My name is Johan Bengtsson-Palme. I am doing research in microbiology and microbial ecology, primarily focusing on investigating antibiotic resistance and interactions in bacterial communities using metagenomics and bioinformatics. Currently, I am on a leave from my position as assistant professor at the Sahlgrenska Academy, and instead work in the Jo Handelsman lab at University of Wisconsin-Madison, studying antibiotic resistance, invasion processes in microbial communities, effects of pharmaceuticals in the environment, and molecular taxonomy. See my complete research interests here.

I did my PhD thesis for Prof. Joakim Larsson, with co-supervision by Erik Kristiansson at Chalmers University of Technology. During my PhD, I studied the effects of antibiotics in the environment, primarily using metagenomic approaches. I have also been involved in projects related to toxicology in marine environments. When I am not in Madison, Wisconsin, I reside in Gothenburg, on the Swedish west coast. To contact me, feel free to send an e-mail to my

Address during 2018:
Wisconsin Institute of Discovery, Room 3135E-2
330 North Orchard Street
Madison WI 53715

Address University of Gothenburg (not valid during 2018):
Joakim Larsson Lab, Avd. för Klinisk bakteriologi/Virologi
Guldhedsgatan 10
SE-413 46 Göteborg

Office phone (not valid through 2018):
Sahlgrenska, main number: +46 (0) 31 – 342
Followed by the office code: 46 26

– Wisconsin Institute for Discovery, University of Wisconsin-Madison
– Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
– Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg

Merits and employments
2017 – Assistant professor, Sahlgrenska Academy, University of Gothenburg
2017 – Postdoctoral Associate in the group of Prof. Jo Handelsman, Wisconsin Institute for Discovery, University of Wisconsin-Madison
2016-2017 – Postdoctoral researcher in the group of Prof. Joakim Larsson (University of Gothenburg)
2011-2016 – PhD in medicine at the Sahlgrenska Academy, University of Gothenburg
2009-2011 – MSc in systems biology at the University of Gothenburg
2006-2009 – BSc in biology at the University of Gothenburg

I have published more than 40 papers in peer-reviewed journals, which have been cited more than 2500 times. I have also released more than 10 freely available software packages. Please see “Publications” at the top-right of the page for my complete publication list. Here is a list of selected key publications:

  • Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053 [Paper link] (Editor’s choice)
  • Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P: Structure and function of the global topsoil microbiome. Nature, 560, 7717, 233–237 (2018). doi: 10.1038/s41586-018-0386-6 [Paper link]
  • Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399 [Paper link]
  • Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Souza F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. Methods in Ecology and Evolution, 4, 10, 914–919 (2013). doi: 10.1111/2041-210X.12073 [Paper link]
  • Bengtsson-Palme J: The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants – but not always. Microbiome, 6, 125 (2018). doi: 10.1186/s40168-018-0508-2 [Paper link]
  • Bengtsson-Palme J, Larsson DGJ: Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation. Environment International, 86, 140-149 (2016). doi: 10.1016/j.envint.2015.10.015 [Paper link]
  • Bengtsson-Palme J, Larsson DGJ, Kristiansson E: Using metagenomics to investigate human and environmental resistomes. Journal of Antimicrobial Chemotherapy, 72, 2690–2703 (2017). doi: 10.1093/jac/dkx199 [Paper link]
  • Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648 [Paper link]
  • Bengtsson-Palme J, Angelin M, Huss M, Kjellqvist S, Kristiansson E, Palmgren H, Larsson DGJ, Johansson A: The human gut microbiome as a transporter of antibiotic resistance genes between continents. Antimicrobial Agents and Chemotherapy, 59, 10, 6551-6560 (2015). doi: 10.1128/AAC.00933-15 [Paper link]
  • Bengtsson-Palme J, Larsson DGJ: Antibiotic resistance genes in the environment: prioritizing risks. Nature Reviews Microbiology, 13, 369 (2015). doi: 10.1038/nrmicro3399-c1 [Paper link]

Major grants

Please see this page for a complete listing of grants.

Research platform participation

  • CARe
    Centre for Antibiotic Resistance Research at University of Gothenburg (2016-)
    The database for DNA identification of fungi (2013-)
    Gothenburg Bioinformatics Network (2012-)
  • MistraPharma
    A MISTRA-funded project to assess risks of human pharmaceuticals in the environment (2011-2016)
    A FORMAS-funded project to investigate co-selection of metal, biocide and antibiotic resistance (2012-2017)
  • Ecotoxicology from Gene to Ocean (EGO)
    at the Faculty of Science, University of Gothenburg (2008-2012)
  • GoBiG
    Gothenburg Bioinformatics Group for Junior Scientists (2012-2015)

Invited talks

  • Antibiotic resistance is in the air, but what does that mean?
    The (un)recognised pathways of AMR: Air pollution and food, Healthcare Without Harm Webinar, 2017-03-28
  • Antibiotic pollution from manufacturing
    Antimicrobial resistance: the environmental impact, Healthcare Without Harm Webinar, 2016-11-03
  • Elucidating biocide and metal co-selection for antibiotic resistance in sewage treatment plants using metagenomics
    The role of metals and biocides in the selection of antibiotic resistant bacteria, Stockholm, Sweden, 2016-03-15
  • Kan läkemedelsutsläpp påverka spridningen av antibiotikaresistens i miljön? – Ledtrådar från sekvensering och metagenomik
    NGS Seminar day, Laboratoriemedicin, Sahlgrenska University Hospital, Gothenburg, Sweden, 2013-05-23
  • Identification of detoxification systems in marine environments using sequence collections from global ocean sampling.
    Open Day in Life Sciences, organized by the Faculty of Science, University of Gothenburg, 2011-05-02

Other committees etc.

  • Member of the GOTBIN organisation group, University of Gothenburg (2016-)
  • Member of the expert panel for refinement of the criteria used for procurement of medicines in Sweden (2016-2017)
  • Member of the Department Board at the Department of Cell and Molecular Biology, University of Gothenburg (2008-2010)
  • Member of the Biology Programme Committee, University of Gothenburg (2008-2011)
  • Member of the Systems Biology Programme Committee, University of Gothenburg (2009-2011)

Peer reviewing
I serve on the editorial board of Metabarcoding & Metagenomics, and have acted as reviewer for the following academic journals:

AMBIO, Annals of the New York Academy of Sciences, Applied Microbiology and Biotechnology, Biology and Fertility of Soils, Bioinformatics, BMC Bioinformatics, BMC Microbiology, Current Pollution Reports, Data, Diversity, eLife, Ecology and Evolution, Environment International, Environmental Pollution, Environmental Reviews, Environmental Science and Pollution Research, Environmental Science & Technology, FEMS Microbiology Ecology, Folia Microbiologica, GERMS, GigaScience, Journal of Antimicrobial Chemotherapy, Journal of Hazardous Materials, Journal of Herbs Spices & Medicinal Plants, Microbial Ecology, Molecular Biology and Evolution, Molecular Ecology Resources, Nature Microbiology, Nature Reviews Microbiology, Nucleic Acids Research, PeerJ, PLoS ONE, Proceedings of the National Academy of Sciences USA (PNAS); Proceedings of the Royal Society B, Processes, Proteomics, Proteomics Clinical Applications, Science of the Total Environment, Scientific Reports, Statistical Applications in Genetics and Molecular Biology, Sustainability, Trends in Microbiology, Water Research, Water Science and Technology: Water Supply

I have also reviewed grants for the following funding agencies:

  • The Irish Health Research Board (HRB)
  • The US National Science Foundation (NSF)
  • The Czech Research Council
  • The German Research Foundation, Deutsche Forschungsgemeinschaft (DFG)
  • Italian Ministry of Education, Universities and Research (Ministero dell’Istruzione dell’Università e della Ricerca)

See also my Publons profile.

Previous positions