Summary of 2018

This was a very different year. In January, the entire family made the move to Madison, Wisconsin, where I spent my working hours as a postdoctoral associate in the Jo Handelsman lab. Moving this far with a newborn and a soon-four-year-old was not without hiccups, but I think we did remarkably well overall, and Madison will be dearly missed by all of us, I think. The stay in the U.S. has given us new friends, perspectives and whole new understanding of American society (and the mid-western kindness!) I am deeply thankful to Jo and her lab for making the stay in Madison so fantastic!

From a publication point of view, this year has been exceptional. Twelve new papers with my name on them saw the light of day this year. It started off with the paper resulting from the fungal annotation workshop in Aberdeen in April 2017, and the paper coming out of the JPIAMR workshop on environmental antibiotic resistance in Gothenburg in the fall of 2017. In addition, some of the longer running projects finally came out this year; Nadine’s paper on ciprofloxacin selective concentrations in microbial communities and our description of the structure of a new sialic acid symporter both came out in the spring, as well as our big paper describing the Metaxa2 Database Builder.

In the summer, I also published a paper entirely on my own, describing the degree to which the diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants (it works, but not always!) And close to that paper in time, Mohammad Bahram and his colleagues managed to get their big topsoil microbiome survey (in which I played part) in Nature. Kudos to Mohammad and the rest of the team for that big achievement!

By the end of the year, we published a paper on the new version of the UNITE database, a paper on breast milk and infant gut microbiota, and the the introduction of a new type of ribosomal tandem repeat barcoding for fungi.

Since the family went with me to the U.S., I cut down on travel this year to focus on my postdoctoral work. We did go to Canada for vacation though.

Before the end of the year, I got (in competition) offered four years of faculty funding and a starting grant for my new lab from the Sahlgrenska Academy at the University of Gothenburg, starting some time in 2019. This will be a great and exciting starting point to continue my academic career in Sweden when I get back from the U.S.! I look forward to this (and some parental leave with my son) in 2019!

Publications

Papers

  • Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J-Y, Naas T, O’Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7, 459 (2018). doi: 10.12688/f1000research.14509.2 [Paper link]
  • Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K: The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47, D1, D259–D264 (2019). doi: 10.1093/nar/gky1022 [Paper link]
  • Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DGJ, Rautava S, Isolauri E, Salminen S, Kumar H, Satokari R, Virta M: Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nature Communications, 9, 3891 (2018). doi: 10.1038/s41467-018-06393-w [Paper link]
  • Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH: Introducing ribosomal tandem repeat barcoding for fungi. Molecular Ecology Resources, 19, 1, 118–127 (2019). doi: 10.1111/1755-0998.12944 [Paper link]
  • 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: 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]
  • Richardson RT, Bengtsson-Palme J, Gardiner MM, Johnson RM: A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data. PeerJ, 6, e5126 (2018). doi: 10.7717/peerj.5126 [Paper link]
  • Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH: Metaxa2 Database Builder: Enabling taxonomic identification from metagenomic and metabarcoding data using any genetic marker. Bioinformatics, 34, 23, 4027–4033 (2018). doi: 10.1093/bioinformatics/bty482 [Paper link]
  • Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach C-F, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Ploy M-C, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel A, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson A-S: Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environment International, 117, 132–138 (2018). doi: 10.1016/j.envint.2018.04.041 [Paper link]
  • Wahlgren WY°, North RA°, Dunevall E°, Paz A, Scalise M, Bisognano P, Bengtsson-Palme J, Goyal P, Claesson E, Caing-Carlsson R, Andersson R, Beis K, Nilsson U, Farewell A, Pochini L, Indiveri C, Grabe M, Dobson RCJ, Abramson J, Ramaswamy S, Friemann R: Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a novel Na+ site. Nature Communications, 9, 1753 (2018). doi: 10.1038/s41467-018-04045-7 [Paper link]
  • Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach C-F, Larsson DGJ: Selective concentration for ciprofloxacin in Escherichia coli grown in complex aquatic bacterial biofilms. Environment International, 116, 255–268 (2018). doi: 10.1016/j.envint.2018.04.029 [Paper link]
  • Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršenaite R, Martin-Sánchez PM, Meyer W, Oh S-O, Sampaio JP, Seifert KA, Sklenár F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg J, Wurzbacher C, Van den Wyngaert S, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K: Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from an April 10-11, 2017 workshop (Aberdeen, UK). MycoKeys, 28, 65–82 (2018). doi: 10.3897/mycokeys.28.20887 [Paper link]
  • 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] (Published in 2017, but noted as a 2018 paper)
  • Bengtsson-Palme J°, Gunnarsson L°, Larsson DGJ: Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing? Journal of Cleaner Production, 171, 137–146 (2018). doi: 10.1016/j.jclepro.2017.09.247 [Paper link] (Published in 2017, but noted as a 2018 paper)
  • Bengtsson-Palme J, Larsson DGJ: Protection goals must guide risk assessment for antibiotics. Environment International, 111, 352–353 (2018). doi: 10.1016/j.envint.2017.10.019 [Paper link] (Published in 2017, but noted as a 2018 paper)

Book chapters

  • Bengtsson-Palme J: Assessment and management of risks associated with antibiotic resistance in the environment. In: Roig B, Weiss K, Thoreau V (Eds.) Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment, 243–263. Elsevier, UK (2019). doi: 10.1016/B978-0-12-813290-6.00010-X [Paper link]

Posters

  • Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DGJ, Rautava S, Isolauri E, Salminen S, Kumar H, Satokari R, Virta M: Maternal gut and breast milk microbiota affect the infant gut antibiotic resistome and mobilome. ISME16 Conference, Leipzig, Germany, 2018.
  • Bengtsson-Palme J: The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants – but not always. WID Symposium, Madison, WI, USA, 2018.
  • Garavito MF, Hurley A, Li C, Bengtsson-Palme J, Juang DC, Heinritz JR, Lozano GL, Jona O, Meinholz K, Beebe D, Handelsman J: Dynamics and interactions within a multi-phylum model biofilm community. Madison Microbiome Meeting, Madison, WI, USA, 2018.

Conferences and workshops

  • Madison Microbiome Meeting
    in Madison, Wisconsin, USA (poster)
  • WID Symposium
    in Madison, Wisconsin, USA (poster)

Research platforms and projects

  • CARe
    Centre for Antibiotic Resistance Research at University of Gothenburg
  • UNITE
    The database for DNA identification of fungi

Other committees etc.

  • Member of the expert panel for refinement of the criteria used for procurement of medicines in Sweden
  • Member of the JRC external expert group for implementation of NGS in the coordinated action plan against antimicrobial resistance
  • Reviewed manuscripts for Bioinformatics, Science of the Total Environment, Environmental Science & Technology, Ecology & Evolution, PeerJ, Scientific Reports, Environmental Reviews, Trends in Microbiology, PLoS ONE, Nature Microbiology, Environmental Pollution, Annals of the New York Academy of Sciences, Environmental Science and Pollution Research, Biology and Fertility of Soils, Sustainability, Journal of Hazardous Materials, Proceedings of the National Academy of Science (PNAS), Ecological Applications, Nature Springer Books, BMC Microbiology, Environment International, Environmental Microbiology, and Pathogens
  • Reviewed grant applications for the US National Science Foundation (NSF), the Czech research council, and Deutsche Forschungsgemeinschaft (DFG)