Biologist, Lab Fellow
Biological Sciences
Biologist, Lab Fellow
Biological Sciences


Janet Jansson is Chief Scientist for Biology in the Biological Sciences Division and a Laboratory Fellow at the Pacific Northwest National Laboratory (PNNL). Jansson has more than 30 years of experience in microbial ecology. Jansson earned an Soil Microbiology at Colorado State University (1983) and a Microbial Ecology at Michigan State University (1988). Jansson was a researcher in Sweden for 20 years from 1988 - 2007 and was Professor, Chair of Environmental Microbiology, and Vice Dean at the Swedish University of Agricultural Sciences prior to moving back to the United States in 2007. Before coming to PNNL in June 2014, Jansson was a senior staff scientist at Lawrence Berkeley National Laboratory (2007-2014). From 2012-2014, Jansson was an adjunct professor at the University of California, Berkeley and at the University of Copenhagen, Denmark.

Jansson's specific expertise is in the use of molecular approaches (omics) to study complex microbial communities, such as those residing in soil, sediments, and the human gut. Jansson is studying the impact of climate change on microbial communities in prairie and arctic ecosystems, including a focus on the impact of warming on permafrost soil microbiomes and drought on grassland soils. Her research also focuses on the human microbiome, including the impacts of diet, host genetics and inflammatory bowel disease on gut microbial functions.

Currently, Jansson is Co-Principal Investigator for the DOE Office of Science-funded Phenotypic Response of the Soil Microbiome to Environmental Perturbations Science Focus Area. Jansson is a Fellow of the American Academy of Microbiology and the Washington State Academy of Science. In addition, she was recently appointed by the National Academy of Science to the U.S. National Committee on Soil Sciences. She as authored ~200 publications, and is the editor of two books on molecular microbial ecology and a textbook on soil microbiology. She previously served as President of the International Society for Microbiology (ISME) and on numerous advisory panels, including the National Academy of Science Committee on Science Breakthroughs for Food and Agriculture by 2030.

Research Interest

  • Environmental microbiology
  • Molecular microbial ecology
  • Human microbiome


  • B.S. Biology & Soil Science (dual), New Mexico State University, 1980
  • M.S. Soil Microbiology, Colorado State University, 1983
  • Ph.D. Microbial Ecology, Michigan State University, 1988
  • Postdoc. Biochemistry, Stockholm University, 1991

Affiliations and Professional Service

  • President: International Society of Microbial Ecology (ISME) (2014-2016); Vice President/President elect (2012-2014)
  • Conference chair: Gordon Research Conference on Applied and Environmental Microbiology (2013; Vice Chair 2011); Co-Chair: ASM Beneficial Host-Microbe conference, San Antonio, TX (2012); Session Chair: "Permafrost Microbiology," AGU conference, San Francisco (2012); Conference chair: 10th Symposium on Bacterial Genetics and Ecology (BAGECO-10), Uppsala, Sweden (2009).
  • Co-Editor-in-Chief, The ISME Journal (2010-2012); Senior Reviews Editor (2013-present).
  • Editor, Mbio (2014-present)
  • Editorial Board member Environmental Microbiology, Current Opinion in Biotechnology, Applied and Environmental Microbiology, FEMS Microbiology Ecology, Microbiome
  • Steering Committee Member: Earth Microbiome Project (; NSF RCN TerraGenome (
  • Advisory Board Member: SciLifeLab (Sweden) > 2014
  • Invited expert to White House Roundtable on the Microbiome, Washington DC (2014)
  • Coordinator of the Swedish Network of Excellence: Uppsala Microbiomics Center (2006-2007)
  • Member of the Swedish Gene Technology Advisory Board (2000-2006)
  • Member of the Swedish Royal Academy of Sciences, National Committee for Biology (2006-2007)
  • Swedish representative for the International Union of Biological Sciences (2006-2007)
  • Coordinator of EU project: MAREP, Marker/reporter genes in Microbial Ecology with 26 partners from 11 different countries (1997-1999)

Awards and Recognitions

  • Top 1% Highly Cited Researchers in the World, Thompson Reuters (2016, 2018, 2019, 2021, 2022)

  • Committee Member: National Academy of Science’s Biological Science Panel for the Decadal Study on Biological and Physical Sciences in Space (2022 – present)

  • Recipient of Honorary Doctorate, University of Helsinki, Finland (2022)

  • Committee Member: US National Committee on Soil Sciences (2021-present)

  • President of the International Society of Microbial Ecology, ISME (2012-2013); ISME Executive Board (2010-2017)

  • Invited White House expert: Microbiome Initiative (2014–2016)

  • Scientific Advisory Board Member: SciLifeLab, Sweden (2015-present); CeMist Consortium, Denmark (2017- present); Collaborative Crop Resilience Program, CCRP, Denmark and U.S.A. (2020-present); Microbiome Insights, Canada (2015–present); Joint Genome Institute Prokaryotic Super Program (2014–present); MicrobiomeSupport, Austria, (2019-2022); SEED Health (2020-present), Applied Microbiology International (2023-present).

  • Conference Chair: Multi-Omics for Microbiomes, Richland, WA - 150 & 200 participants, respectively (2015 & 2017); Gordon Research Conference on Applied and Environmental Microbiology, Mt Holyoke, NC - 150 participants (2013); ASM Beneficial Host-Microbes Conference, San Antonio, TX - 200 participants (2012); 10th International Conference on Bacterial Genetics and Ecology (BAGECO-10), Uppsala, Sweden - 250 participants (2009); Marker/Reporter Genes in Microbial Ecology, Stockholm, Sweden - 200 participants each time (1997 & 1999).

  • Recipient of Distinguished Alumni Award, Colorado State University (2018)

  • Nature Journal’s Nominee to Science Futures Panel hosted by President of Chile (2017)

  • National Academy of Science Committee Member: Science Breakthroughs to Advance Food and Agricultural Research by 2030 (2017-2018)

  • Rubbo Orator Award, Australian Society of Microbiology (2015)

  • Senior Editor: ISME Journal (2010-2012); mSystems (2017- present)

  • Chair of the External Advisory Committee for the University of Copenhagen, Denmark (2018)

  • Laboratory Fellow, Pacific Northwest National Laboratory (2017)
  • Fellow, American Academy of Microbiology (2013)
  • Faculty 1000 (2013)
  • Distinguished Francis C. Clark Lecture, Soil Science Society of America: recognizing achievements in soil biology (2013).
  • Frequent Invited Speaker at National and International Conferences & Universities (recent examples): University of Helskinki (2022); South by Southwest (SXSW), Austin, TX (2023); American Society of Microbiology, ASM Microbe Conference, Houston, TX (2023); American Society of Plant Biologists (ASPB), Savannah, GA (2023)

  • Recent Distinguished Lectures/Keynote addresses: AAAS Cutting Edge: The Art and Science of Climate Change (May 1, 2014) Washington, DC; Novartis: Multi-omics of the gut microbiome (Oct. 29, 2014) Emeryville, CA; Argonne Soil Metagenomics Conference: Permafrost soil metagenomics (Oct. 2-3, 2014) Chicago, IL; ASM Beneficial Microbes Symposium: Multi-omics of the gut microbiome (Sept. 28-30, 2014) Boston, MA; Complex Soil Systems Conference: Untangling complexity of soil microbiomes (Sept. 4, 2014) Berkeley, CA; International Society of Microbial Ecology: Omics of the gut microbiome (Aug. 22-28, 2014) Seoul, S. Korea; Monsanto Fellows Symposium (Jan. 7-8, 2014) Saint Louis, MO; Keynote debate, Danish Society of Microbiology (Nov. 19, 2013), Copenhagen, Denmark; Frontiers in Biology Distinguished Lecture Series, Department of Biological Sciences, University of Alberta, (Sept. 12, 2013) Edmonton, Canada; Distinguished lecture, 8th CeBiTec Symposium, (Oct. 28-30, 2013) Bielefeld, Germany. Inspiring Wisdom Distinguished Lecture of State Key Laboratory of Microbial Metabolism (SKMML) (June 3, 2013) Shanghai Jiao Tong University, China; Distinguished Lecture. Microbial Sciences Initiative at Harvard, (April 14, 2012), Harvard, MA; UT/ORNL/KBRIN Bioinformatics Summit: (March 30-April 1, 2012), Louisville, KY; AAAS: Earth Microbiome Project (Feb. 16-20, 2012) Vancouver, BC.



  • Zhang Y., R.E. Komorek, Z. Zhu, Q. Huang, W. Chen, J.K. Jansson, and G.C. Jansson, et al. 2022. "Mass Spectral Imaging Showing the Plant Growth-Promoting Rhizobacteria’s Effect on the Brachypodium Awn." Biointerphases 17, no. 3:Art. No. 031006. doi:10.1116/6.0001949
  • Wu R., E.M. Bottos, V.G. Danna, J.C. Stegen, J.K. Jansson, and M.R. Davison. 2022. "RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost." mSystems. doi:10.1128/msystems.00582-22
  • Lee J., H.D. Mitchell, M.C. Burnet, R. Wu, S.C. Jenson, E.D. Merkley, J.K. Jansson and E.S. Nakayasu, et al. 2022. "Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics." Journal of Proteome Research 21, no. 8:2023–2035. doi:10.1021/acs.jproteome.2c00334
  • Wu R., C. Smith, G.W. Buchko, I.K. Blaby, A. Paez-Espino, N.C. Kyrpides, J.K. Jansson and Y. Yoshikuni, et al. 2022. "Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase." Nature Communications 13, no. 1:Art. No. 5485. doi:10.1038/s41467-022-32993-8
  • Jansson J.K., and R. Wu. 2022. "Soil Viral Diversity, Ecology and Climate Change." Nature Review Microbiology. doi:10.1038/s41579-022-00811-z
  • Wu R.,G. Trubl,N. Tas, and J.K. Jansson. 2022. “Permafrost as a potential pathogen reservoir.” One Earth 5, no. 4:351-360. doi:10.1016/j.oneear.2022.03.010
  • Shaffer J.P., L. Nothias, L.R. Thompson, J.G. Sanders, R.A. Salido, S.P. Couvillion, J.K. Jansson and A. Brejnrod, et al. 2022. "Multi-omics profiling of Earth’s biomes reveals patterns of turnover, nestedness, and co-occurrence in microbial and metabolite composition across environments." Nature Microbiology.  doi:10.1038/s41564-022-01266-x
  • McClure R.S., Y. Farris, R.E. Danczak, W.C. Nelson, H. Song, A. Kessler, J.K. Jansson and J. Lee, et al. 2022. "Interaction Networks are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes." mSystems 7, no. 5:Art. No. e00372-22. doi:10.1128/msystems.00372-22
  • Naylor D., R.S. McClure, and J.K. Jansson. 2022. "Trends in microbial community composition and function by soil depth." Microorganisms 10, no. 3:Art. No. 540. doi:10.3390/microorganisms10030540


  • Neal A.L., D. Hughes, I.M. Clark, J.K. Jansson, and P.R. Hirsch. 2021. "Microbiome Aggregated Traits and Assembly are More Sensitive to Soil Management than Diversity." mSystems
  • Boiteau R.M., L. Markillie, D.W. Hoyt, D. Hu, R.K. Chu, H.D. Mitchell, J.K. Jansson and L. Pasa-Tolic, et al. 2021. "Metabolic interactions between Brachypodium and Pseudomonas fluorescens under 1 controlled iron-limited conditions." mSystems 6, no. 1:e00580-20. doi:10.1128/mSystems.00580-20
  • McClure R.S., Y. Farris, M.R. Davison, N.C. Sadler, H. Song, R.E. Danczak, J.K. Jansson and W.C. Nelson, et al. 2021. "Interspecies Interactions During Chitin Decomposition in a Naturally Enriched Model Soil Microbial Consortium." Abstract submitted to 2021 Biological System Sciences Division Principle Investigators' Meetings-Genomic Science Program, Online, United States. 
  • Jurelevicius D., S.R. Cotta, L.F. Montezzi, A. Dias, O.U. Mason, R.C. Picao, and J.K. Jansson, et al. 2021. "Enrichment of potential pathogens in marine microbiomes with different degrees of anthropogenic activity." Environmental Pollution 268. doi:10.1016/j.envpol.2020.115757
  • Wu R., M.R. Davison, W.C. Nelson, Y. Gao, C.D. Nicora, J.E. McDermott, J.K. Jansson and K.E. Burnum-Johnson, et al. 2021. "Soil moisture impacts composition, activity and ecosystem functions of soil DNA and RNA viruses." Abstract submitted to 2021 Biological System Sciences Division Principle Investigators' Meetings-Genomic Science Program, Online, United States.
  • Song H., N.C. Sadler, J. Lee, A. Bhattacharjee, C.R. Anderton, R.S. McClure, and E. Zegeye, et al. 2021. "Prediction of Spatial Assemblies in Soil Microbiomes Governed by Interspecies Interactions and Environmental Gradients." Abstract submitted to 2021 Biological System Sciences Division Principle Investigators' Meetings-Genomic Science Program, Online, United States.
  • Zegeye E., N.C. Sadler, G.X. Lomas, I.K. Attah, J.K. Jansson, K.S. Hofmockel, and C.R. Anderton, et al. 2020. "Activity-based protein profiling of chitin catabolism." Chembiochem. doi:10.1002/cbic.202000616
  • Lipton M.S., K.K. Weitz, M.L. Smith, T.O. Metz, S.P. Couvillion, K.J. Bloodsworth, J.K. Jansson and V.L. Paurus, et al. 02/22/2021. "Unraveling the Molecular Mechanisms Underlying the Microbiome Response to Soil Rewetting." Abstract submitted to 2021 Biological System Sciences Division Principle Investigators' Meetings-Genomic Science Program, Online, United States.
  • Bhattacharjee A., C.R. Anderton, D. Velickovic, J. Richardson, O. Qafoku, L.N. Anderson, J.K. Jansson and S.P. Couvillion, et al. 02/22/2021. "Fungal Nutrient Acquisition and Transport in Soil Micromodels is Regulated by Organic Acid Chelation and Specific Membrane Transporters." Abstract submitted to 2021 Biological System Sciences Division Principle Investigators' Meetings-Genomic Science Program, Online, United States.
  • Handakumbura P., A. Rivas-Ubach, T. Varga, A. Battu, T.W. Wietsma, J.K. Jansson, and G.C. Jansson, et al. 2021. "3D Cartography of the Sorghum Rhizosphere." Abstract submitted to GSP PI Meeting (virtual), Richland, Washington. PNNL-SA-159894.
  • Couvillion S.P., D.T. Naylor, M.L. Smith, K.G. Stratton, V.L. Paurus, K.J. Bloodsworth, J.K. Jansson and Y. Farris, et al. 2021. "Significant remodeling of the soil lipidome following extreme moisture and temperature shifts." The ISME Journal. PNNL-SA-161488. [Unpublished]
  • Weitz K.K., M.L. Smith, K.K. Hixson, E.A. Hill, J.K. Jansson, K.S. Hofmockel, and M.S. Lipton. 2021. "Real-Time Mass Spectrometry Measurements of Respiration Rates in Biological Systems." Journal of the American Society for Mass Spectrometry 32, no. 3:648-652. doi:10.1021/jasms.0c00251
  • Nayfach S., S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, Jansson J.K. and D. Wu, et al. 2021. "A genomic catalog of Earth’s microbiomes." Nature Biotechnology 39, no. 4:499–509. doi:10.1038/s41587-020-0718-6
  • Wu R., M.R. Davison, Y. Gao, C.D. Nicora, J.E. McDermott, K.E. Burnum-Johnson, Jansson J.K. and K.S. Hofmockel, et al. 2021. "Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses." Communications Biology 4, no. 1:992. doi:10.1038/s42003-021-02514-2
  • Trubl G., J. Kimbrel, J. Liquet-Gonzalez, E. Nuccio, P.K. Weber, J. Pett-Ridge, and J.K. Jansson, et al. 2021. "Active virus-host interactions at sub-freezing temperatures in Arctic peat soil." Microbiome 9, no. 1:Article No. 208. doi:10.1186/s40168-021-01154-2
  • Anderson L.N., A. Bhattacharjee, O. Qafoku, J. Richardson, L.M. Bramer, D.J. Orton, J.K. Jansson and Z. Zhu, et al. 2021. "Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization Data Package DOI (KS4A-Omics1.0_FspDS682)." 
  • Wu R., M.R. Davison, W.C. Nelson, E.B. Graham, S.J. Fansler, Y. Farris, J.K. Jansson and S.L. Bell, et al. 2021. "DNA viral diversity, abundance and functional potential vary across grassland soils with a range of historical moisture regimes." mBio 12, no. 6:e02595-21. doi:10.1128/mBio.02595-21
  • Neal A.L., D. Hughes, I.M. Clark, J.K. Jansson and P.R. Hirsch. 2021. "Microbiome Aggregated Traits and Assembly are More Sensitive to Soil Management than Diversity." mSystems 6, no. 3:e01056-20. doi:10.1128/mSystems.01056-20
  • Xu C., S.P. Couvillion, R.L. Sontag, N.G. Isern, Y. Maezato, S.R. Lindemann, J.K. Jansson and T.R. Chowdhury, et al. 2021. "MetFish: A Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments." mSystems 6, no. 3:e01058-20. doi:10.1128/mSystems.01058-20
  • Weitz K.K., M.L. Smith, K.K. Hixson, E.A. Hill, J.K. Jansson, K.S. Hofmockel, and M.S. Lipton. 2021. "Real-Time Mass Spectrometry Measurements of Respiration Rates in Biological Systems." Journal of the American Society for Mass Spectrometry 32, no. 3:648-652. doi:10.1021/jasms.0c00251


  • Bradley R., B. Langley, J. Ryan, J. Phipps, D.A. Hanes, E. Stack, and J.K. Jansson, et al. 2020. "Xanthohumol Microbiome and Signature in Healthy Adults (the XMaS trial): A phase 1 triple-masked, placebo-controlled clinical trial." Trials 21. PNNL-SA-152346. doi:10.1186/s13063-020-04769-2
  • Suskind D., D. Lee, Y. Kim, G. Wahbeh, N. Singh, K. Braly, and M. Nuding, et al. 2020. "The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn’s Disease: A Randomized Diet Controlled Trial." Nutrients 12, no. 12:3749. PNNL-SA-152828. doi:10.3390/nu12123749
  • Nayfach S., S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, and D. Wu, et al. 2020. "A genomic catalog of Earth’s microbiomes." Nature Biotechnology. PNNL-SA-150672. doi:10.1038/s41587-020-0718-6. [Unpublished]
  • Weitz K.K., M.L. Smith, K.K. Hixson, E.A. Hill, J.K. Jansson, K.S. Hofmockel, and M.S. Lipton. 2020. "Real-Time Mass Spectrometry Measurements of Respiration Rates in Biological Systems." Journal for the American Society of Mass Spectrometry. PNNL-SA-154008. doi:10.1021/jasms.0c00251. [Unpublished]
  • Bhattacharjee A., A.M. Thompson, K.C. Schwarz, M.C. Burnet, Y. Kim, J. Nunez, and S.J. Fansler, et al. 2020. "Soil microbial EPS resiliency is influenced by carbon source accessibility." Soil Biology and Biochemistry 151. PNNL-SA-153321. doi:10.1016/j.soilbio.2020.108037
  • Starke R., Y. Kim, M.R. Williams, R.D. Stedtfeld, E.M. Zink, K.K. Weitz, and R.B. Crawford, et al. 2020. "Metabolomic and Proteomic Investigations on Gnotobiotic C57BL/6 Mice Colonized with Segmented Filamentous Bacteria (SFB) and Bacteroides fragilis Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin." BMC Microbiome. PNNL-SA-154406. [Unpublished]
  • Zegeye E., N.C. Sadler, G.X. Lomas, I.K. Attah, J.K. Jansson, K.S. Hofmockel, and C.R. Anderton, et al. 2020. "Activity-based protein profiling of chitin catabolism." Chembiochem. PNNL-SA-156004. doi:10.1002/cbic.202000616
  • Mao, J.-H., Y.-M. Kim, Y.-Xia Zhou, D. Hu, C. Zhong, H. Chang, C.J. Brislawn, S. Fansler, S. Langley, Y. Wang, B.Y. Loulou Peisl, S.E. Celniker, D.W. Threadgill, P. Wilmes, G. Orr, T.O. Metz, J.K. Jansson* and A.M. Snijders* (*Shared corresponding, senior authors). 2020. Genetic and metabolic links between the murine microbiome and memory. Microbiome. 8:53 /
  • Jansson, J.K. and K.S. Hofmockel. 2020. Soil microbiomes and climate change. Nature Reviews Microbiology. 18:35-46.
  • McClure, R.S., D. Naylor, Y. Farris, M. Davison, S. Fansler, K.S. Hofmockel and J.K. Jansson. 2020. Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome.  Frontiers in Microbiology. in press.
  • Bhattacharjee A., D. Velickovic, T.W. Wietsma, S.L. Bell, J.K. Jansson, K.S. Hofmockel, and C.R. Anderton. 2020. Visualizing Microbial Community Dynamics Via a Controllable Soil Environment. mSystems 5:e00645-19. PNNL-SA-147223. doi:10.1128/mSystems.00645-1902/11/2020
  • Ma B., Y. Wang, S. Ye, S. Liu7, E. Stirling, J.A. Gilbert, K. Faust, R. Knight, J.K. Jansson, C. Cardona, L. Rottjers and J. Xu. 2020. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. Microbiome. 8:82.
  • Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica. 2020. Science of the Total Environment (STOTEN) in press
  • Naylor D.T., S.J. Fansler, C.J. Brislawn, W.C. Nelson, K.S. Hofmockel, J.K. Jansson, and R.S. McClure. 2020. Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. mBIO. 11, no. 4:e01349-20. PNNL-SA-153705. doi:10.1128/mBio.01349-20
  • Naylor D.T., N.C. Sadler, A. Bhattacharjee, E.B. Graham, C.R. Anderton, R.S. McClure, and M.S. Lipton, K.S. Hofmockel and J.K. Jansson. 2020. Soil Microbiomes under Climate Change and Implications for Carbon Cycling. Annual Review of Environment and Resources.45:X-X. PNNL-SA-150059. in press.  
  • McClure R.S., J. Lee, T. Chowdhury, E.M. Bottos, R.A. White, Y. Kim, and C.D. Nicora, T.O. Metz, K.S. Hofmockel, J.K. Jansson and H.-S. Song. 2020. Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations. Scientific Reports. 10:10882. PNNL-SA-153633. doi:10.1038/s41598-020-67878-7
  • Anderson L.N., W.C. Nelson, J.E. McDermott, R. Wu, J.K. Jansson, K.S. Hofmockel, and S.L. Bell, et al. 2020. Terabase Metagenome Sequencing of Grassland Soil Microbiomes. Microbiology Resource Announcements. PNNL-SA-153752. doi:10.1128/MRA.00718-20
  • Lee J., N.C. Sadler, R.G. Egbert, C.R. Anderton, K.S. Hofmockel, J.K. Jansson, and H. Song. 2020. Deep Learning Predicts Microbial Interactions from Self-organized Spatiotemporal Patterns. Computational and Structural Biotechnology Journal. 18:1259-1269. PNNL-SA-150281. doi:10.1016/j.csbj.2020.05.023
  • Kabwe M.H., S. Vikram, K. Mulaudzi, J.K. Jansson, and T.P. Makhalanyane. 2020. The gut microbiota of rural and urban individuals is shaped by geography and lifestyle. BMC Microbiology 20:257. PNNL-SA-153154
  • Kim Y., A.M. Snijders, C.J. Brislawn, K.G. Stratton, E.M. Zink, S.J. Fansler, and T.O. Metz, J.-H. Mao and J.K. Jansson. 2019. Light-stress influences the composition of the murine gut microbiome, memory function, and plasma metabolome. Frontiers in Molecular Biosciences. 6. PNNL-SA-144001. doi:10.3389/fmolb.2019.00108


  • Xu C., S.P. Couvillion, R.L. Sontag, N.G. Isern, Y. Maezato, S.R. Lindemann, and T.R. Chowdhury, et al. 2019. "MetFish: A New Metabolomics Platform for Studying Microbial Communities in Chemically Extreme Environments." bioRxiv. PNNL-SA-132977. doi:10.1101/518647. [Unpublished]
  • Ma B., Y. Wang, S. Ye, S. Liu, E. Stirling, J.A. Gilbert, and K. Faust, et al. 2019. "Global Microbial Association Network Derived from the Earth Microbiome Project's dataset." Nature Communications. PNNL-SA-148818. [Unpublished]
  • Boiteau R.M., L. Markillie, H.D. Mitchell, D. Hu, R.K. Chu, D.W. Hoyt, and L. Pasa Tolic, et al. 2019. "Iron deficiency response of interactions between Brachypodium and rhizosphere Pseudomonas fluorescens." mSystems. PNNL-SA-147916. [Unpublished]
  • Graham E.B., A. Paez-Espino, C.J. Brislawn, R.Y. Neches, K.S. Hofmockel, R. Wu, and N.C. Kyrpides, et al. 2019. "Untapped Viral Diversity in Global Soil Metagenomes." Nature Microbiology. PNNL-SA-142148. [Unpublished]
  • Kim, Y.-M., A.M. Snijders, C.J. Brislawn, K.G. Stratton, E.M. Zink, S.J. Fansler, T.O. Metz, J.-H. Mao and J.K. Jansson. 2019. Light-stress influences the composition of the murine gut microbiome, memory function and plasma metabolome. Frontiers in Molecular Biosciences. 6 (108): 1-9. doi:10.3389/fmolb.2019.0108.
  • Cavicchioli R., W.J. Ripple, K.N. Timmis, F. Azam, L. Bakken, M. Bayliss, M. Behrenfeld, A. Boetius, P.W. Boyd, A.T. Classen, T.Crowther, R. Danovaro, C. Foreman, J. Huisman, D.A. Hutchins, J.K. Jansson, D. Karl, B. Koskella, M.D. Welch, J. Martiny, M.A. Moran, V.J. Orphan, D. Reay, J. Remais, V. Rich, B.K. Singh, L. Stein, F. Stewart, M.B. Sullivan, M. van Oppen, S.C. Weaver, E.A. Webb, N. Webster. 2019. "Scientists’ Warning to Humanity: Microorganisms and Climate Change." Nature Reviews Microbiology. doi:10.1038/s41579-019-0222-5
  • Committee Author. Science Breakthroughs to Advance Food and Agricultural Research by 2030. 2019. National Academy of Sciences.
  • Lloyd-Price J., C. Arze, A. Ananthakrishnan, M. Schirmer, J. Avila-Pacheco, T. Poon, E. Andrews, N. Ajami, K. Bonham, C.J. Brislawn, D. Casero, H. Courtney, A. Gonzalez, T. Graeber, B. Hall, K. Lake, C. Landers, H. Malick, D. Plichta, M. Prasad, G. Rahnavard, J. Sauk, D. Shungin, Y. Vazquez-Baeza, R. White III, J. Braun, T. Denson, J.K. Jansson, R. Knight, S. Kugathasan, D. McGovern, J. Petrosino, T. Stappenbeck, H.Winter, C. Clish, E. Franzosa, H. Vlamakis, R. Xavier, C. Huttenhower. 2019. "Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases." Nature 569. doi:10.1038/s41586-019-1237-9
  • Bjorkqvist O., D. Repsilber, M. Seifert, C.J. Brislawn, J.K. Jansson, L. Engstrand, I. Rangel, and J. Halfvarson. 2019. "Alterations in the relative abundance of Faecalibacterium prausnitzii correlate with changes in fecal calprotectin in patients with ileal Crohn’s disease: a longitudinal study." Scandinavian Journal of Gastroenterology 54, no. 5:557-585. doi:10.1080/00365521.2019.1599417
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  • Koeberl M., R.A. White, S. Erschen, T.F. El-Arabi, J.K. Jansson, G. Berg.  2015. Draft Genome Sequence of Paenbacillus Polymyxa Strain Mc5Re-14, an Antagonistic Root Endophyte of Matricaria chamomilla. Genome Announcements. doi:10.1128/genomeA.00861-15
  • Walters, W., E.R. Hyde, D. Berg-Lyons, G. Ackermann, G. Humphrey, A. Parada, J.A. Gilbert, J.K. Jansson, G. Caporaso, J.A. Fuhrman, A. Apprill, R. Knight. 2015. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems. doi:10.1128/mSystems.00009-15
  • Mao J.H., S.A. Langley, Y. Huang, M. Hang, K.E Bouchard, S.E. Celniker, J.B. Brown, J.K. Jansson, G.H. Karpen. A.M. Snijders. 2015. Identification of Genetic Factors that Modify Motor Performance and Body Weight Using Collaborative Cross MiceScientific Reports. doi:10.1038/srep16247
  • Hultman, J., M.P. Waldrop, R. Mackelprang, M.M. David, J. McFarland, S.J. Blazewicz, J. Harden, M.R. Turetsky, A.D. McGuire, M.B. Shah, N.C. VerBerkmoes, L.Ho Lee, K. Mavrommatis, J.K. Jansson.  2015. Multi-Omics of Permafrost, Active Layer and Thermokarst Bog Soil Microbiomes. Nature.521:208-212. doi:10.1038/nature14238.
  • Keravec, M., J. Mounier, E. Presstat, S. Vallet, J.K. Jansson, G. Burgaud, S. Rosec, S. Bouriou, G. Rault, E. Coton, G. Barbier, G. Hery-Arnaud. 2015. Insights into the Respiratory Tract Microbiota of Patients with Cystic Fibrosis During Early Pseudomonas Aeruginosa Colonization. SpringerPlus. doi:10.1186/s40064-015-1207-0
  • Koeberl, M., R.A. White III, S. Erschen, T.F. El-Arabi, H. Muller, J.K. Jansson G. Berg. 2015. Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11: A Desert Isolate with Broad-Spectrum Antagonism against Soil-Borne Phytopathogens. Genome Announcements. doi:10.1128/genomeA.00860-15
  • Lipson, D.A., T.K. Raab, M. Parker, S.T. Kelley, C.J. Brislawn, J.K. Jansson. 2015. Changes in Microbial Communities along Redox Gradients in Polygonized Arctic Soils. Environmental Microbiology Reports. doi:10.1111/1758-2229.12301
  • Carrillo-Araujo, M., N. Tas, R.J. Alcantara-Hernandez, O. Gaona, J.E. Schondube, R.A. Medellin, J.K. Jansson L.I. Falcon. 2015. Phyllostomid Bat Microbiome Composition is Associated to Host Phylogeny and Feeding Strategies. Frontiers in Microbiology. doi:10.3389/fmicb.2015.00447
  • Schostag, M., M. Stibal, C.S. Jacobsen, J. Baelum, N. Tas, B. Elberling, J.K. Jansson, P. Semenchuk, A. Prieme. 2015. Distinct Summer and Winter Bacterial Communities in the Active Layer of Svalbard Permafrost Revealed by DNA- and RNA-Based Analyses. Frontiers in Microbiology. doi:10.3389/fmicb.2015.00399

Selected Publications


  • Gilbert, J.A, J.K. Jansson, R. Knight. 2014. The Earth Microbiome Project: Successes and Aspirations. BMC Biology. doi:10.1186/s12915-014-0069-1
  • Woo, H.L., N.R. Ballor, T.C. Hazen, J.L. Fortney, B. Simmons, K. Walston Davenport, L. Goodwin, N. Ivanova, N.C. Kyrpides, K. Mavromatis, T. Woyke, J.K. Jansson, J. Kimbrel, K.M. DeAngelis. 2014. Complete Genome Sequence of the Lignin-Degrading Bacterium Klebsiella Sp. Strain BRL6-2. Standards in Genomic Sciences. doi:10.1186/1944-3277-9-19
  • Scott, N.N., M. Hess, N.J. Bouskill, O.U. Mason, J.K. Jansson, J.A. Gilbert. 2014. The Microbial Nitrogen Cycling Potential is Impacted by Polyaromatic Hydrocarbon Pollution of Marine Sediments. Frontiers in Microbiology.
  • Prestat, E., M.M. David, J. Hultman, N. Tas, R. Lamendella, J. Dvornik, R. Mackelprang, D.D. Myrold, A. Jumpponen, S. Tringe, E. Holman, K. Mavromatis, J.K. Jansson. 2014. FOAM: Functional Ontology Assignments for Metagenomes: a Hidden Markov Model (HMM) Database with Environmental Focus. Nucleic Acids Res. doi: 10.1093/nar/gku702
  • Myrold, D.D., L.H. Zeglin, J.K Jansson. 2014. The Potential of Metagenomic, and Other Omic, Approaches for Understanding Soil Microbial Processes. Soil Science. Society of America. doi:10.2136/sssaj2013.07.0287dgs
  • Hawley E.R., H. Piao, N.M. Scott, S. Malfatti, I. Pagani, M. Huntemann, A. Chen, et al. 2014. Metagenomic Analysis of Microbial Consortium from Natural Crude Oil That Seeps Into The Marine Ecosystem Offshore Southern California. Standards in Genomic Sciences. doi:10.4056/sigs.5029016
  • Mason, O.U., J. Han, T. Woyke J.K. Jansson. 2014. Single-Cell Genomics Reveals Features of a Colwellia Species that was Dominant during the Deepwater Horizon Oil Spill. Frontiers in Microbiology. doi:10.3389/fmicb.2014.00332
  • Lamendella, R., S. Borglin, R. Chakraborty, S. Strutt, N. Tas, O.U. Mason, J. Hultamn., E. Prestat, T. Hazen, J.K. Jansson. 2014. Assessment of the Deepwater Horizon Oil Spill Impact on Gulf Coast Microbial Communities. Frontiers in Microbiology. doi:10.3389/fmicb.2014.00130.
  • Kyrpides N.C., Hugenholtz P., Eisen J.A., Woyke T., Göker M., Parker C.T., Amann R., Beck B.J., Chain P.S.G., Chun J., Colwell R.R., Danchin A., Dawyndt P., Dedeurwaerdere T., DeLong E.F., Detter J.C., De Vos P., Donohue T.J., Dong X-Z, Ehrlich D.S., Fraser C., Gibbs R, Gilbert JA, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A., Lee J-S, Li W-J, Juncai M., Markowitz V., Moore E.R.B., Morrison M., Meyer F., Nelson K.E., Ohkuma M., Ouzounis C.A., Pace N., Parkhill J., Qin N., Rossello-Mora R., Sikorski J., Smith D., Sogin M., Stevens R., Stingl U., Suzuki K-I., Taylor D., Tiedje J.M., Tindall B., Wagner M., Weinstock G., Weissenbach J., White O., Wang J., Zhang L., Zhou Y-G, Field D., Whitman W.B., Garrity G.M., Klenk H-P. 2014. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. PLoS Biology. doi: 10.1371/journal.pbio.1001920.
  • David, M.M., S. Cecillon, B.M. Warne, E. Prestat, J.K. Jansson T.M. Vogel. 2014. Microbial Ecology of Chlorinated Solvent Biodegradation. Environmental Microbiology. doi:10.1111/1462-2920.12413
  • Howe, A.C., J.K. Jansson, S. Malatti, S.G. Tringe, J.M. Tiedje, C.T. Brown. 2014. Tackling Soil Diversity with the Assembly of Large, Complex Metagenomes. Proceedings of the National Academy of Science (PNAS).doi:10.1073/pnas.1402564111
  • Jansson, J.K., N. Tas. 2014. The Microbial Ecology of Permafrost. Nature Microbiology Reviews. doi:10.1038/nrmicro3262.
  • Hawley, E.R., Malfatti, S.A., Pagani, J., Huntemann, M., Chen, A., Foster, B., Copeland, A., Glavina del Rio, T., Pati, A., Jansson, J.R., Globert, J.A., Tringe S.G, Lorenson, T.D., Hess, M. Netagenomes from Two Microbial Consortia Associated with Santa Barbara Seep Oil. Marine Genomics, 18. doi.10.1016/j.margen.2014.06.003
  • Tas, N., E. Prestat, J.W. McFarland, K.P. Wickland, R. Knight, A.A. Berhe, T. Jorgenson, M.P. Waldrop, 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. doi: 10.1038/ismej.2014.36
  • 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, J.K. Jansson. 2014. Metagenomics Reveals Sediment Microbial Community Response to Deepwater Horizon Oil Spill. The ISME Journal. doi:10.1038/ismej.2013.254


  • Jansson, J.K. 2013. Microbiology: The Life Beneath our Feet. Nature. doi: 10.1038/494040a
  • Lozupone, C.A., J. Stombaugh, A. Gonzalez, G. Ackermann, D. Wendel, Y. Vazquez-Baeza, J.K. Jansson, J.I. Gordon, R. Knight. 2013. Meta-analysis of Studies of the Human Microbiota. Genome Res. doi:10.1101/gr.151803.112.
  • Jansson, J.K. 2013. Soil metagenomics. In K.E. Nelson (ed) Encylopedia of Metagenomics. Article ID: 309151. Chapter ID: 701. SpringerReference. doi: 10.1007/978-1-4614-6418-1_701-4
  • Nicora, C., B. Anderson, S. Callister, A. Norbeck, S. Purvine, J. Jansson, O. Mason, D. Jurelevicius, M. David, R. Smith. M. Lipton. 2013. Amino Acid Treatment Enhances Protein Recovery from Sediment and Soils for Metaproteomic Studies. Proteomics. doi:10.1002/pmic.201300003


  • Lozupone, C.A., J. Stombaugh, J.K. Jansson, J.I. Gordon, R. Knight. 2012. Diversity, Stability and Resilience of the Human Gut Microbiota. Nature. doi:10.1038/nature11550.
  • Lamendella, R., N. Verberkmoes, J.K. Jansson. 2012. Omics of the Mammalian Gut – New Insights into Function. Current Opinion in Biotechnology. doi:10.1016/j.copbio.2012.01.016
  • Methe, B.A., K.E. Nelson, M. Pop, H.H. Creasy, M.G. Giglio, J.K. Jansson & et al. 2012. A Framework for Human Microbiome Research. Nature. doi:10.1038/nature11209
  • Huttenhower, C., Jansson, J.K., &  et al., 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486:207-214. doi: 10.1038/nature11234
  • 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. doi: 10.1038/ismej.2012.59
  • 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. doi: 10.1371/journal.pone.0049138.
  • 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. doi: 10.1111/j.1462-2920.2012.02780.x
  • 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. doi: 10.1038/nbt.2235
  • 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. doi: 10.1038/ismej.2011.163
  • 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. doi: 10.1038/ismej.2011.91
  • 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. doi: 10.1111/j.1462-2920.2011.02518.x


  • Mackelprang, R., M.P. Waldrop, K.M. DeAngelis, K.L. Chavarria, S.J. Blazewicz, E.M. Rubin and J.K. Jansson. (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature. 480:368-371. doi:10.1038/nature10576.
  • 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.
  • Jansson, J.K. (2011) Towards Tera-Terra: Terabase sequencing of terrestrial metagenomes. Microbe. 6:309-315.
  • 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. doi: 10.1038/nbt.1823


  • 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. doi: 10.1126/science.1195979
  • 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. doi: 10.1021/pr100787q
  • 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. doi: 10.4056/aigs.1443528
  • 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. doi: 10.1053/j.gastro.2010.08.049
  • 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).  doi: 10.1371/journal.pone.0009836
  • 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. doi: 10.1097/MCG.0b013e3181c87e02.
  • 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. doi: 10.1099/mic.0.040618-0.
  • 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. doi: 10.1016/j.apsoil.2010.04.003
  • 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. doi: 10.1111/j.1574-6941.2009.00801.x


  • 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. doi: 10.1038/nrmicro2119-c3
  • 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). doi: 10.1371/journal.pone.0006386.
  • 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. doi: 10.1039/b817611f
  • 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 doi: 10.1038/nrmicro2119
  • 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. doi: 10.1021/pr800897c
  • 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. doi: 10.1002/ibd.20783.
  • 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. doi: 10.1099/jmm.0.007302-0.
  • 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. doi: 10.1038/ismej.2008.108


  • Jäderlund, L. M. Hellman, I. Sundh, M. Bailey and J.K. Jansson. 2008. Use of a novel non-antibiotic triple marker gene cassette to monitor high survival of Pseudomonas fluorescens SBW25 on winter wheat in the field. FEMS Microbiology Ecology.63:156-168. doi: 10.1111/j.1574-6941.2007.00420.x
  • Unell, M., K. Nordin, C. Jernberg, J. Stenström and J.K. Jansson. 2008. Degradation of mixtures of phenolic compounds by Arthrobacter chlorophenolicus A6. Biodegradation 19:495-505. doi: 10.1007/s10532-007-9154-2
  • Bjerketorp, J. A.N.T. Chiang, K. Hjort, M. Rosenquist, W-T. Liu and J.K. Jansson. 2008. Rapid lab-on-a-chip profiling of human gut bacteria. Journal of Microbiological Methods. 72:82-90. doi: 10.1016/j.mimet.2007.10.011
  • Jäderlund, L., V. Arthurson, U. Granhall and J.K. Jansson. 2008. Specific interactions between arbuscular mycorrhizal fungi and plant growth/promoting bacteria as revealed by different combinations. FEMS Microbiology Letters. 287:174-180. doi: 10.1111/j.1574-6968.2008.01318.x..
  • Edlund, A., F. Hårdeman, J.K. Jansson and S. Sjöling. 2008. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. Environmental Microbiology 10:2051-2063. doi: 10.1111/j.1462-2920.2008.01624.x
  • Edlund, A. and J.K. Jansson. 2008. Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phananthrene-enriched polluted Baltic Sea sediments. FEMS Microbiology Ecology. 65:513-525.  doi: 10.1111/j.1574-6941.2008.00513.x
  • Van Elsas, J.D., J. Jansson, S. Sjoling, M. Bailey, R. Nalin, T. Vogel, R. Costa and L.V. Overbeek. 2008.The soil metagenome–a recalcitrant, yet explorable goldmine for gene hunters. Trends in Biotech.26:591-691.
  • Dicksved, J., J. Halfvarson, M. Rosenquist, G. Järnerot, C. Tysk, J. Apajalahti, L. Engstrand and J.K. Jansson. 2008. Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. The ISME Journal .2:716-727. doi: 10.1038/ismej.2008.37


  • Jernberg, C., S. Löfmark, C. Edlund and J.K. Jansson. 2007. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME Journal.1:56-66. doi: 10.1038/ismej.2007.3.
  • Steger, K., Å.M. Sjögren, Å. Jarvis, J.K. Jansson and I. Sundh. 2007. Development of compost maturity and Actinobacteria populations during full-scale composting of organic household waste. Journal of Applied Microbiology.103:487-498. doi: 10.1111/j.1365-2672.2006.03271.x
  • Hjort, K., A. Lembke, A. Speksnijder, K. Smalla and J.K. Jansson. 2007. Community structure of actively growing bacterial populations in plant pathogen suppressive soil. Microbial Ecology. 53:399-413. doi: 10.1007/s00248-006-9120-2
  • Dicksved, J., H. Flöistrup, A. Bergström, M. Rosenquist, G. Pershagen, A. Scheynius, S. Roos, J.S. Alm, L. Engstrand, C. Braun-Fahrländer, E. von Mutius and J.K. Jansson. 2007. Molecular fingerprinting of the fecal microbiota of children raised according to different lifestyles. Applied and Environmental Microbiology. 73:2284-2289. doi: 10.1128/AEM.02223-06.
  • Unell, M., N. Kabelitz, J. Jansson and H. Heipieper. 2007. Adaptation of the psychrotroph Arthrobacter chlorophenolicus A6 to growth temperature and the presence of phenols by changes in the anteiso/iso ration of branched fatty acids. FEMS Microbiology Letters. 266:138-143. doi: 10.1111/j.1574-6968.2006.00502.x


  • Toljander, J., V. Artursson, L.R. Paul, J.K. Jansson and R.D. Finlay. 2006. Attachment of different soil bacteria to arbuscular mycorrhizal fungal extraradical hyphae is determined by hyphal vitality and fungal species. FEMS Microbiology Letters. 254:34-40. doi: 10.1111/j.1574-6968.2005.00003.x
  • Lofmark, S., C. Jernberg, J. Jansson and C. Edlund. 2006. Clindamycin induced enrichment and long term persistence of resistant Bacteroides spp. and resistance genes. Journal of Antimicrobial Chemotherapy. 58:1160-1167. doi: 10.1093/jac/dkl420.
  • Edlund, A., T. Soule, S. Sjöling and J.K. Jansson. 2006. Microbial community structure in Baltic Sea sediment along a pollution gradient. Environmental Microbiology. 8:223-232. doi: 10.1111/j.1462-2920.2005.00887.x
  • Edlund, A. and J.K. Jansson. 2006. Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments. Applied and Environmental Microbiology 72:6800-6807. doi: 10.1128/AEM.00971-06
  • Bjerketorp, J., S. Håkansson, S. Belkin and J.K. Jansson. 2006. Advances in preservation methods: how to keep microbial biosensors alive and active? Current Opinion in Biotechnology. 17:43-49. doi: 10.1016/j.copbio.2005.12.005
  • Artursson, V. R. Finlay and J.K. Jansson. 2006. Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth. Environmental Microbiology. 8:1-10. doi: 10.1111/j.1462-2920.2005.00942.x


  • Nordin, K., M. Unell and J.K. Jansson. 2005. A novel 4-chlorophenol degradation gene cluster and degradation route via hydroxyquinol in Arthrobacter chlorophenolicus A6. Applied and Environmental Microbiology 71:6538-6544. doi: 10.1128/AEM.71.11.6538-6544.2005
  • Von der Weid, I., V. Artursson, L. Seldin and J.K. Jansson. 2005. Antifungal and root surface colonization properties of GFP-tagged Paenibacillus bransilensis PB177. World Journal of Microbiology and Biotechnology 12:1589-1595. doi:10.1007/s11274-005-8123-3
  • Jernberg, C., Å. Sullivan, C. Edlund and J.K. Jansson. 2005. Monitoring antibiotic induced alterations in the human intestinal microflora and detection of probiotic strains by the use of T-RFLP. Applied and Environmental Microbiology. 71:501-506. doi: 10.1128/AEM.71.1.501-506.2005.
  • Artursson, V., R.D. Finlay and J.K. Jansson. 2005. Combined bromodeoxyuridine immunocapture and terminal restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation of plant species.  Environmental Microbiology. 7:1952-1956.


  • Lu, Z., R. Tombolini, S. Woo, S. Zeilinger, M. Lorito and J.K. Jansson. 2004. In vivo study of Trichoderma-pathogen-plant interactions with constitutive and inducible GFP reporter systems. Applied and Environmental Microbiology. 70:3073-3081. doi: 10.1128/AEM.70.5.3073-3081.2004
  • Maraha, N., A. Backman and J.K. Jansson. 2004. Monitoring physiological status of GFP-tagged Pseudomonas fluorescens SBW25 under different nutrient conditions and in soil by flow cytometry. FEMS Microbiology Ecology 51:123-132. doi: 10.1016/j.femsec.2004.07.007
  • Backman, A., N. Maraha and J.K. Jansson. 2004. Impact of temperature on the physiological status of a potential bioremediation inoculant, Arthrobacter chlorophenolicus A6. Applied and Environmental Microbiology. 70:2952-2958. doi: 10.1128/AEM.70.5.2952-2958.2004
  • Backman, A. and J.K. Jansson. 2004. Degradation of 4-chlorophenol at low temperature and during extreme temperature fluctuations by Arthrobacter chlorophenolicus A6. Microbial Ecology. 48:246-253. doi: 10.1007/s00248-003-2026-3


  • Jansson, J.K. 2003. Marker and reporter genes: illuminating tools for environmental microbiologists. Current Opinion in Microbiology. 6:310-316. doi: 10.1016/j.mib.2003.09.011
  • Artursson, V. and J.K. Jansson. 2003. Use of Bromodeoxyuridine Immunocapture to Identify Active Bacteria Associated with Arbuscular Mycorrhizal Hyphae. Applied and Environmental Microbiology.69:6208-6215. Editor’s choice: Science. 2003. 302:1117. doi: 10.1128/AEM.69.10.6208-6215.2003


  • Jernberg, C. and J.K. Jansson. 2002. Impact of genetically modified Arthrobacter chlorophenolicus inoculum on soil microbial community structure during bioremediation of 4-chlorophenol contaminated soil. FEMS Microbiology Ecology.42:387-397. doi: 10.1111/j.1574-6941.2002.tb01028.x


  • Unge, A. and J.K. Jansson. 2001. Monitoring population size, activity and distribution of gfp/luxAB-tagged Pseudomonas fluorescens SBW25 during colonisation of wheat. Microbial Ecology. 41: 290-300. doi:10.1007/s002480000047
  • Elväng, A. M., C. Jernberg, K.  Westerberg and J.K. Jansson. 2001. Monitoring bioremediation of 4-chlorophenol-contaminated soil using gfp or luc-tagged Arthrobacter chlorophenolicus A6. Environmental Microbiology. 3:1-12.
  • Räsänen, L.A., A.M. Elväng, J.K. Jansson and K. Lindström. 2001. Effect of heat stress on the cell activity and cell morphology of tropical rhizobia Sinorhizobium arboris cells. FEMS Microbiology Ecology 34:267-278. doi: 10.1111/j.1574-6941.2001.tb00777.x


  • Jansson, J.K., K. Björklof, A. Möller  and K. Jörgensen. 2000. Biomarkers for monitoring efficacy of bioremediation by inoculants. Environmental Pollution.107:217-223. doi: 10.1016/S0269-7491(99)00140-2
  • Lowder, M., A. Unge, N. Maraha, J.K. Jansson, J. Swiggett and J.D. Oliver. 2000. Effect of starvation and the viable-but nonculturable state on green fluorescent protein (GFP) fluorescence in GFP-tagged Pseudomonas fluorescens A506. Applied and Environmental Microbiology. 66:3160-3165. doi: 10.1128/AEM.66.8.3160-3165.2000
  • Westerberg, K., A. M. Elväng, E. Stackebrandt and J.K. Jansson. 2000. Arthrobacter chlorophenolicus sp. nov., a new species capable of degrading high concentrations of 4-chlorophenol. International Journal of Systematic and Evolutionary Microbiology. 50:2083-2092. doi: 10.1099/00207713-50-6-2083
  • Jansson, J.K., S. Molin and M. Romantschuk. 2000. Test methods for monitoring genetically modified microorganisms (GMMs) in nature. Nordtest technical report 455, 23 p. NT Project number: 1473-99.


  • Westerberg, K., C. Jernberg, A. M. Elväng and J.K. Jansson. 2001. Arthrobacter chlorophenolicus A6: the complete story of a 4-chlorophenol degrading bacterium. Proceedings of the Sixth International In Situ and On-Site Bioremediation Symposium. San Diego, CA, Battelle Press.


  • Tombolini, R., D.J. Van der Gaag, B. Gerhardson and J.K. Jansson. 1999. Colonization pattern and in situ visualization of the biocontrol strain, Pseudomonas chlororaphis MA342 during early stages of barley seed germination. Applied and Environmental Microbiology. 65:3674-3680.
  • Unge, A., R. Tombolini, L. Molbak and J.K. Jansson. 1999. Simultaneous Monitoring of Cell Number and Metabolic Activity of Specific Bacterial Populations with a Dualgfp-luxAB Marker System. Applied and Environmental Microbiology 65:813-821.


  • Moller A. and J.K. Jansson. 1998. Detecttion of firefly luciferase tagged bacteria in environmental samples. Methods in Molecular Biology. 102:269-283.


  • Moller, A., and J.K. Jansson. 1997. Quantification of genetically–tagged cyanobacteria in Baltic Sea sediment by competitive PCR. BioTechniques. 22:512-518.
  • Tombolini, R., A. Unge, M.E. Davey, F.J. de Bruijn and J.K. Jansson. 1997. Flow cytometric and microscopic analyses of GFP-tagged Pseudomonas fluorescens. FEMS Microbiology Ecology 22:117-28. doi: 10.1016/S0168-6496(96)00068-2
  • Jansson, J.K. and J. Prosser. 1997. Quantification of the presence and activity of specific microorganisms in nature. Molecular Biotechnology 7:103-120.
  • Brostedt, E., A. Lindblad, J. Jansson and S. Nordlund. 1997. Electron transport to nitrogenase in Rhodospirillum rubrum: the role of NAD(P)H as electron donor and the effect of fluoroacetate on nitrogenase activity. FEMS Microbiol. Letters. 150: 263-267. doi: 10.1016/S0378-1097(97)00127-4


  • Lindblad, A., J.K. Jansson, E. Brostedt, M. Johansson, U. Hellman and S. Nordlund. 1996. Sequence and partial characterization of a nifJ gene in the photosynthetic bacterium, Rhodospirillum rubrum. Molecular Microbiology. 20:559-568.


  • Moller, A., A.M. Norrby, K. Gustafsson and J.K. Jansson. 1995. Luminometry and PCR-based monitoring of genetically modified cyanobacteria in Baltic Sea microcosms. FEMS Letters. 129:43-50. 10.1111/j.1574-6968.1995.tb07555.x
  • Jansson, J.K. 1995. Tracking genetically engineered microorganisms in nature. Current Opinion in Biotechnology. 6:275-283. 10.1016/0958-1669(95)80048-4


  • Moller, A., K. Gustafsson and J.K. Jansson. 1994. Specific monitoring by PCR amplification and bioluminescence of Firefly luciferase gene-tagged bacteria added to environmental samples. FEMS Microbiology Ecology 15:92-106.


  • Gustafsson, K., and J.K. Jansson. 1993. Ecological risk assessment of the deliberate release of genetically modified microorganisms. Ambio. 22:236-242.


  • Tiedje, J.M., J.K. Jansson, W.W. Mohn, W.E. Holbena nd J.F. Quensen, III. 1991. Biotechnology for biodegradation: Reductive dechlorination and nucleic acid probe tracking methods. In L. Gololeva (ed) Microbial Biodegradation of Xenobiotics. UNEP Training Course. United Nations Environmetal Programme, USSR Commission for UNEP, USSR Academy of Sciences. Pushchino, Moscow, USSR, pp. 84-106.


  • Jansson, J.K., W.E. Holben, and J.M. Tiedje. 1989. Detection in soil of a deletion in an engineered DNA sequence by using DNA probes. Applied and Environmental Microbiology. 55:3022-3025.


  • Holben, W.E., J.K. Jansson, B.K. Chelm, and J.M. Tiedje. 1988. DNA probes method for the detection of specific miocroorganisms in the soil bacterial community. Applied and Environmental Microbiology. 54:703-711.


  1. Liu, W-T. and J.K. Jansson (eds) 2010. Environmental Molecular Microbiology. Caister Academic Press.
  2. Van Elsas, J.D., J.K. Jansson and J. Trevors (eds) 2007. Modern Soil Microbiology. CRC Press, Taylor and Francis.
  3. 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.

Book chapters

  1. Lozada M., H.M. Dionisi, F.J. Espinola, P.A. Calderoli, M.A. Musumeci, J.A. Gonzalez, and J.A. Lopez, et al. 2019. "Contribution of Metagenomics to our Understanding of Microbial Processes in Antarctic and Sub-Antarctic Coastal Sediments." In Microbial Ecology: Current Advances from Genomics, Metagenomics and Other Omics, edited by Diana Marco. 64-106. doi:10.21775/9781912530021.05
  2. van Elsas J.D., A. Hartmann, M. Schloter, J.T. Trevors, and J.K. Jansson. 2019. "The Bacteria and Archaea in Soil." In Modern Soil Microbiology, Third Edition, edited by Jan Dirk van Elsas, Jack T. Trevors, Alexandre Soares, Paolo Nannipieri. 49 - 64. Boca Raton, Florida:CRC Press Taylor & Francis Group. ISBN: 9781498763530.
  3. Jansson, J.K. Soil Metagenomics. 2012. In K. Nelson (ed). Encyclopedia of Metagenomics.
  4. Jansson, J.K. 2011. Microbiota and inflammatory bowel disease. In Finlay, B. (ed.), Microbiota: Agents for Health and Disease, The Biomedical & Life Sciences Collection, Henry Steward Talks Ltd. London (online at
  5. Willing, B.P. and J.K. Jansson. 2011. The Gut Microbiota: Ecology and Function. In Sadowsky, M.J. and R.L Whitman (eds). The Fecal Bacteria. ASM Press. Pp.39-66.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Jansson, J.K. 2002. Antibiotic, Chromogenic, and Luminescent Markers for Bacteria. Manual of Environmental Microbiology. ASM Press, Washington, D.C. pp. 604-614.
  11. 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.
  12. 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.
  13. 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.
  14. Unge, A., R. Tomboliini, M.E. DAvey, J.F. de Bruijn and J.K. Jansson. 1997. GFP as a marker gene. In A.D.. Akkermans, J.D. van Elsas and F.J. de Bruijn (eds) Molecular Microbial Ecology Manual. Kluwer Academic Publishers. Dordrecht, The Netherlands.
  15. Tombolini, R. and J.K. Jansson. 1997. Monitoring of GFP tagged bacterial cells. In R. LaRossa (ed) Bioluminescent Protocols. Methods in Molecular Biology. Human Press. doi: 10.1385/0-89603-520-4:285
  16. Moller A. and J.K. Jansson. 1997. Detection of Firefly luciferase-tagged bacteria in environmental samples. In R. LaRossa (ed) Bioluminescent Protocols. Methods in Molecular Biology. Human Press.
  17. 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.

Popular scientific articles and Reports

  • Jansson, J.K. 2003. Chapter 8. Bakterier-hot och möjligheter. In. Genklippet? Risker och möjligheter med den nya biologin. FORMAS, Sweden.
  • de Bruijn, F.J.,  M. Givskov, A. Glover, P. Hill, J.K. Jansson, M. Karp, S. Molin, O. Nybroe, J. Oliver, A. Palomares, J. Prosser, M. Romantschuk, W. Selbitschka, D. Springael, C. Tebbe, V. Torsvik,J. Vanderleyden and J.D. Van Elsas. 2001. Monitoring methods for specific microorganisms and microbial communities in nature. An opinion. J.K. Jansson (ed) European Commission Biotechnology Programme, DGXII.
  • Jansson, J.K., S. Molin and M. Romantschuk. 2000. Test methods for monitoring genetically modified microorganisms (GMMs) in nature. Nordtest Tech. Report 455.
  • Bailey, M., P. Corbisier, A. Glover, P. Hill, J.K. Jansson, K. Killham,S. Lindow, S. Molin, J. Oliver, J. Prosser, A. Palomares, C. Tebbe, J.D. Van Elsas. 2000. Reporter genes for monitoring microbial cell activity and/or the environment. An opinion. J.K. Jansson (ed) European Commission Biotechnology Programme, DGXII.
  • Jansson, J.K. and H. Kruse. 1997. The use of antibiotic resistance genes as marker genes in genetically modified organisms. Norwegian Pollution Control Authority Report 97:03.
  • Nytt Liv i Vår Herres Hage (New Life in Our Lord’s Garden). 1993. Written by the science journalist, Peter Sylvan, in collaboration with J.K. Jansson. Royal Swedish Academy of Science.