R. A. Gilbert

Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria

The rumen is known to harbor dense populations of bacteriophages (phages) predicted to be capable of infecting a diverse range of rumen bacteria. While bacterial genome sequencing projects are revealing the presence of phages which can integrate their DNA into the genome of their host to form stable, lysogenic associations, little is known of the genetics of phages which utilize lytic replication. These phages infect and replicate within the host, culminating in host lysis, and the release of progeny phage particles. While lytic phages for rumen bacteria have been previously isolated, their genomes have remained largely uncharacterized. Here we report the first complete genome sequences of lytic phage isolates specifically infecting three genera of rumen bacteria: Bacteroides, Ruminococcus, and Streptococcus. All phages were classified within the viral order Caudovirales and include two phage morphotypes, representative of the Siphoviridae and Podoviridae families. The phage genomes displayed modular organization and conserved viral genes were identified which enabled further classification and determination of closest phage relatives. Co-examination of bacterial host genomes led to the identification of several genes responsible for modulating phage:host interactions, including CRISPR/Cas elements and restriction-modification phage defense systems. These findings provide new genetic information and insights into how lytic phages may interact with bacteria of the rumen microbiome.

Ruminal Viruses (Bacteriophages, Archaeaphages)

Viruses of prokaryotes (phages) are ubiquitous to the gastrointestinal tracts of all animals, and particularly dense and diverse populations occur in the rumen of herbivores. Although knowledge of their existence dates back to the 1960s, very few studies were undertaken until the late 1980s and 1990s, when a number of investigators examined rumen phages at both the individual and ecosystem level. Despite the fact that these viruses have characteristics that can be both detrimental (reduce feed efficiency, transfer toxin genes) and advantageous (bacterial population balance, lateral gene transfer, phage therapy, novel enzymes), very little is known about their biological properties or genetic make-up. With recent technical advances in molecular biology, particularly developments in high-throughput sequencing, the field of rumen phage research is predicted to rapidly change, with individual phage isolates and the entire virus fraction (viral metagenome or virome) being characterised in ways never previously possible. The overall importance of phage-host interactions in relation to the functioning of the rumen microbial ecosystem and the nutrition of the animal remains elusive, but these viruses are likely to impact on the bacterial population balance and the flow of genetic material between microorganisms within the ecosystem.

In vitro detection and primary cultivation of bacteria producing materials inhibitory to ruminal methanogens.

A novel method for screening bacterial isolates for their potential to inhibit the growth of ruminal methanogenic Archaea was developed using a modification of the soft agar overlay technique, formally used for the isolation of lytic bacteriophages. This method may be used in the specific, hydrogen-rich conditions required for the growth of ruminal methanogenic Archaea.

Phage therapy in livestock methane amelioration.

Viruses of prokaryotes (phages) are obligate microbial pathogens that can, in the lytic phase of development, infect and lyse their respective bacterial or archaeal hosts. As such, these viruses can reduce the population density of their hosts rapidly, and have been viewed as possible agents of biological control (phage therapy). Phage therapy is becoming increasingly important as a means of eradicating or controlling microbial populations as the use of antibiotics and chemical treatments becomes both less effective and less publicly acceptable. Phage therapy has therefore been raised as a potential strategy to reduce methane (CH4) emissions from ruminants, providing an innovative biological approach, harnessing the potent, yet targeted, biocidal attributes of these naturally occurring microbial predators.

Modulation of the rumen microbiome

Rosalind Gilbert, Diane Ouwerkerk and Athol Klieve Rumen Ecology Unit, Department of Agriculture and Fisheries, Level 2A East, EcoSciences Precinct, Dutton Park, Qld 4102, Australia Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld 4067, Australia School of Agriculture and Food Sciences, University of Queensland, Gatton Campus, Gatton, Qld 4343, Australia Corresponding author. Tel: +61 7 3255 4289, Email: Ros.Gilbert@daff.qld.gov.au Tel: + 61 7 3255 4291, Email: Diane.Ouwerkerk@daff.qld.gov.au Tel: +61 7 546