Microbial Genomics

Microbial genomics is the study of the total genomic content of a microbial strain or the total of an individual organism's genes.

Microbes have modest-sized genomes - averaging 4 to 5 million bases compared with 3 billion bases in the human and other mammalian genomes. As such, they can be used to explore and understand life processes at a whole-system level. These analyses allow researchers to learn about microbes at their most fundamental level and to ask questions about how the basic parts work together to form a functioning organism.

By sequencing the genome, we are identifying genes and proteins, as well as patterns of gene expression during various conditions.

Our recent genomics studies include analysis of some novel microbial isolates:

  • Anoxybacillus flavithermus – a moderately thermophilic bacterial species implicated in the catalysis of silica sinter formation.(1)
  • Methylacidophilum infernorum – a methanotrophic obligate acidophile isolated from geothermal soils at Tikitere, Hells Gate.(2-3)

References:

  1. Saw, J.H., Mountain, B.W., Feng, L., Omelchenko, M.V., Hou, S., Saito, J.A., Stott, M.B., Li, D., Zhao, G., Wu, J., Galperin, M.Y., Koonin, E.V., Makarova, K.S., Wolf, Y.I., Rigden, D.J., Dunfield, P.F., Wang, L. & Alam M. 2008. Encapsulated in silica: genome, proteome and physiology of thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biology, 9, R161.
  2. Op den Camp, H.J.M., Islam, T., Stott, M.B., Harhangi, H.R., Hynes, A., Schouten, S., Jetten, M.S.M., Birkeland, N-K., Pol, A., and Dunfield, P.F. 2009. Minireview: Environmental, genomic, and taxonomic perspectives on methanotrophic Verrucomicrobia. Environmental Microbiology Reports, doi:10.1111/j.1758-2229.2009.00022.x.
  3. Hou, S., Makarova, K.S., Saw, J.H., Senin, P., Ly, B.V., Zhou, Z., Ren, Y., Wang, J., Galperin, M.Y., Omelchenko, M.V., Wolf, Y.I., Yutin, N.Y., Koonin, E.V., Stott, M.B., Mountain, B.W., Crowe, M.A., Smirnova, A.V., Dunfield, P.F., Feng, L., Wang, L. & Alam, M. 2008. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biology Direct, 3, 26.