A comparison of microbial profiles of different regions of the equine hindgut

The microbial profiles of the luminal content of five hindgut segments of one healthy horse were compared with rectal sample to elucidate the effect of anatomical region on bacterial and archaeal community structure and to evaluate the use of faeces as a representative model of large intestine. The qualitative and quantitative changes of the microbial community composition of caecum, right ventral colon, left ventral colon, left dorsal colon, right dorsal colon and faeces were monitored by denaturing gradient gel electrophoresis (DGGE) and real-time PCR using universal primers amplifying the V3 region of 16 S rDNA. DGGE fingerprints revealed extensive bacterial as well as archaeal diversity in all studied samples and reflected shifts in the community structure among the caecum, the different segments of the colon and the faeces. Archaeal DGGE pattern of the caecum differed from all the other parts of the hindgut. Microbial profile similarities were found between the left and the right dorsal colon and between the left ventral colon and the faeces. The excised DGGE bands were related to uncultured bacteria and methanogens, the dominant archaeal bands of caecum and faeces were related to Methanocorpusculum sp. Diversity indices indicated the higher diversity for bacteria than for archaea and the dominance of some methanogenic species. The real-time PCR revealed the differences in the microbial quantitative composition of each segment, showing the highest number of total bacteria and archaea in the right ventral colon. The analyses of bacterial and archaeal composition along the one equine hindgut indicate that the faecal sample is similar to that of the left ventral colon, but does not represent the microbial community of the caecum and other parts of the colon.