Microbial Communities and Metabolites of Rumens from Various Ruminants using a Barcoded Pyrosequencing and 1H NMR Spectroscopy

A combination of barcoded pyrosequencing and 1H-NMR technique was applied to investigate the ruminal microbial communities and metabolites of four typical Korean ruminants, Hanwoo with growing stage (HGS), Hanwoo with late-fattening stage (HFS), Holstein-Friesian dairy cattle (HDC), and Korean native goats (KNG). Ruminal samples were collected from the ruminants 3 h after feeding. Pyrosequencing analysis based on 16S rRNA gene sequences showed that the rumens had highly diverse microbial communities containing many unexploited microorganisms. Bacterial classifications revealed that the bacterial sequencing reads were predominantly affiliated with four phyla, Bacteriodetes, Firmicutes, Fibrobacteres, and Proteobateria in all ruminants, but, interestingly the bacterial reads belonging to Fibrobacteres were present at a very low abundance (< 0.1%) in only KNG with low ruminal pH. Archaeal community analysis showed that almost all archaeal reads were classified into methanogens of the phylum Euryarchaeota, but the sequences were not clustered with known methanogenic sequences. Community and metabolite analysis showed that the microbial communities and metabolites of KNG were clearly distinguished from those of other ruminants. The analyses also showed that bacterial communities and metabolite profiles of Hanwoo (HGS and HFS) were relatively similar even though they had different growth stages and diets, and their profiles were a little different from those of other ruminants. In conclusion, bacterial communities as well as metabolites of the rumens were differentiated statistically with respect to ruminant species, which suggested that ruminant ages and diets as well as ruminant species might be important factors to influence on their microbial communities and metabolites.