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Mircea Podar |
Description of Research:
Our research combines the use of experimental and computational approaches to study the evolution of microbial genomes, adaptation to various environments and the composition and dynamics of microbial communities.
The exponential increase in microbial genomic and metagenomic data provides new opportunities to understanding functional diversification in gene families and evolution of genome size/composition as part of organism adaptation to specific niches. Analyzing large genomic datasets and especially metagenomic data presents however computational challenges in terms of gene identification, functional inferences and taxonomical assignments. We are integrating computational genomics and phylogenetic approaches to correlate genomic and metagenomic data with the ecology and evolution of individual microbes and communities. Microbial systems under study include species relevant to bioremediation and bioenergy, the mammalian gut microbiome, species and communities from extreme environments and oceanic niches. We are also applying the concept of targeted genomics of single cells and specific populations to sequence the genomes of uncultured bacteria and archaea. This approach bridges the gap between characterization of cultured organisms, which represent a minute fraction of the microbial diversity and metagenomics, which provides only a glimpse of the genomic information of complex communities. We are developing experimental and computational tools necessary to achieve reliable isolation and genomic sequencing of any specific microbes, rare or abundant, from any type of community.
Other research interests include the study of Nanoarchaeota, a recently described group of hyperthemophilic archaea. The only cultivated representative of this group, Nanoarchaeaum equitans appears to be a parasite by living attached to another archaeon, Ignicoccus hospitalis. The genomes of both organisms have been sequenced and we will use functional genomic and proteomic approaches to study this unique symbiotic system. As nanoarchaea have been detected in numerous high temperature environments based on ribosomal sequences, we will also aim at isolating other representatives in laboratory culture and study them using traditional microbiology as well as genomics and proteomics.Selected Publications:
- Podar M, Wall MA, Makarova KS, Koonin EV. (2008). The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system. Biology Direct, 3, 2.
- Warnecke, F., Luginbuhl, P., Ivanova, N., Ghassemian, M., Richardson, T., Stege, J., Cayouette,M., Djordjevic, G., Aboushadi, N., Sorek, R., Tringe, S., Podar, M., Martin, H., Kunin, V., Dalevi, D., Madejska, J., Kirton, E., Platt, D., Szeto, E., Salamov, A., Barry, K., Mikhailova, N., Kyrpides, N., Matson, E., Ottesen, E., Zhang, X., McHardy, A., Hernández, M., Murillo, C., Acosta, L., Rigoutsos, I., Tamayo, G., Green, B., Chang, C., Rubin, E., Mathur, E., Robertson, D., Hugenholtz, P. and Leadbetter, J. (2007). Metagenomic and functional analysis of the hidgut bacteria of a wood-feeding higher termite. Nature, 450, 560-565.
- Podar, M., Abulencia, C., Wachter, M., Hutchinson, D., Zengler, K, Garcia, J., Hausser, L and Keller, M. (2007) Targeted access to the genomes of low-abundance bacteria in complex microbial communities. Applied and Environmental Microbiology, 73:3205-3214.
- Podar, M. Two component systems in microbial communities: Approaches and resources for generating and analyzing metagenomic data sets. (2007). Methods in Enzymology, 422:32-46
- Podar, M. and Reysenbach, A.L. (2006). New opportunities revealed by biotechnological explorations of extremophiles. Current Opinions in Biotechnology, 17:1-6.
- Podar, M., Eads, J. and Richardson, T.H. (2005). Evolution of a microbial nitrilase gene family: An environmental genomics study. BMC Evolutionary Biology, 5:42-48.
- Giovannoni, S., Tripp, J., Givan, S., Podar, M., Vergin, K., Bibbs, L., Eads, J., Richardson, T., Noordewier, M., Rappé, M., Short, J. and Mathur, E. (2005). Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Science, 309: 1242-1245.
- Tringe, S.G., Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P. and Rubin, E.M. (2005) Comparative metagenomics of microbial communities. Science, 308: 554-557.
- Waters, E, Hohn, M.J., Ahel, I., Graham, D.E., Adams, M.D., Barnstead, M., Beeson, K.Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X., Mathur, E., Ni, J., Podar, M., Richardson, T., Sutton, G.G., Simon, M., Söll, D., Stetter, K.O., Short, J. and Noordewier, M. (2003). The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. U.S.A. 100, 12984-12988.