Rumen Methanogens Diversity in Native Cattle under Different Feeding Regimen using 16s Metagenomic Techniques

Abstract

Background: Pulikulam cattle is an indigenous cattle breed native to south India, Understanding the rumen microbiome is an important step to develop effective strategies to minimize their enteric methane emission. The rumen microbiome of this breed has not been documented. Hence, a study was executed in Pulikulam cattle, fed different diets, to investigate the diversity of rumen methanogens using metagenomic techniques. Methods: Twenty recently calved Pulikulam cattle with mean body weight of 200 Kg were randomly distributed into four treatments, with five animals per treatment. The animals were fed their respective diets as per their treatment for 30 days, after which the rumen liquor was collected. DNA from the samples were extracted and subjected for 16s rRNA gene amplification using region specific primers. Result: Methanogens belonging to five orders, four classes and eleven families were identified. Order Methanomassiliicoccales was not present in treatment group fed with high energy diet. The methanogens affiliated to the order Methanomicrobiales were predominant in treatment 1 (14%) and treatment 2 (16.30%). Order methanococcales (15%) was predominant in treatment 3 and order Methanosarcinales (18%) was predominant in treatment 4. Archaeal order belonging to Thermoplasmatales were also identified in Pulikulam cattle fed different dietary regimen except in treatment 3. Archaeal family Methanothermaceae belonging to the order Methanobacteriales was identified in Pulikulam cattle. Methanocorpusculum labreanum was the predominant species in all the treatment groups. Sulfolobus acidocaldarius, Sulfolobus islandicus, Sulfolobus solfataricus, Sulfolobus sp. A20 and Sulfolobus tokodaii were identified in treatment 1, which had higher dietary crude protein. It was concluded that methanogen diversity varied under different feeding regimen and predominant methanogen is varied in Pulikulam breed of cattle. M. labreanum was the predominant methanogen in Pulikulam cattle fed with different dietary regimen.