Study of the Cow Rumen Stationary and Mobile Metagenome

Ruminal bacteria perform vital functions on behalf of their hosts, from the breakdown of cellulose and other plant cell wall components to the production of fatty acids and vitamins. Little investigation, however, has been carried out on rumen metagenomes and mobile metagenomes. The rumen environment is extremely attractive for the isolation and identification of plasmids, for three main reasons:

1.      The study of horizontal gene transfer within a confined natural environment.

2.      Isolating new enymatic functions from this unexplored environment, such as cellulolytic enzymes that may used for generating clean energy from cellulosics.

3.      Isolating plasmids that may serve as a shuttle vector for the genetic manipulation of the rumen microflora, to enhance such aspects as the harvesting of energy from and milk production by the ruminant.

We are applying a novel experimental approach for characterising the mobile metagenome of ruminants. Our aim is to create tools for the isolation and study of the rumen mobile metagenome and to utilise these tools in metagenomic profiling and function analysis. For this purpose we have designed an experimental approach which allows for the purification of plasmids from environmental samples without compromising on the quantity, quality, diversity and integrity of the palsmid DNA. We have subjected our plasmid samples to new-generation sequencing methods and these are currently being assembled. Our plan is to thoroughly analyse the rumen mobile metagenome in terms of sequencing and functionality.

Figure 1: A fistulated dairy cow. Rumen fluid is recovered from the fistula as a source for rumen microbes. DNA is recovered from the rumen microbiome and analyzed by next generation (Solexa) sequencing to mine the metagenomes.

collaboration:  Dr Itzhak Mizrahi from the department of dairy sciences, Volcani research center.