A self-heating field-scale composter treating agro-industrial wastes within a period of 30 d was analyzed by denaturing gradient gel electrophoresis (DGGE) (Pedro et al., J. Biosci. Bioeng., 91, 159-165, 2001). Three major bands were derived from Propionibacterium acnes, Methylobacterium mesophilicum or M. radiotolerans, and Bacillus thermocloacae. Strains MSP09A and MSP06G with close affiliation to P acnes and A thermocloacae, respectively, were successfully isolated. Based on quantitative-PCR results, the relative population of MSP09A increased towards the end of the composting process (mesophilic stage) while MSP06G seemed to predominate during the middle period (thermophilic stage). These results correlated highly with their growth temperatures. MSP09A and MSP06G had different metabolic profiles which were largely affected by culture conditions. MSP09A was able to utilize large complex molecules of lipids and proteins. An interspecies relationship in terms of metabolites such as propionic acid was expected between the two microorganisms.