Associate Professor
Canada Research Chair in Environmental Genomics
CIFAR Scholar

Research Summary

My lab investigates the ecological and biogeochemical roles of uncultivated microbial communities in natural and engineered ecosystems with a particular emphasis on defining metabolic interactions. We combine plurality and single-cell genome sequencing with functional screening and the development of computational tools to predict latent and expressed metabolic potential and recover genomic scaffolds with biotechnological applications. To permit improved metabolic pathway prediction from environmental sequence information we have developed MetaPathways, a modular annotation and analysis pipeline for pathway inference that uses the PathoLogic algorithm to map functional annotations onto the MetaCyc collection of reactions and pathways, and construct environmental Pathway/Genome Databases (ePGDBs) compatible with the editing and navigation features of Pathway Tools. We use MetaPathways to predict metabolic interactions between sequenced isolates or environmental clones that can be validated in co-culture experiments using traditional genetic and biochemical methods. Other project space includes the use of microfluidic digital chip technology for single-cell genome sequencing and the use of biosensors to detect small molecule production or substrate conversion by environmental clones in plate-based or cell-sorting screens.

Spin-Offs

In 2013, the lab spun-off a synthetic biology company called MetaMixis (http://www.metamixis.com), that uses proprietary platform screening technology to discover and evolve small molecules and industrial catalysts from uncultivated microbial communities inhabiting natural and engineered ecosystems.

Intellectual Property

Sequential screening for co-culture based detection of metagenomic elements conferring heterologous metabolite secretion. 14-036 (Tech 14-0238) and Modular protein class structures for combinatorial lignin transformation in E. coli. 14-076 (Tech 14-0465)

Provisional patents based on 14-036 and 14-076 has been filed in the United States and Canada with serial numbers 61/936,448 and 62/013,369, respectively.

Bio

Steven Hallam is a University of California Santa Cruz and MIT trained molecular biologist, microbial ecologist, entrepreneur, and innovator. With over 20 years of experience in field and laboratory research and innovation at disciplinary interfaces, Hallam is an Associate Professor in the Department of Microbiology and Immunology at the University of British Columbia, Canada Research Chair in Environmental Genomics and Canadian Institute for Advanced Research Scholar in integrated microbial biodiversity, a program dedicated to studying the molecular, morphological and community complexity of the microbial world.

Following an undergraduate degree from Sarah Lawrence College concentrating on Biology and Religion, Steven spent several years working as an oncology research technician at the Montifiore Medical Center. He went on to receive a PhD from the University of California Santa Cruz where he conducted research on developmental regulation of neuronal asymmetry and synaptic remodeling. Motivated by this experience in network dynamics, Steven became a postdoctoral research fellow at the Monterey Bay Aquarium Research Institute and later, Massachusetts Institute of Technology, where he studied microbial ecology and environmental genomics.

Steven’s current academic research intersects microbial ecology, synthetic biology and bioinformatics with specific emphasis on the creation of functional screens and computational tools that reveal hidden metabolic powers of uncultivated microbial communities. His laboratory has developed MetaPathways, a modular annotation and analysis pipeline to predict metabolic interactions from environmental sequence information. Other research areas include the use of microfluidic digital chip technology for single-cell genome sequencing and biosensor development for environmental monitoring and enzyme discovery. He was recently elected a fellow in the American Association for the Advancement of Science for distinguished contributions to the fields of environmental genomics and microbial ecology.

Dr. Hallam has filed provisional patents applications on platform screening technology for biosensor development and biorefining process improvements through his faculty position with the University of British Columbia. He recently co-founded MetaMixis, a synthetic biology company that uses this screening technology to discover and evolve small molecules and industrial catalysts from uncultivated microbial communities inhabiting natural and engineered ecosystems.

Steven is an underwater enthusiast. A former NAUI SCUBA instructor and scientific diver he has had the opportunity to ride in deep-sea submersibles exploring slow spreading centers and interact with remotely operated vehicles probing hydrocarbon seeps on continental margins.

Teaching

I have a particular interest in network and scaling relationships in biological systems. This brings me to teach about microbial genomes, pathways and communities in relation to ecosystem functions and the services that humans enjoy.

Lead Instructor, MICB425 Microbial Ecological Genomics and Genetics (2012-present)

Co-instructor, MICB405 Bioinformatics (2012-present)

Lead Instructor, SCIE113 First-Year Seminar in Science (2011)

Lead Instructor, MICB409 Microbial Genetics (2007-2010)

In addition to classroom instruction I am committed to student training across undergraduate, graduate and postgraduate levels and encourage my trainees to participate in the design and implementation of MICB425.

Graduate students supervised (17 total; 9 PhD and 8 MSc; 12 current)

Postdoctoral fellows supervised (12 total; 5 current)

Technicians, co-op, interns and undergraduates supervised (54 total; 15 current)

Directed Studies students supervised (18 total; 4 current)

Recently I became a faculty mentor for the UBC International Genetically Engineered Machine (iGEM) team. Working with the team has helped me refocus my own research program to include the paradigm of emergent or distributed metabolism in natural and engineered ecosystems.

Mentor, International Genetically Engineered Machine Team (2012-present) http://www.hallam.microbiology.ubc.ca/iGEM

Awards

2013 American Association for the Advancement of Science (AAAS) Fellow

2013 UBC Killam Teaching Prize

2010 Canadian Society for Microbiology (CSM) Fisher Scientific Early Career Award

2007 Peter Wall Institute for Advanced Studies Early Career Scholar

2007 Canadian Institute for Advanced Research (CIFAR) Fellow, Integrated Microbial Diversity

2006 Canada Research Chair in Environmental Genomics

2000 MBARI Postdoctoral Fellowship

Publications

I have been cited 3,579 times since 1995 with 2,433 of those citations occurring since 2009, resulting in a cumulative h-index of 23 and i10-index of 36. Trainees are underlined. For a complete citation index, see my Google Scholar profile page.

  1. Strachan C.R., D. VanInsberghe, R. Singh, K. Ievdokymenko, K. Budwill, W.W. Mohn, L.D. Eltis & S.J. Hallam. 2014. Metagenomic scaffolds enable combinatorial lignin transformation by Escherichia coli. PNAS. 111(28):10143–10148, doi: 10.1073/pnas.1401631111
  2. Hanson, N.W., K. M. Konwar, A. K. Hawley, T. Altman, P. Karp, and S. J. Hallam. 2014. Metabolic pathways for the whole community. BMC Bioinformatics 15:619 doi:10.1186/1471-2164-15-619
  3. Hawley, A. K., H M., Brewer, A.D. Norbeck, L. Pasa-Tolic and S. J. Hallam. 2014. Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. PNAS doi: 10.1073/pnas.1322132111
  4. Hanson, N.W., K. M. Konwar, S. Wu, and S. J. Hallam. 2014. Metapathways 2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds. Computational Intelligence in Bioinformatics and Computational Biology, 2014 IEEE Conference on. doi:10.1109/CIBCB.2014.6845516
  5. Hurwitz, B.L., S.J. Hallam* and M.B. Sullivan*. 2013. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biology. 14(11):R123 doi:10.1186/gb-2013-14-11-r123 [corresponding author (*)]
  6. Wright, J.J., K. Mewis, N. W. Hanson, K. M. Konwar, K. R. Mitchell and S. J. Hallam. 2013. A potential role for Marine Group A bacteria in the marine sulfur cycle. ISME Journal 8(2):455-468 doi:10.1038/ismej.2013.152
  7. Mewis, K., Z. Armstrong, Y.C. Song, S.A. Baldwin, S. Withers and S. J. Hallam. 2013. Biomining active cellulases from a passive mining bioremediation system, Journal of biotechnology 167(4):462-471 doi:pii: S0168-1656(13)00311-8. 10.1016/j.jbiotec.2013.07.015
  8. An D., S. M. Caffrey, J. Soh, A. Agrawal, D. Brown, K. Budwill, X. Dong, P. F. Dunfield, J. Foght, L. M. Gieg, S. J. Hallam, N. W. Hanson, Z. He, T. R. Jack, J. Klassen, K. M. Konwar, E. Kuatsjah , C. Li, S. Larter, V. Leopatra, C. L. Nesbø, T. B. Oldenburg, A. P. Page, E. Ramos-Padron, F. Rochman, A. Saidi-Mehrabad, C. W. Sensen, P. Sipahimalani, Y. C. Song , S. Wilson, G. Wolbring, G. Wong, and G. Voordouw . 2013. Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common. Environ. Sci. Technol. 47(18):10708–10717 doi:10.1021/es4020184
  9. Konwar, K. M., N. W. Hanson, A. P. Pagé, and S. J. Hallam. 2013. MetaPathways: A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information. BMC Bioinformatics 14(1):202. doi: 10.1186/1471-2105-14-202
  10. Swan B.K., B. Tupper, A. Sczyrba, F. M. Lauro, M. Martinez-Garcia, J. M. González, H. Luo, J. J. Wright, Z. C. Landry, N. W. Hanson, B. P. Thompson, N. J. Poulton, P. Schwientek, S. G. Acinas, S. J. Giovannoni, M. A. Moran, S. J. Hallam, R. Cavicchioli, T. Woyke and R. Stepanauskas. 2013. Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean. Proc. Natl. Acad. Sci. USA 110(28):11463-8. doi: 10.1073/pnas.1304246110
  11. Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson, J. Cheng, A. Darling, S. Malfatti, B. K. Swan, E. A. Gies, J. A. Dodsworth, B. P. Hedlund, G. Tsiamis, S. M. Sievert, W. Liu, J. A. Eisen, S. J. Hallam, N. C. Kyrpides, R. Stepanauskas, E. M. Rubin, P. Hugenholtz and T. Woyke. 2013. Insights into the Phylogeny and Coding Potential of Microbial Dark Matter. Nature 499(7459):431-7 doi:10.1038/nature12352
  12. Durno E., N. W. Hanson, K. M. Konwar and S. J. Hallam. 2013. Expanding the boundaries of local similarity analysis, BMC Genomics 14 Suppl 1:S3. doi: 10.1186/1471-2164-14-S1-S3
  13. Allers, E†., J. J. Wright†, K. M. Konwar, C. G. Howes, E. Beneze, S. J. Hallam* and Matthew J. Sullivan*. 2012. Diversity and population structure of Marine Group A bacteria in the oxygen minimum zone of the Northeast subarctic Pacific Ocean. ISME Journal 7(2):256-68. doi: 10.1038/ismej.2012.108 [co-first author (†), corresponding author (*)]
  14. Hartmann, M., C. G. Howes, D. VanInsberghe, H. Yu, D. Bachar, R. Christen, R. H. Nilsson, S. J. Hallam and W.W. Mohn. 2012. Significant and Persistent Impact of Timber Harvesting on Soil Microbial Communities in Northern Coniferous Forests. ISME Journal. 6:2199-2218 doi:10.1038/ismej.2012.84
  15. Leung, K., H. Zahn, T. Leaver, K. M. Konwar, N. W. Hanson, A.P. Pagé, C. Lo, P. S. Chain, S.J. Hallam, and C. L. Hansen. 2012. Programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc. Natl. Acad. Sci. USA 109(20):7665-70 doi: 10.1073/pnas.1106752109
  16. Orsi, W†., Y.C. Song†, S.J. Hallam and V. Edgcomb. 2012. Effect of Oxygen Minimum Zone Formation on Communities of Marine Protists. ISME Journal 6(8):1586-1601 doi:10.1038/ismej.2012.7
  17. Schulze-Makuch, D., S. Haque, M. Resendes de Sousa Antonio, D. Ali, R. Hosein, Y.C. Song, J. Yang, E. Zaikova, D.M. Beckles, E. Guinan, H.J. Lehtoand S.J. Hallam. 2011. Microbial life in a liquid asphalt desert, Astrobiology Apr;11(3):241-58 doi:10.1089/ast.2010.0488
  18. Zaikova, E., D. A. Walsh, C. P. Stilwell, W.W. Mohn, P. D. Tortell, and S. J. Hallam, 2010. Microbial community dynamics in a seasonally anoxic fjord: Sannich Inlet British Columbia, Environmental Microbiology, 12(1):172-91 doi: 10.1111/j.1462-2920.2009.02058.x
  19. Walsh, D. A., E. Zaikova, C. G. Howes, Y. C. Song., J.J. Wright, S. Tringe, P. D. Tortell, and S. J. Hallam, 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones, Science, 326(5952):578-82 DOI: 10.1126/science.1175309

Selected Book Chapters and Reviews

  1. Hawley, A. K., S. Kheirndish, A. Mueller, A.D. Norbeck, H. Brewer, L. Pasa-Tolic and S. J. Hallam. 2013. Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters. Meth. Enzymol. 531:305-329 doi.org/10.1016/B978-0-12-407863-5.00016-2
  2. Wright, J.J. K. Konwar, and S.J. Hallam. 2012 Microbial Ecology of Expanding Oxygen Minimum Zones. Nat. Rev. Microbiol. 10, 381-94 doi:10.1038/nrmicro2778
  3. Walsh D.A. and S.J. Hallam. 2011. Bacterial community diversity and population dynamics in a seasonally anoxic fjord: Saanich Inlet, Chapter 25:253-267 Handbook of Molecular Microbial Ecology II: Metagenomics and Complementary Approaches, Wiley-Blackwell, Ed. Frans de Bruijn
  4. Taupp, M., K. Mewis and S.J. Hallam. 2011. The art and design of functional metagenomic screens. Curr. Opin. Biotechnol. Jun;22(3):465-72, doi:10.1016/j.copbio.2011.02.010.
  5. Taupp, M., L. Constan, S.J. Hallam. 2010. The biochemistry of anaerobic methane oxidation Part 17 in the Handbook of Hydrocarbon Microbiology, doi: 10.1007/978-3-540-77587-4_63
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