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Comparative analysis of methanogen compositions in the feces of horse and pony was carried out by constructing the   α  -subunit of methyl coenzyme-M reductase ( mcrA ) gene and 16S ribosomal RNA gene (16S rRNA) clone libraries. The  mcrA  clone library analysis indicated that Methanomicrobiales was predominant in both horse and pony. Furthermore, most of the clones of the 16S rRNA gene library showed that Methanomicrobiales was also predominant in horse and pony, but the LIBSHUFF analysis showed that the horse and pony libraries were significantly different ( P  < 0.05). Most of operational taxonomic units (OTUs) showed low similarity to the identified methanogens in both the  mcrA  and the 16S rRNA clone libraries. The results suggest that horse and pony harbor unidentified and novel methanogens in their hindgut. The methanogen population was higher in horse than in pony; however, the anaerobic fungal population was similar in horse and pony. The methanogen diversity was different between two breeds of  Equus caballus .

Comparative Analysis of the Methanogen Diversity in Horse and Pony by UsingmcrAGene and Archaeal 16S rRNA Gene Clone Libraries