Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Janet Jansson's Publications

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Publications (Last 5 years)

      1. Howe, A.C., J.K. Jansson, S. Malfatti, S.G. Tringe, J.M. Tiedje and C. T. Brown. 2014. Tackling soil diversity with the assembly of large, complex metagenomes. PNAS (in press).
      2. David, M.M., S. Cecillon, B.M. Warne, E. Prestat, J.K. Jansson and T.M. Vogel. 2014. Microbial ecology of chlorinated solvent biodegradation. Environmental Microbiology Reports. In press.
      3. Tas, N., E. Prestat, J. W. McFarland, K. P. Wickland, R. Knight, A. A. Berhe, T. Jorgenson, M. P. Waldrop, and J. K. Jansson. 2014. Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. The ISME Journal (in press).
      4. Mason, O.U., N. M. Scott, a. Gonzalez, A. Robbins-Pianka, J. Baelum, J. Kimbrel, N.J. Bouskill, E. Prestat, S. Borglin, D. C. Joyner, J.L. Fortney, D. Jurelevicius, W.T. Stringfellow, L. Alvarez-Cohen, T.C. Hazen, R. Knight, J.A. Gilbert and J.K. Jansson. 2014. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. The ISME Journal.
      5. Nicora, C., B. Anderson, S. Callister, A. Norbeck, S. Purvine, J. Jansson, O. Mason, D. Jurelevicius, M. David, R. Smith and M. Lipton. 2013. Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics. 13:2776-2785.
      6. Jansson, J.K. and N. Tas. 2013. Permafrost microbial ecology. Nature Microbiology Reviews (invited, in preparation).
      7. Lozupone, C.A., J. Stombaugh, A. Gonzalez, G. Ackermann, D. Wendel, Y. Vazquez-Baeza, J.K. Jansson, J.I. Gordon and R. Knight. 2013. Meta-analysis of studies of the human microbiota. Genome Research. 23:1704-1714. PMCID: PMC3787266.
      8. Jansson, J.K. 2013. Soil metagenomics. In K.E. Nelson (ed) Encylopedia of metagenomics. Article ID: 309151. Chapter ID: 701. SpringerReference. 
      9. Nicora, C., B. Anderson, S. Callister, A. Norbeck, S. Purvine, J.K. Jansson, O. Mason, D. Jurelevicius, M. David, R. Smith and M. Lipton. 2013. Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics. 13:2776-2785.
      10. Howe, A.C., J. Pell, R. Canino-Koning, R. Mackelprang, S.G. Tringe, J. Jansson, J.M. Tiedje, C.T. Brown. 2012. Preprint arXiv:1212.0159.
      11. Howe, A.C., J.K. Jansson, S.A. Malfatti, S.G. Tringe, J.M. Tiedje. C.T. Brown. 2012. Assembling large complex environmental metagenomes. Preprint arXiv:1212.2832.
      12. Lozupone, C.A., J.I. Stombaugh, J.I. Gordon, J.K. Jansson and R. Knight. 2012. Diversity stability and resilience of the human gut microbiota. Nature. 489:220-230. doi: 10.1038/nature11550. PMC3577372.
      13. Lamendella, R., N. Verberkmoes and J.K. Jansson. 2012. “Omics” of the mammalian gut – new insights into function. Current Opinion in Biotechnology. 23:1-10. 
      14. Methe, B.A., K. E. Nelson, M. Pop, H.H. Creasy, M.G. Giglio, et al. 2012. A framework for human microbiome research. Nature. 486:215-221. 
      15. Huttenhower et al., 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486:207-214. 
      16. Mason,O.U., T.C. Hazen, S. Borglin, P.S.G. Chain, E.A. Dubinsky, J.L. Fortney, J. Han, H.-Y. N. Holman, J. Hultman, R. Lamendella, R. Mackelprang, S. Malfatti, L.M. Tom, S.G. Tringe, T. Woyke, J. Zhou, E.M. Rubin and J.K. Jansson. 2012. Metagenome, metatranscriptome and single cell sequencing reveal microbial response to Deepwater Horizon oil spill. The ISME Journal. 6:1715-1727. 
      17. Erickson, A.R., B.L. Cantarel, R. Lamendella, Y. Darzi, E. F. Mongodin, C. Pan, M. Shah, J. Halfvarson, C. Tysk, B. Henrissat, J. Raes, N.C. Verberkmoes, C.M. Fraser, R.L. Hettich and J.K. Jansson. 2012. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease. PLoS One. 1212;7(11) e49138. 
      18. Baelum, J., S. Borglin, R. Chakraborty, J.L. Fortney, R. Lamendella, O.U. Mason, M. Auer, M. Zemla, M. Bill, M.E. Conrad, S.A. Malfatti, S.G. Tringe, H.-Y. Holman, T.C. Hazen and J.K. Jansson. 2012. Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environmental Microbiology. 14: 2405-2416.
      19. Knight, R., J.K. Jansson, D. Field, N. Fierer, N. Desai, J.A. Fuhrman, P. Hugenholtz, D. van der Lelie, F. Meyer, R. Stevens, M.J. Bailey, J.I. Gordon, G. A. Kowalchuk and J.A. Gilbert. 2012. Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology. 30:513-520.
      20. Graham, D.E., M.D. Wallenstein, T.A. Vishnivetskaya, M.P. Waldrop, T.J. Phelps, S.M. Pfiffner, T.C. Onstott, L.G. Whyte, E.M. Rivkina, D.A. Gilichinsky, D.A. Elias, R. Mackelprang, N.C. VerBerkmoes, R.L. Hettich, D. Wagner, S.D. Wullschleger and J.K. Jansson. 2012. Microbes in thawing permafrost: the unknown variable in the climate change equation. The ISME Journal. 6:709-712. 
      21.  Mackelprang, R., M.P. Waldrop, K.M. DeAngelis, K.L. Chavarria, S.J. Blazewicz, E.M. Rubin and J.K. Jansson. (2011) Deep metagenome sequencing illuminates permafrost response to thaw. Nature. 480:368-371. 
      22. Cantarel, B.L., A.R. Erickson, N.C. Verberkmoes. B.K. Erickson, P.A. Carey, C. Pan, M. Shah, E. F. Mongodin, J.K. Jansson, C.M. Fraser-Liggett and R.L. Hettich. 2011. Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. PLoS One. 6(11):e27173.doi:10.1371/journal.pnoe.0027173. 
      23.  Jansson, J.K. (2011) Towards "Tera-Terra": Terabase sequencing of terrestrial metagenomes. Microbe. 6:309-315.
      24. Lu, Z., Y. Deng, J. D. Van Nostrand, Z. He, J. Voordeckers, A. Zhou, Y-J. Lee, O. Mason, E. Dubinsky, K. Chavarria, L. Tom, J. Fortney, R. Lamendella, J.K. Jansson, P.D’haeselleer, T.C. Hazen and J. Zhou. 2012. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. The ISME Journal. 6:451-460.
      25. Hazen, T.C., E.A. Dubinsky, T.Z. DeSantis, G.L.Andersen, Y.M. Piceno, N. Singh, J.K. Jansson, et al. 2010. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science. 330:204-208.
      26.  Jansson, J.K., J.D. Neufeld, M.A. Moran and J.A. Gilbert. 2012. Omics for understanding microbial functional dynamics. Environmental Microbiology. 14:1-3.
      27. Chourey, K., J.K. Jansson, N. VerBerkmoes, M. Shah, K. Chavarria, L. Tom, E. Brodie and R. Hettich. 2010. A direct cellular lysis/protein extraction protocol for soil metaproteomics. Journal of Proteome Research. 9:6615-6622.
      28. Yilmaz, P., R. Kottmann, D. Field, R. Knight, J.R. Cole, L. Amaral-Zettler, J.A. Gilbert, I. Karsch-Mizrachi, A. Johnston, G. Cochrane, R. Vaughan, C. Hunter, J. Park, N. Morrison, P. Rocca-Serra, P. Ster, M. Arumugam, M. Bailey, L. Baumgartner, B.W. Birren, M.J. Blaser, V. Bonazzi, T. Booth, P. Bork, F.D. Bushman, P. L. Buttigieg, P.S.G. Chain, E. Charlson, E.K Costello, H. Huot-Creasy, P. Dawyndt, T. DeSantis, N. Fierer, J.A. Fuhrman, F.E. Gallery, D. Gevers, R.A. Gibbs, I.San Gil, A. Gonzalez, J.I. Gordon, R. Guralhnick, W. Hankeln, S. Highlander, P. Hugenholtz, J. Jansson, et al., (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29:415-420.
      29. Gilbert, J.A., F. Meyer, J. Jansson, J. Gordon, N. Pace, J. Tiedje, R. Ley, N. Fierer, D. Field, N. Krypides, F.-O. Glockner, H.P. Klenk, K.E. Wommack, E. Glass, K. Docherty, R. Gallery, R. Stevens and R. Knight. 2010. The Earth Microbiome Project: Meeting report of the 1st EMP meeting on sample selection and acquisition. Standards in Genomic Science. 3:3.
      30. Willing, B., J. Dicksved, J. Halfvarson, A. Andersson, M. Lucio, Z. Zeng, G. Jarnerot, C. Tysk, J.K. Jansson, L. Engstrand. (2010) A pyrosequencing study in twins shows that GI microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology.139:1844-1854.
      31.  Jakobsson, H., C. Jernberg, A.F. Andersson, M.Sjöland-Karlsson, J.K. Jansson and L. Engstrand. 2010. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One. 5(3):1-12(e9836).
      32. Khoruts, A., J. Dicksved, J.K. Jansson and M. J. Sadowsky. 2010. Changes in the composition of the human fecal microbiome following bacteriotherapy for recurrent Clostridium difficile-associated diarrhea.  Journal of Clinical Gastroenterology. 44:354-360.
      33. Jernberg, C., S. Lofmark, C. Edlund and J.K. Jansson. 2010. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology. 156:3216-3223.
      34. Wessen, E., K. Nyberg, J.K. Jansson and S. Hallin. 2010. Responses of bacterial and archaeal ammonia oxidizers to soil organic matter under long-term management. Applied Soil Ecology. 45:193-200.
      35. Hjort, K., M. Bergström, M. Adesina, J.K. Jansson, K. Smalla and S. Sjöling. 2010. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen suppressive soil. FEMS Microbiology Ecology 71:197-207. LBNL-2732E.
      36. Vogel, T.M., P.R. Hirsch, P. Siumonet, J.K. Jansson, J.M. Tiedje, J.D. van Elsas, R. Nalin, L. Philippot and M.J. Bailey. 2009. Advantages of the metagenomic approach for soil exploration: reply from Vogel et al. Nature Reviews Microbiology. Published on line. 
      37. Jansson, J. K., B. Willing, M. Lucio, A. Fekete, J. Dicksved, J. Halfvarson, C. Tysk, and P. Schmitt-Kopplin.2009. Metabolomics reveals metabolic biomarkers of Crohn’s disease. LBNL-2153. PLoS One. 4 (7):1-10 (e6386).
      38. Zhigang, Wu, B. Willing, J. Bjerketorp, J.K. Jansson and K. Hjort. 2009. Soft inertial microfluidics for high throughput separation of bacteria from human blood cells. Lab on a Chip. 9:1193-1199.
      39. Vogel, T.M., P. Simonet, J.K. Jansson, P.R. Hirsch, J.M. Tiedje, J.D. van Elsas, M. J. Bailey, R. Nalin L. Philippot 2009. TerraGenome: a consortium for the sequencing of a soil metagenome. Nature Reviews Microbiology.7:1
      40. Unell, M., P. E. Abraham, M. Shah, B. Zhang, C. Ruckert, N.C. VerBerkmoes and J. Jansson. 2009. Impact of phenolic substrate and growth temperature on the Arthrobacter proteome. J.Proteome Res. 8:1953-1964.
      41. Willing, B., J. Halfvarson, J. Dicksved, M. Rosenquist, G. Jarnerot, L. Engstrand, C. Tysk and J.K. Jansson. 2009. Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn’s disease. Inflammatory Bowel Diseases. 15:653-660.
      42.  Dicksved, J., M. Lindberg, M. Rosenquist, H. Enroth, J.K. Jansson and L. Engstrand. 2009. Molecular Characterization of the Stomach Microbiota in Patients With Gastric Cancer and Controls. Journal of Medical Microbiology. 58:509-516.
      43. VerBerkmoes, N.C., A.L. Russell, M. Shah, A. Godzik, M. Rosenquist, J. Halfvarson, M.G. Lefsrud, J. Apajalahti, C. Tysk, R.L.Hettich and J.K. Jansson. 2009. Shotgun metaprotomics of the human distal gut microbiota. The ISME Journal. 3:179-189.

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          Books and Book Chapters

          1. Willing, B.P. and J.K. Jansson. 2011. The Gut Microbiota: Ecology and Function. In Sadowsky, M.J. and R.L Whitman (eds) 2011. The Fecal Bacteria. ASM Press. pp.39-66.
          2. Liu, W-T. and J.K. Jansson (eds) 2009. Environmental Molecular Microbiology. Caister Academic Press. (in press)
          3. Prosser, J., J.K. Jansson and W.-T. Liu. 2010. Nucleic-acid-based characterization of community structure and function. In Liu, W-T. and J.K. Jansson (eds) Environmental Molecular Microbiology. Caister Academic Press. pp. 63-86.
          4. Dicksved, J., L. Zhao and J.K. Jansson. 2010. Human Environment. In Liu, W-T. and J.K. Jansson Environmental Molecular Microbiology. Caister Academic Press. pp 167-190.
          5. Van Elsas, J.D., J.K. Jansson and J. Trevors (eds) 2007. Modern Soil Microbiology. CRC Press, Taylor and Francis.
          6. Van Elsas, J.D., V. Torsvik, A. Hartmann, L. Øvreås and J.K. Jansson. 2007. The bacteria and archaea in soil. In. J.D. van Elsas, J.K. Jansson and J. Trevors (eds). Modern Soil Microbiology. CRC Press, Taylor and Francis pp. 83-106.
          7. Bloemberg, G.V., A. Lagopodi, F. J. De Bruijn and J.K. Jansson. 2004. Visualisation of microbes and their interactions in the rhizosphere using auto fluorescent proteins as markers. In A.D.L. Akkermans, J.D. van Elsas and F.J. de Bruijn (eds) Molecular Microbial Ecology Manual, 2nd edition. Kluwer Academic Publishers. Dordrecht, Netherlands, 6.05:1257-1280.
          8. Jansson, J.K. 2002. Antibiotic, Chromogenic, and Luminescent Markers for Bacteria. Manual of Environmental Microbiology. ASM Press, Washington, D.C. pp. 604-614.
          9. Jansson, J.K., Bailey, M. and van Elsas, J.D. (eds) 2000. Tracking Genetically Engineered Microorganisms. Biotechnology Intelligence Unit. Landes Bioscience, EUREKAH.COM. Austin, TX. 164 pages.
          10. Stoltzfus, J.R., J.K. Jansson and F.J. de Bruijn. 2000. Using green fluorescent protein (GFP) as a biomarker or bioreporter for bacteria. In J.K. Jansson, Bailey, M. and van Elsas, J.D. (eds) 2000. Tracking Genetically Modified Microorganisms. Biotechnology Intelligence Unit. R.G. Landes Company, Austin, TX. pp. 101-112.
          11. Jansson, J.K. and F.J. de Bruijn. 1999.  Biomarkers and bioreporters. In Arnold Demain and Julian Davies (eds) Manual of Industrial Microbiology and Biotechnology, 2nd Edition. ASM Press, Washington, D.C., pp.651-665.
          12. Unge, A., R. Tombolini, A. Möller, and J.K. Jansson. 1997. Optimization of GFP as a marker for detection of bacteria in environmental samples. In J.W. Hastings, L.J. Kricka and P.E. Stanley (eds) Bioluminescence and Chemiluminescence: Molecular Reporting with Photons.John Wiley & Sons, Sussex, UK. pp. 391-394.
          13. Jansson, J.K. and T. Leser. 1996. Quantitative PCR of environmental samples. In A.D.L. Akkermans, J.D. van Elsas and F.J. de Bruijn (eds) Molecular Microbial Ecology Manual. Kluwer Academic Publishers. Dordrecht, Netherlands, ch. 2.7.4.

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          Current Invited Speaker Presentations

            • Distinguished Speaker Presentations
              • Monsanto Fellows Symposium, Monsanto, Saint Louis, MO. January 7-8, 2014.
              • Francis E. Clark Distinguished Lectureship on Soil Biology. Keynote address, Soil Science Society of America International Meeting, Tampa, FL. November 3-6, 2013.
              • Frontiers in Biology Distinguished Lecture Series. Department of Biological Sciences, University of Alberta, Edmonton, CA. September 12, 2013.
              • Distinguished lecture, 8th CeBiTec Symposium, Bielefeld, Germany. October 28-30, 2013.
              • Omics of the human gut microbiome in health and Disease. Inspiring Wisdom Distinguished Lecture of State Key Laboratory of Microbial Metabolism (SKMML). Shanghai Jiao Tong University, June 3, 2013.
              • Omics analysis of the impact of thaw on permafrost microbiomes. Lectures at the Leading Edge Distinguished Lecture Series. University of Toronto. January 30, 2013.
              • Soil metagenomics – “Illumina”-tion of climate change impacts on soil microbial communities Microbial Sciences Distinguished Lecture Initiative at Harvard, MA. April 14, 2012.
              • “Illumina”tion of soil microbial community functions using metagenomics. UT/ORNL/KBRIN Bioinformatics Summit Distinguished Lecture Series. Louisville, KY. March 30-April 1, 2012
            • Keynote lectures
              • Keynote Debate "Omics": Danish Society of Microbiology. Copenhagen, Denmark. November 19, 2013.
              • Omics of the Deepwater Horizon Oil Spill. 4th International Symposium on Applied Microbiology and Molecular Biology in Oil Systems. Rio de Janiero, Brazil. August 25-28, 2013.
              • Microbial succession in thawing permafrost. Evolution and Ecology of Microbiota Workshop. University of Basel, Switzerland. September 12-14, 2012.
              • Birds Eye View Keynote lecture. 14th International Symposium on Microbial Ecology (ISME 14). Copenhagen, Denmark. August 19024, 2012.
              • Soil Metagenomics – “Illumina” tion of climate change impacts on soil microbial communities. Inauguration of Center for Permafrost (CENPERM). Copenhagen, Denmark. June 1, 2012.
            • Other seminars
              • Impact of climate change on permafrost microbial communities and processes. UC Berkeley, Plant and Microbial Biology Department seminar, November 9, 2012
              • Use of “omics” to explore the human gut microbiome, UC Davis, Invited semianr, October 31, 2012
            • Other recent invited speaker presentations
              • Next Generation Ecosystem Experiment (NGEE) in the Arctic. American Geophysicial Union’ 45h Annual Fall Meeting. San Francisco, CA, December 3-7, 2012.
              • Permafrost metagenomics. 19th International Microbial Genomes Conference. Lake Arrowhead, CA, September 16-20, 2012.
              • Impact of perturbation on the human gut microbiome. American Society of Microbiology. San Francisco, CA. June 16-19, 2012.
              • Soil metagenomics. MGM Workshop. JGI (twice yearly, Spring and Fall, 2011-2013)
              • Earth Microbiome Project. AAAS, Vancouver, CA. February 16-20, 2012.

              Invention Disclosure

              Metabolite signatures of Crohn’s disease

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