Metagenomic insights into the rumen microbial fibrolytic enzymes in Indian crossbred cattle fed finger millet straw

V Lyju Jose,A Sha Arun,Thulasi Appoothy,Ravi P More

doi:10.1186/s13568-016-0310-0

Abstract

The rumen is a unique natural habitat, exhibiting an unparalleled genetic resource of fibrolytic enzymes of microbial origin that degrade plant polysaccharides. The objectives of this study were to identify the principal plant cell wall-degrading enzymes and the taxonomic profile of rumen microbial communities that are associated with it. The cattle rumen microflora and the carbohydrate-active enzymes were functionally classified through a whole metagenomic sequencing approach. Analysis of the assembled sequences by the Carbohydrate-active enzyme analysis Toolkit identified the candidate genes encoding fibrolytic enzymes belonging to different classes of glycoside hydrolases(11,010 contigs), glycosyltransferases (6366 contigs), carbohydrate esterases (4945 contigs), carbohydrate-binding modules (1975 contigs), polysaccharide lyases (480 contigs), and auxiliary activities (115 contigs). Phylogenetic analysis of CAZyme encoding contigs revealed that a significant proportion of CAZymes were contributed by bacteria belonging to genera Prevotella, Bacteroides, Fibrobacter, Clostridium, and Ruminococcus. The results indicated that the cattle rumen microbiome and the CAZymes are highly complex, structurally similar but compositionally distinct from other ruminants. The unique characteristics of rumen microbiota and the enzymes produced by resident microbes provide opportunities to improve the feed conversion efficiency in ruminants and serve as a reservoir of industrially important enzymes for cellulosic biofuel production.

Highlights

Ruminants represent a substantial proportion of domesticated animal species worldwide and are the main source of milk, meat, and other dairy products
The host as such cannot produce any enzymes that degrade the plant material, so they take advantage of the symbiotic association with rumen microflora to release the energy in form of carbohydrates and sugars from the recalcitrant plant polysaccharides
The results obtained in our studies confirm the earlier reports where the bacteria belonging to phyla Bacteroidetes and Firmicutes are the major contributors of different classes of Carbohydrate-Active Enzymes (CAZymes) in the cattle rumen ecosystem

Summary

Introduction

Ruminants represent a substantial proportion of domesticated animal species worldwide and are the main source of milk, meat, and other dairy products. Ruminants have the ability to digest large amounts of plant polysaccharides by virtue of the composite microflora present in the rumen. The rumen has evolved into an efficient and effective fermentation vat for fiber degradation and the rumen is inhabited by a consortium of microorganisms consisting of bacteria, archaea, fungi, protozoa, and viruses (Miron et al 2001; Pope et al 2012), which interact and contribute significantly towards the health of ruminants. Among the various domains of microorganisms resident. The extensive rumen microbiota are endowed with the potential to hydrolyze the plant polymers into simpler forms that provides nutrients to the host, predominantly in the form of volatile fatty acids and microbial proteins. The rumen essentially functioning as an anaerobic fermenter, has the ability to absorb the digested plant polysaccharides by the resident microflora (Jami and Mizrahi 2012). Studies on the symbiotic rapport between the rumen microbial communities and the mammalian host

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