Summary of 2012

During 2012, I have mainly been working with the impact of antibiotic selection pressure on environmental communities – from many different perspectives. I have published two papers during the year – one on the software tool Megraft, and one on guidelines for quality control of ITS sequences. Somewhat disappointing, neither of the GOS paper and the periphyton paper is yet out – sometimes the publication wheels turn extremely slowly.

However, I have had the opportunity to present my work on various conferences, e.g. I had oral presentations on this year’s ISME conference in Copenhagen, and on the SocBiN conference in Stockholm. I have also brought posters to a number of other occasions.

Upcoming publications in the pipeline include a paper on a software tool for improved ITS sequence detection and extraction, but also the antibiotic resistance work I have been doing for the last year will start to bear fruit in 2013.

A very nice thing that happened during the year was the group secured 25 million SEK (~2.5 million EUR) in funding over five years for a collaboration project on antibiotic resistance and metal/biocide resistance coselection (INTERACT). This will bring us closer together with the Hans Blanck, Dan Andersson and Mats Tysklind groups, which most probably will be welcome interactions. We have also started up the Gothenburg Bioinformatics Group for PhD Students (GoBiG), which has spurred very interesting discussions among the people working with bioinformatics in Gothenburg. Hopefully, the group’s activities will continue and broaden in 2013.

Publications

Papers

  • Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH: Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes. Research in Microbiology. Volume 163, Issues 6–7 (2012), 407–412, doi: 10.1016/j.resmic.2012.07.001. [Paper link]
  • Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson-Palme J, Eriksson KM, Larsson K-H, Larsson E, Kõljalg U: Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys. Issue 4 (2012), 37–63. doi: 10.3897/mycokeys.4.3606 [Paper link]

Posters

  • Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Using Large-Scale Sequencing Metagenomics to Assess the Antibiotic Resistome. 4th Next Generation Sequencing Congress, London, Great Britain, 2012.
  • Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities. ISME14 Conference, Copenhagen, Denmark, 2012.
  • Bengtsson-Palme J, Hartmann M, Eriksson KM, Nilsson RH: High-Throughput Diversity Analysis and Quality Control of Environmental Data Derived from Next-Generation Sequencing Studies. ISME14 Conference, Copenhagen, Denmark, 2012.
  • Eriksson KM, Sanli K, Bengtsson-Palme J, Nilsson RH, Alm Rosenblad M, Blanck H: Starting to unravel the layer of life on surfaces in the sea: Metagenomics of complex marine biofilm communities. ISME14 Conference, Copenhagen, Denmark, 2012.
  • Bengtsson J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Comprehensive Analysis of Antibiotic Resistance Genes Using Metagenomic DNA Sequencing: Studies of Contaminated River Sediment, Well Water and Soil Microbial Communities. SocBiN Bioinformatics Conference 2012, Stockholm, Sweden, 2012

Conferences and workshops

Talks

  • Analyzing antibiotic resistance using metagenomics
     SocBiN Bioinformatics Conference 2012, Stockholm, Sweden, 2012-06-13
  • Comprehensive analysis of antibiotic resistance genes using metagenomic DNA sequencing
    ISME14 Conference, Copenhagen, Denmark, 2012-08-23

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
  • Ecotoxicology from Gene to Ocean (EGO)
    at the Faculty of Science, University of Gothenburg
  • GoBiG
    Gothenburg Bioinformatics Group for PhD students

Other committees etc.

  • Reviewed manuscripts for Environmental Science and Technology and PLoS ONE.

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