Summary of 2015

During the first half of 2015, I spent most of my time taking care of our daughter who turned one this spring. Working 20% for about six months has taught me that 1) working 20% in academia is generally not possible and is therefore a bad idea; 2) supporting three different software packages while working 20% is even less possible; and 3) parental leave is fantastic. Thanks to patient, productive co-workers, and an understanding family, it has still been possible to both publish some papers and supervise a master student.

This year have seen the publication of several important papers in which I have been involved. First, in February, the paper describing the Metaxa2 software was published, after a rather length review process. This paper not only describes an important update to the Metaxa software, but also shows that Metaxa2 outperforms other commonly used tools for community analysis based on shotgun metagenomic sequence data. Judging from the number of questions I have received about the Metaxa2 software, I think it has been quite well received in the community. Particularly, I got a very nice e-mail from Australia, which essentially only contained a “thank you” for the software; an e-mail that certainly made my day!

In March, two papers in which I played a minor role came out. One described the European technical report for aquatic monitoring, to which I wrote the parts on metagenomics and sequencing. The other described the ITS chimera control reference dataset now deposited in the UNITE database.

Late December 2014, José Martínez, Teresa Coque and Fernando Baquero published an opinion paper in Nature Reviews Microbiology on ranking the risks associated with antibiotic resistance gene findings in metagenomes. Although myself and Joakim Larsson thought this was a rather good paper, we disagreed on the relative risk rankings and therefore wrote a response letter to Nature Reviews Microbiology, which was published in April. In our response we outlined that the potentially disastrous consequences that transfer of previously unknown resistance determinants from the environmental resistome to pathogens could have are often under-appreciated. We also stressed that the abundances of resistance genes, and not only their presence, should be accounted for when estimating risks.

In August, we published our findings that travel does not only contribute to the spread of ESBL resistant bacteria, but also to dissemination of a range of other resistance genes. Although this has been suspected for quite some time, the scope of resistance carrying in healthy individuals has been unknown. The study generated quite a bit of buzz, and we were interviewed both on Swedish national news, and on a local radio program where I got to speak at length about the issue. The paper was also discussed a lot on Twitter.

Towards the end of the year two more papers got published. The first described the metagenomes of marine periphyton communities, a project that started off as my master thesis in 2010. The second described the co-selection potential between resistance genes against antibiotics, biocides and metals, based on data from fully sequenced bacterial genomes and plasmids.

My most important contribution this year, however, may be the paper published most recently, in which we predict concentrations of antibiotics that would not be selective for antibiotic resistance. The paper provides upper boundaries for selective concentrations (MSCs) for 111 different antibiotics and predicts the no effect concentrations (PNECs) for resistance selection. We intend the paper to be used as guidance for implementation of compound-specific emission limits, and hope that the data will be of great use in environmental risk assessments, in efforts by industries, regulatory agencies or purchasers of medicines to define acceptable environmental emissions of antibiotics, in the implementation of environmental monitoring programs, for directing mitigations, and for prioritizing future studies on environmental antibiotic resistance.

Papers aside, I also released additional software to the community: the Metaxa2 Diversity Tools included with Metaxa2 version 2.1 and later, and the FARAO genomics visualization toolkit. I went to two conferences this year; the EDAR3 conference in Germany, and the Swedish Bioinformatics Workshop in Stockholm. Both were truly great events, and I already look forward to the next iterations of them!

So, what will happen in 2016? Well, I have two papers in revision – one on experimentally determined minimal selective concentrations that relates nicely to my last paper published in 2015; and one on the Helicobacter pylori in vivo (meta-)transcriptome. Late this spring I will defend my PhD thesis, so much of my focus is at finishing the thesis at the moment. There are rumors that Michael Gillings will pay a visit to Gothenburg, which would be awesome. Finally, there’s a large bunch of papers waiting to be finished, so there are many reasons to believe that 2016 will be an exciting and productive year!

Publications

Papers

  • 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]
  • Wernersson A-S, Carere M, Maggi C, Tusil P, Soldan P, James A, Sanchez W, Dulio V, Broeg K, Reifferscheid G, Buchinger S, Maas H, Van Der Grinten E, O’Toole S, Ausili A, Manfra L, Marziali L, Polesello S, Lacchetti I, Mancini L, Lilja K, Linderoth M, Lundeberg T, Fjällborg B, Porsbring T, Larsson DGJ, Bengtsson-Palme J, Förlin L, Kienle C, Kunz P, Vermeirssen E, Werner I, Robinson CD, Lyons B, Katsiadaki I, Whalley C, den Haan K, Messiaen M, Clayton H, Lettieri T, Negrão Carvalho R, Gawlik BM, Hollert H, Di Paolo C, Brack W. Kammann U, Kase R: The European technical report on aquatic effect-based monitoring tools under the water framework directive. Environmental Sciences Europe, 27, 7 (2015). doi: 10.1186/s12302-015-0039-4 [Paper link] (Highly accessed on BMC)
  • Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker D, de Sousa F, Gamper HA, Larsson E, Larsson K-H, Kõljalg U, Edgar R, Abarenkov K: A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments, 30, 2, 145-150 (2015). doi: 10.1264/jsme2.ME14121 [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]
  • 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]
  • Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM: Metagenomic sequencing of marine periphyton: Taxonomic and functional insights into biofilm communities. Frontiers in Microbiology, 6, 1192 (2015). doi: 10.3389/fmicb.2015.01192 [Paper link]
  • Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics, 16, 964 (2015). doi: 10.1186/s12864-015-2153-5 [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]
  • Wang X-C, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang J-H, Cai D, Li J-Q: ITS1: A DNA barcode better than ITS2 in eukaryotes? Molecular Ecology Resources, 15, 3, 573-586 (2015). doi: 10.1111/1755-0998.12325 [Paper link] (Bizarrely noted as a 2015 paper, despite being published in September 2014.)

Posters

  • Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of resistance genes to antibiotics, biocides and metals on bacterial chromosomes and plasmids reveals novel insights into their co-selection potential. ICETAR 2015: International Conference on the Evolution and Transfer of Antibiotic Resistance, Amsterdam, The Netherlands, 2015.

  • Flach C-F, Svensson C-J, Pal C, Bengtsson-Palme J, Östman M, Kristiansson E, Larsson DGJ: Antifouling paint co-selects for antibiotic resistant bacteria in the marine environment. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.

Conference talks
Presenting author indicated by *

  • Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Large-scale analysis of resistance genes towards antibiotics, biocides and metals in bacterial genomes and plasmids uncovers their co-selection potential. ICETAR 2015: International Conference on the Evolution and Transfer of Antibiotic Resistance, Amsterdam, The Netherlands, 2015.
  • Lundström S*, Östman M, Bengtsson-Palme J, Pal C, Rutgersson C, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibacterial agents in complex aquatic bacterial communities. 6th Congress of European Microbiologists (FEMS 2015), Maastricht, The Netherlands, 2015.
  • Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Turn up the signal – wipe out the noise: Gaining insights into antibiotic resistance of bacterial communities using metagenomic data. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  • Pal C*, Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Co-occurrence of antibacterial biocide, metal and antibiotic resistance genes in bacterial genomes and plasmids reveals novel insights in their co- selection potential. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  • Lundström S*, Östman M, Bengtsson-Palme J, Pal C, Rutgersson C, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Determining the minimal selective concentrations of antibacterial agents in complex aquatic bacterial communities. 3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015.
  • Bengtsson-Palme J*, Kristiansson E, Larsson DGJ: Turn up the signal – wipe out the noise: Gaining insights into bacterial community functions using metagenomic data. Swedish Bioinformatics Workshop, Stockholm, Sweden, 2015.

Conferences and workshops

Talks

  • Turn up the signal – wipe out the noise: Gaining insights into antibiotic resistance of bacterial communities using metagenomic data
    3rd International symposium on the environmental dimension of antibiotic resistance (EDAR2015), Wernigerode, Germany, 2015-05-18
  • Turn up the signal – wipe out the noise: Gaining insights into bacterial community functions using metagenomic data
    Swedish Bioinformatics Workshop, Stockholm, Sweden, 2015-09-24.

Research platforms and projects

  • MistraPharma
    A MISTRA-funded project to assess risks of human pharmaceuticals in the environment
  • INTERACT
    A FORMAS-funded project to investigate co-selection of metal, biocide and antibiotic resistance
  • UNITE
    The database for DNA identification of fungi
  • GoBiG
    Gothenburg Bioinformatics Group for junior scientists

Other committees etc.

  • Reviewed manuscripts for Folia Microbiologica, GigaScience, FEMS Microbiology Ecology.
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