Summary of 2013

During 2013, my research is still centered around the impact of antibiotic selection pressure on environmental communities from a vast range of perspectives. In addition, I have spent some time on molecular barcoding for taxonomic inferences, this year particularly focused on the Internal Transcribed Spacer (ITS) region. I have published three papers during the year; one on a software tool for use in DNA barcoding using the ITS region (ITSx), one on the BacMet database (which actually will be noted as a 2014 paper), and I have also been a co-author on a paper paving the way for better fungal systematics, related to the UNITE database. In addition, I have also published an entry in the Encyclopedia of Metagenomics on Metaxa.

It has not been an intensive conference year, although in the last months of 2013 I managed to get away to the Swedish Bioinformatics Workshop in Skövde, the 5th Next Generation Sequencing Congress in London, and the 2nd Thünen Symposium on Soil Metagenomics in Braunschweig. Especially the Soil Metagenomics Symposium was incredibly interesting and rewarding.

At the end of the year, there were some nice funding news for our group as well! We got 11.4 million SEK (~1.3 million EUR) from the Swedish Research Council over four years for a project on finding new carbapenemase genes – abbreviated NoCURE. This means a long-term collaboration with Ørjan Samuelsen in Tromsø, Norway, and it will be very nice to collaborate with him.

As I have noted previously, the finishing of certain papers can take ages. So there’s still a lot of stuff in the pipeline for 2014 (or later?), for example some more work utilizing the ITS region for fungal and eukaryotic barcoding, a paper on an updated version of Metaxa (yes, Metaxa2 is coming this spring!), some metagenomics work on marine communities, both as biofilms and plankton, and – of course – my main papers on using metagenomics to investigate antibiotic resistance (which I have now presented posters on numerous times). There’s no reason to think that 2014 won’t be an exciting year!



  • Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TT, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Senés C, Smith ME, Suija A, Taylor DE, Telleria MT, Weiß M, Larsson KH: Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, Volume 22, Issue 21 (2013), 5271–5277. doi: 10.1111/mec.12481 [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, Volume 4, Issue 10 (2013), 914–919. doi: 10.1111/2041-210X.12073 [Paper link]
  • Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DGJ: BacMet: Antibacterial Biocide and Metal Resistance Genes Database. Nucleic Acids Research, Volume 42, Issue D1 (Database issue) (2014), D737-D743. doi: 10.1093/nar/gkt1252 [Paper link]

Book chapters and similar

  • Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH: Metaxa, overview. In:Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference ( Springer-Verlag Berlin Heidelberg (2013). [Link]


  • Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Sequencing depth is central to capture the diversity of antibiotic resistance genes in the environment. 5th Next Generation Sequencing Congress, London, Great Britain, 2013.
  • Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Metagenomics Unravels the Antibiotic Resistome of Indian Soils. 2nd Thünen Symposium on Soil Metagenomics, Braunschweig, Germany, 2013.
  • Sanli K, Eriksson KM, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H: Metagenomic Analysis of Periphyton: Taxonomic and Functional Insights into Marine Biofilm Communities. Swedish Bioinformatics Workshop, Skövde, Sweden, 2013.

Conferences and workshops


  • 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 (invited talk, in Swedish)
  • Depth Matters: Sequencing depth is central to capture the diversity of antibiotic resistance genes in the environment
    Swedish Bioinformatics Workshop 2013, Skövde, Sweden, 2013-11-05

Research platforms and projects

  • MistraPharma
    MISTRA-funded project to assess risks of human pharmaceuticals in the environment
    A FORMAS-funded project to investigate co-selection of metal, biocide and antibiotic resistance
  • GoBiG
    Gothenburg Bioinformatics Group for PhD students

Other committees etc.

  • Reviewed manuscripts for PLoS ONE and Applied Microbiology and Biotechnology.

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