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Characterization of Microbial Communities

Characterization of Microbial Communities

Title: Unbiased Characterization of Microbial Communities

Microbial communities play a vital role in most processes in the biosphere and are essential for solving present and future environmental challenges, such as treatment of water and wastewater, recovery of resources (e.g. phosphorus), production of “green” chemicals (e.g. bioplastics), and production of bioenergy (methane, electricity). However, a prerequisite realizing the full potential of microbial communities is to be able to identify the key organisms. The current approach for microbial identification is rRNA amplicon sequencing, but this method has several severe biases and drawbacks that need to be solved. In this project the aim is to overcome these limitations by the development of novel methods and apply these for an unbiased view of microbial communities.


The project is funded by The Danish Council for Independent Research (FNU) in the period 2016-2019.

Project content:

  • Development of primer-free full-length 16S rRNA sequencing
  • Establish a comprehensive full-length 16S rRNA databases in Environmental Biotechnology
  • Re-design of primers and high-throughput screening of ecosystems in Environmental Biotechnology.
  • Re-design of FISH probes and in situ investigations

Project participants:

Aalborg University, Center for Microbial Communities:

  • Per Halkjær Nielsen, Professor (project leader)
  • Jannie Munk Kristensen, PhD student
  • Mads Albersen, Post.Doc.
  • Morten Dueholm, Assistant Professor
  • Simon McIlroy, Post.Doc.
  • Marta Nierychlo, Post.doc.


  • Professor Dr. Michael Wagner, Department of Microbial Ecology, Univ. of Vienna