Exploring diet-dependent shifts in methanogen and methanotroph diversity in the rumen of Mehsani buffalo by a metagenomics approach

In this study, metagenomics was applied to characterize microbial communities, specifically methanogens and methanotrophs, and to discover their functional activities under two different dietary treatments. To retrieve an overall rumen microbial community profile and to check the abundance of methanogenic and methanotrophic bacteria therein, semiconductor shotgun sequencing of DNA isolated from the rumen fluid of Mehsani buffalo treated with two different diets, i.e. 50% green roughage/50% concentrate (M50GL) and 100% green roughage (M100GL), was carried out. The study revealed that the M50GL group harboured more Proteobacteria than the M100GL group, which harboured more Bacteroidetes. The classes of Proteobacteria (methanotrophs) differed significantly in response to the change in diet. α-Proteobacteria and β-proteobacteria were found to be significantly (p < 0.05) higher in the M100GL group, whereas γ-proteobacteria were significantly more abundant in the M50GL group than in the M100GL group. Different species of methanogens were more abundant in the M100GL group than in the M50GL group. The enzymes involved in the serine pathway (glycine hydroxyl methyltransferase) carried out by type II methanotrophs, i.e. α-proteobacteria and β-proteobacteria, were found in higher abundance in the M100GL group, which correlates with the taxonomic abundance of the same classes in the M100GL group.