Diversity of Gut Methanogens and Functional Enzymes Associated With Methane Metabolism in Smallholder Dairy Cattle

Abstract Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; six rumen and 42 dung contents were collected and analyzed using a shotgun metagenomic approach. The results indicated archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P<0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and in dung (~44%). The most abundant (~17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic classes were not classified (~ 6% in the rumen and ~4% in the dung). Furthermore, five functional enzymes: Glycine/Serine hydroxy methyltransferase, Formylmethanofuran—tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, Anaerobic carbon monoxide dehydrogenase and Catalase-peroxidase were associated with methane metabolism. KO0600 module and Enzyme Commissions (1.11.1.6 & 2.1.2.1) were common for dung and rumen fluid’s enzymatic pathways. Functional analysis for the enzymes identified were significant (P<0.05) for 5 metabolism processes. Breeding for tolerable methane emitting dairy cattle for a sustainable environment should be undertaken.