° C. for a HRT of at least thirteen days; and replacing the contents drawn from the first reactor with more waste from the waste stream. Alternately, the waste stream may be initially treated in a mesophilic reactor, followed by treatment in a thermophilic reactor, or a single stage thermophilic reactor may be used.