A reference set of rumen microbial genomes: The Hungate1000 project

The Hungate1000 project (www.Hungate1000.org.nz) seeks to produce a reference set of rumen microbial genome sequences from cultivated rumen bacteria and archaea, together with representative cultures of rumen anaerobic fungi and ciliate protozoa. The resulting data will be used for two main purposes; 1) to support international efforts to develop methane mitigation and rumen adaptation technologies and, 2) to initiate genome-based research aimed at understanding rumen function, feed conversion efficiency, methanogenesis and plant cell wall degradation in order to find a balance between food production and greenhouse gas emissions. It will underpin the analysis and comprehension of rumen metagenomic and metatranscriptomic sequence datasets and broaden our knowledge of rumen microbial phylogenetic diversity through genome sequencing of novel microorganisms.

Ruminants have evolved a symbiotic relationship with a complex microbiome located in their forestomach (reticulo-rumen) that allows these animals to use the lignocellulose component of plant material as their main energy source. Bacteria are the most numerous organisms in the rumen microbiome, being present at 1010 to 1011/g of content and making up more than 50% of the cell mass. Studies of rumen bacteria have revealed a bacterial community that includes both generalists and specialists able to convert large plant polymers to a variety of smaller organic compounds that are used by the ruminant for growth.

To guide the selection of bacteria for sequencing through the Hungate1000, we performed a metaanalysis of rumen 16S rRNA-based studies overlaid with cultured representative data. We identified cultivated rumen bacteria belonging to 88 different bacterial genera while a survey of international culture collections gave 146 bacterial cultures of rumen origin. While these culture collection isolates cover all the major taxonomic groups and include several well described organisms known to have key roles in rumen function, they do not represent the full diversity of the rumen microbiome. Consequently, studies focused on bringing additional rumen organisms into cultivation are important to this project.

The Hungate1000 project currently has genome sequencing in progress for more than 220 bacterial cultures, with sequence information already available for 90 cultures. These belong in 14 different bacterial families from five phyla and include several organisms that are not yet taxonomically described and only identified to the family level. When combined with genomes sequenced by other research groups ~120 genomes of rumen bacteria are now available. While not yet comprehensive, this collection will be a valuable resource for researchers interested in the microbiology of gut environments.