Research background
Our
research focuses on microbial genomics,
ecology, and systematics, and interactions between these research areas.
Genomics, which explores the biology of organisms
through their genetic blueprints, has profoundly affected microbiology. It has
led us to revise our definitions of microbial entities, reconsider their
capabilities, and re-evaluate the microbiological toolbox of methods and
approaches. In the breadth of its
influence on various subdisciplines of microbiology (e.g., metabolism,
physiology, ecology, host-pathogen relationships, industrial microbiology), and
its interaction with other disciplines (e.g., human and veterinary medicine,
agriculture, evolutionary biology, structural biology), the impact of genomics
on microbiology is arguably unrivaled in this century.
Our
understanding of microbial ecology
has been greatly expanded by molecular and genomic tools. Cultivation-independent methodologies analyze
the small-subunit ribosomal RNA (rRNA) genes of mixed microbial populations
from environmental samples, revealing the diversity of the uncultured
prokaryotic world and providing the basis for studies of microbial
biogeography. Prediction of the
ecological role of members of these communities requires access to the genome,
rather than a single gene, and high-throughput genome sequencing methodologies
provide that access, giving rise to metagenomics.
Questions in microbial systematics
range from the species level to the phylum. The question ,"What is a bacterial
species?" has vexed microbiologists and confounded biologists of "higher"
organisms for years. The availability of genome data from multiple strains of a
species promises to provide a quantitative measure of genome relatedness and
hence species status. At the other end of the taxonomic spectrum, analysis of
members of poorly represented phyla should reveal the true diversity of
microbial genomes and allow us to better resolve phylogenetic relationships
between the phyla. The interface between microbial systematics, evolution, and
genomics also provides an opportunity to re-evaluate the genome as a static
entity, particularly its susceptibility to acquisition and loss of genes by
lateral gene transfer (LGT) within and across the species boundary.
Current and future research
Our
primary research addresses the biology of the planctomycetes, acidobacteria,
and verrucomicrobia, using genomic and post-genomic approaches. These three
groups, while phylogenetically unrelated, are united in having a cosmopolitan
distribution in aquatic and terrestrial environments, and being relatively
understudied and poorly characterized. We are starting to gain an understanding
of their ecological importance - e.g. some planctomycetes have been
recently demonstrated to carry out the anaerobic oxidation of ammonium
("anammox"), and it appears that anammox planctomycetes play a significant role
in the global nitrogen cycle - but much work remains
to be done.
A secondary focus is the structure and function of microbial communities, both free-living (East African savanna soils, deep-sea coral habitats, and Galapagos Rift hydrothermal vents), and associated with the human host (gastrointestinal and reproductive tracts).
Selected recent publications
Ward, N., Ø.
Larsen, J.A. Eisen, H. Khouri, A.S. Durkin, G. Dimitrov, L. Jiang, D. Scanlan,
K. Kang, M. Lewis, L. Bruseth, H. Tettelin, T. Read, B. Methé, I. T. Paulsen, Q. Ren, D. Fouts, H.B.
Jensen, S. Salzberg, R. Seshadri, K.E. Nelson, J.F. Heidelberg, R.T. DeBoy,
R.J. Dodson, W. Nelson, T. Feldblyum, T. Utterback, S. Vanaken, N.K. Birkeland,
I. Eidhammer, S. H. Grindhaug, I. Holt, I. Jonasen, J. Lillehaug, and C.M.
Fraser. 2004. Genomic Insights into Methanotrophy: the Complete Genome Sequence
of Methylococcus capsulatus (
Ward, N., J.T.
Staley, J.A. Fuerst, S. Giovannoni, H. Schlesner, and E. Stackebrandt. 2004. The Order Planctomycetales, including the Genera Planctomyces, Pirellula,
Gemmata, and Isosphaera,
and the Candidatus genera Brocadia, Kuenenia, and Scalindua, In: M.
Dworkin et al., (eds). The Prokaryotes, An Evolving Electronic
Resource for the Microbiology Community, 3rd edition.
Bauer, M., T.
Lombardot, H. Teeling, N.L.
Moran, M. A., A. Buchan, J.M. González, J.F. Heidelberg, J. Henriksen, W.B. Whitman, R.P. Kiene, L. Brinkac, M. Lewis, S. Johri, B. Weaver, G. Pai, J.A. Eisen, G. King, M.R. Belas, C. Fuqua, E. Rahe, W. Sheldon, W. Ye, J.M. Carlton, D.A. Rasko, I.T. Paulsen, Q. Ren, S.C. Daugherty, R.T. Deboy, R.J. Dodson, A.S. Durkin, R. Madupu, W.C. Nelson, S.A. Sullivan, M. J. Rosovitz, D.H. Haft, J. Selengut, and N. Ward. 2004. Genome Sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
Badger, J.H., J.A. Eisen, and N. Ward. 2005. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA-based phylogenetic analysis; implications for the taxonomy of the orders Rhodobacterales and Caulobacterales. International Journal of Systematic and Evolutionary Microbiology 55:1021-6.
Ward, N., and C.M. Fraser. 2005. How genomics has affected the concept of microbiology. Current Opinions in Microbiology. 8(5):564-71.
Ward, N. 2006. New directions and interactions in metagenomics research. FEMS Microbiology Ecology 55:331-8.
Penn, K., D. Wu, and N. Ward. 2006. Characterization
of bacterial communities associated with deep-sea corals on
Haft, D.H., I.T. Paulsen, N.L. Ward, and J.D. Selengut. 2006. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biology 4:29.
Badger, J.H., T.R. Hoover, Y.V. Brun, R.M. Weiner, M.T. Laub, G. Alexandre, Q. Ren, I.T. Paulsen, K.E. Nelson, H. Khouri, D. Radune, J. Sosa, R.J. Dodson, S.A. Sullivan, M.J. Rosovitz, R. Madupu, L.M. Brinkac, A.S. Durkin, S.C. Daugherty, S.P. Kothari, M. GwinnGiglio, L. Zhou, D.H. Haft, J.D. Selengut, T.M Davidsen, Q.Y., N. Zafar and N.L. Ward. 2006. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. Journal of Bacteriology 188:6841-50.
von Mering, C., P. Hugenholtz, J. Raes, S.G. Tringe, T. Doerks, L. J. Jensen, N. Ward, and P. Bork. 2007. Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments. Science 315(5815):1126-30.