Microbial community structure in gastrointestinal tracts of domestic animals: Comparative analyses using rRNA-targeted oligonucleotide probes

The microbial community structure of the gastrointestinal (GI) tracts of various domestic animals (bovine, ovine, caprine, and swine) was evaluated using oligonucleotide probes targeting the small subunit (SSU) ribosomal RNA (rRNA) of major microbial groups. Bacterial, eukaryotic, and archaeal rRNAs were estimated to account for approximately 60-90%, 3-30% and 0.5-3%, respectively, of the total rRNA present in the GI tracts of most of the animals examined in this study. The abundance of phylogenetically defined groups of methanogens and sulfate-reducing bacteria (SRB) was also evaluated. Methanobacteriales were the predominant methanogens in the rumen of bovine and caprine, while Methanomicrobiales predominated in the ovine rumen. A dominant archaeal group could not be identified in other sampling locations of the GI tract of these ruminants and in the GI tract of pigs, using the available collection of group-specific probes. Desulfovibrio species were the most abundant Gram-negative SRB targeted by available probes in the GI tract of nearly all animals.