Evaluation of Rumen Microbes For Milk Fat Yield in Cattle Based on 16S rRNA Amplicon Metagenomic Sequencing

Abstract

Background: Ruminal microbes support growth, lactation and maintenance of animals by providing energy and protein yielding nutrients. Metagenomics is the study of microbial communities directly in their natural environments such as soil, water, gut samples etc. The 16S rRNA gene sequencing is one of the basic genetic markers for the characterisation of prokaryote microorganism community. Current study exploited complex gut microbial communities present in cattle rumen based on variation in milk fat yield. Methods: The study was conducted in cattle reared at University Livestock Farm, Kerala Veterinary and Animal Sciences University. Twelve healthy cattle in the initial stages of lactation (less than three months) were selected and divided into two groups of six each based on high and low milk fat composition. Rumen samples were collected and DNA was isolated. Amplicons of 16S rRNA has been generated from metagenomic DNA targeting V3 and V4 hyper variable regions. Qiime2 was used for analysis for 16S rRNA amplicon sequencing. Result: Results revealed that a total of 38,28,241 sequences were obtained after demultiplexing. Majority of sequence length ranged around 295 to 301 nucleotides for forward reads and 216 to 300 nucleotides for reverse reads. After denoising, a total of 6,62,498 sequences were obtained. Clustering (de-replication) produced 711 unique sequence features. In kingdom level of taxonomy, for bacterial kingdom, there was no significant difference in abundance of organisms for high milk fat yield and low milk fat yield cows. For archaea, significant difference observed between abundance of high milk fat and low milk fat groups at five per cent level in the current study.