Research Interests (old)

My main research interests lies within the use of metagenomics to assess questions about antibiotic resistance, microbial ecology and community structures. I have previously used metagenomics to study detoxification proteins in marine environments and marine periphyton communities. My current main project is to investigate the effects of antibiotic selection pressures on microbial communities, environmental as well as human. I am also interested in DNA barcoding, especially using SSU, LSU and ITS sequences, to assess the species composition of microbial communities.

Current projects

  • Finding and quantifying antibiotic resistance genes in metagenomic data from bacterial communities. This is a central undertaking in a number of projects, and is supervised by Joakim Larsson and Erik Kristiansson. The projects involving resistance genes which I am part of are:
    –  The role of antibiotic pollution in the selection of resistance and subsequent gene transfer to the human microbiome from the environment (funded by VR and FORMAS).
    – MistraPharma; an interdisciplinary research program aiming to understand the promotion of antibiotic resistance in the environment, identify high-risk pharmaceuticals, improve risk management related to pharmaceuticals in the environment, and – importantly – to evaluate removal processes of pharmaceuticals of concern through wastewater treatment. (Funded by MISTRA, web site: www.mistrapharma.se)
    – INTERACT – a research program investigating interactions of metals and biocides with the selection of antibiotic-resistant bacteria in various environmental settings. Within INTERACT, we aim to characterize the biocides and concentrations that promote resistance development, where we find high-risk environments and mixtures, what the genetic basis for co- and cross-resistance is, and whether there is a risk that resistance factors spread from environmental bacteria to human pathogens. (Funded by a FORMAS grant to Joakim Larsson, Hans Blanck, Dan Andersson and Mats Tysklind)
  • The use of metagenomics to look at detoxification proteins in marine environments. This is an extension of my BSc project “Finding genes related to detoxification in metagenomic data”. This project is supervised by Magnus Alm Rosenblad and Anders Blomberg, in close collaboration with Mikael Molin.
  • Comparative analysis of marine metagenomes from the Swedish west coast. With Martin Eriksson and Magnus Alm Rosenblad, in collaboration with Hans Blanck.
  • Developing new and improving on existing bioinformatics methods for metagenome analysis, especially handling of second-generation sequencing data, such as 454 and Illumina.
  • Developing methods for species and OTU identification in community data, such as data from metagenomics projects, community PCR and other targeted sequencing methods; focusing on the SSU, LSU and ITS genetic regions. This is done in collaboration with Martin Eriksson, Martin Hartmann and Henrik Nilsson.

Previous stuff

  • The use of iterative methods to find grey-area genes in vast amount of sequence data. This is my own little hobby project that sprung out of the BSc thesis. Might one day turn into a real method.
  • Visualization of BLAST output and ecological data.