Strategies for improving ruminant utilisation of high grain diets: Pangenome of Streptococcus bovis

Abstract

The field of microbiology is being transformed by the increased ease and reduced costs of DNA sequencing. An initiative of the United States Department of Energy (USDOE), Joint Genome Institute facilitated the establishment of a Community Sequencing Project, the Hungate 1000, an international collaborative venture which aimed to sequence the genomes of bacteria isolated from the rumen and intestinal tract of herbivores. The DAF Rumen Ecology Unit (REU) contributed 36 rumen bacteria and seven bacteriophages to this genome sequencing effort. Thirteen of these bacteria belonged to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). These are virulent, fast-growing commensal bacteria which over-proliferate in the rumen of cattle when they transition too quickly from forage to high grain feedlot rations, causing rumen lactic acidosis. Costly management strategies based on lengthy feed transition times (up to 20 days), and the use of feed additives including rumen modifiers such as monensin and antibiotics, are currently used to control rumen acidosis. This project used the SBEC genome sequences generated by the Hungate 1000, as well as publically available SBEC genome sequences, to create a combined genome dataset or pangenome. This pangenome of 42 genome sequences was then used to identify:
1. factors which enable these organisms to rapidly proliferate on starch-rich diets, for example, carbohydrate degrading enzymes; and
2. new approaches to control these organisms, for example inhibitory peptides (bacteriocins) and enzymes, carried by naturally-occurring viruses predatory to bacteria (known as bacteriophage or phage), which can specifically target and puncture bacterial cell walls.
During the course of the project, technical capacity of the REU was also developed to facilitate the analysis and secure storage of large sequence datasets, with the expansion of high performance computing resources and installation of specialist software. Several of the phage proteins identified by the pangenome analysis were shown to be intact and functional, with the formation and release of phage particles from bacterial host cells verified by transmission electron microscopy and proteomics analysis. These phage proteins represent potential candidates for further investigation as antimicrobials to control SBEC, and will be used as background proof of concept for the development of project proposals for submission to funding agencies.