About Us

Our Background

The Microbial Genomics Team began in 2003 as a result of funding from the Foundation for Research Science and Technology (FRST) New Economy Research Fund (NERF). Our team has continued to expand since then and has developed a range of microbial genomics programmes with a strong emphasis on meeting challenges facing New Zealand agriculture.

Our Aims

  • to strengthen microbial genomic research efforts in New Zealand.
  • to provide a platform for the development of new microbial genomics capability.
  • to provide a forum for interaction and learning for emerging microbial genomic researchers.

Our Science

We undertake multidisciplinary collaborative research with the aim of sequencing and analysing microbes of importance within the mammalian gut environment.

Our Current Projects

Butyrivibrio proteoclasticus genome project (FRST funded, 2003-2008)

Butyrivibrio proteoclasticus is a Gram-positive, butyrate-forming bacterium isolated from the rumen of a cow grazing pasture in New Zealand. It is involved in protein breakdown and lipid transformation in the rumen, but the primary focus of the genome sequencing project is on the ability of B. proteoclasticus to breakdown hemicellulose, an important component of plant structural carbohydrates.

Accessing the Uncultured Rumen Microbiome project (FRST funded, 2008-2013)

The microbial community attached to plant material in the rumen is not well represented by the microbes currently in held in culture collections and it is these uncultivated microbes that account for most of the lignocellulose degrading capacity in the rumen. The focus of this project is to identify and access the genomes of these attached microbes (referred to collectively as the "microbiome") and characterise the enzyme systems that they use to degrade lignocellulose.

The project consists of 5 objectives:

  • Cultivation and FISH, (led by Dr. Peter Janssen, AgResearch), which will develop improved cultivation techniques to retrieve more of the plant-adhered microbiome and provide information on its species composition in the rumen.
  • Metagenomics (led by Dr Christina Moon, AgResearch) will use metagenomic techniques to learn about the structure of the attached microbial community by amplifying and sequencing ssrRNA gene sequences from rumen samples and identifying the types of lignocellulose-degrading enzymes present by activity screening of metagenomic expression libraries.
  • Functional Genomics (led by Dr. Bill Kelly, AgResearch). The genomes of at least two predominant microbes obtained in pure culture will be sequenced and the nature of their lignocellulose-degrading systems will be examined using functional genomics techniques.
  • Protein structure and function (led by Assoc. Prof. Vic Arcus, University of Waikato) The structure/function relationships of genes important in lignocellulose degradation will be elucidated via gene expression, scaled-up protein production and crystallisation for determination of enzyme structures.
  • Modelling (led by Dr. Kumar Vetharaniam, AgResearch) will model data from the microbial population, gene and protein expression experiments to determine the extent to which components of lignocellulose digestion affect each other, and predict the sensitivity of the system to changes in individual components and inputs.

Rumen Methanogens genome project (PGGRC funded)

Methanobrevibacter ruminantium is a methane-forming organism originally isolated from the rumen of a cow, and based on cultivation and molecular detection data it is know to be present in the rumen under a variety of dietary conditions. Methane is a potent greenhouse gas and is formed in the rumen by the action of methanogens, (part of the domain Archaea) mainly from the substrates H2 and CO2. The genome of M. ruminantium is being sequenced as part of a research consortium (Pastoral Greenhouse Gas Research Consortium) to gain a better understanding of their biology and identify gene and protein targets for technologies to reduce methane emissions from ruminant animals. We have also started the genome sequencing of another rumen methanogen, Methanobrevibacter sp. strain SM9, and have plans to sequence at least one other rumen methanogen.