Sequencing and Assembly Analysis of Goat’s Rumen Bacterial Metagenomes for the Discovery of Genes Involved in Important Biological Processes

In this study, bacterial metagenomic DNA was isolated from goat’s rumen fluid. Approximately 0.1 microgram of genomic DNA sample was converted to a sequencing library using Nextera DNA Sample prep kits (Illumina) according to the manufacturer’s protocol. The resulting libraries had a range of fragments from approximately 200 bp to 400 bp and were quantified using a Qubit spectrofluorometer (Invitrogen). The pooled libraries were sequenced on an Illumina HiSeq 2000 using TruSeq SBS kit v3 for paired-end 100 bp sequencing. The library was also sequenced on an Illumina Hiseq 2500 using paired-end 120 bp sequencing. The assembly of the NGS data produced 7 million contigs. The assembled sequences have 7492064 nodes, n50 of 410, and the maximum contig length is 140,000bp. These contigs were translated into peptides using Prodigal. Searches in the CAZY database have identified a number of cellulases and related genes. Several of these genes were cloned, sequenced and validated with the putative functions in degrading cellulose substrates. The project is supported by the Pittsburg Supercomputing Center Project TG-DEB140031, USDA-NIFA-2010-02417-223076, USDA-2012-38821-19989