We study microbial communities using shotgun metagenomics and amplicon sequencing and develop methodology for enhancing such studies.

The activities of complex microbial communities shape our planet and affect the health of the humans. In our group we employ metagenomics and taxonomic marker gene sequencing to explore patterns of microbial diversity and reconstruct genomes and metabolic pathways of microbes in environments ranging from the Baltic Sea to the rumen of Moose. We also develop molecular and bioinformatics tools for enhancing the information output from such studies. An introduction to metagenomics and amplicon sequencing can be found here.

Who we are

Anders Andersson (PI)

Anders received his PhD in 2005 at KTH Royal Institute of Technology after graduate studies on functional genomics. Thereafter he conducted postdoctoral studies at the Karolinska Institute, University of California Berkeley, and Uppsala University, working on metagenomics approaches to study microbial communities of different environments (the human gut microbiota, biofilms of acid mine drainage, and bacterioplankton of lakes and the Baltic Sea). In 2010 he returned to KTH, starting his tenure track and building up a group at Science for Life Laboratory in Stockholm. In 2014 he was promoted to associate professor.

Luisa W. Hugerth

Luisa is a PhD student working on microbial communities in the Baltic Sea. She uses shotgun sequencing to reconstruct genomes from uncultured organisms and explore their metabolism. As a complement to that, she applies amplicon sequencing to investigate population dynamics over time.

In collaboration with other groups, Luisa is exploring these same approaches in other environments, such as soils and the human gut.

Conny Sjöqvist

Conny received his PhD in September 2015 at Åbo Akademi University (Finland) after population genetic studies on phytoplankton in the Baltic Sea.

Since October, 2015 he is a Post-doctoral researcher at KTH Royal Institute of Technology studying population genomic patterns of dominant bacterioplankton along environmental gradients in the Baltic Sea. By the use of metagenomic methods he describes microbial communities in the area and aim at revealing patterns of intra-specific diversity and differentiation. Such knowledge may contribute to a better understanding of current selection pressures and evolution of microbial communities in the Baltic Sea.

Johannes Alneberg

With a background in mathematics, statistics and computer science, Johannes is developing Bioinformatic methods to improve the analysis of metagenomic data. He started his PhD studies in May 2014 after doing a master thesis project within the group.

The first projects Johannes have been involved with concerns clustering of metagenomic contigs, reconstructing dominant baltic sea bacterioplankton and using microbial signatures for water quality assessment. Johannes is co-first author of CONCOCT and currently maintaining the code.

Jürg Brendan Logue

Jürg is a PostDoctoral Research Fellow and is currently working on how bacterial communities of different aquatic origin differ in the processing of dissolved organic matter of terrestrial origin (in collaboration with Anders Andersson, KTH Stockholm, and Emma Kritzberg, Lund University).

Jürg's general research interest lies in the ecology of micro-organisms within aquatic ecosystems. He is using microbial communities as model systems to address questions related to community ecology. He is particularly interested in understanding the mechanisms that underlie patterns of microbial species distribution, abundance, and interactions as well as the links between microbial diversity and ecosystem functioning.

Yue Hu

Yue graduated from Wuhan University of Technology in China as Master of Environmental Science, and is now registered in KTH as a Ph.D student. She develops and uses metagenomics methods for environmental monitoring, including tracking contaminations in water systems and plankton monitoring in the Baltic Sea.

Olov Svartström

Olov is a post-doctoral fellow at the department of industrial biotechnology at KTH with Henrik Aspeborg as main supervisor and Anders as a co-supervisor. The project has the ultimate goal to produce new enzymes that efficiently converts renewable plant biomass into biofuels. The strategy is to refine highly potent degraders of lignocellulose (the most abundant renewable biomass on earth) by iterative culturing. The enzymes will be identified by shotgun metagenomics and transcriptomics followed by recombinant gene expression.

Olov received his PhD from the Swedish University of Agricultural Sciences (SLU) investigating a connection with spiral shaped Treponema bacteria and ulcers from which pigs may suffer. In between PhD and post-doctoral studies, Olov spent a year developing next generation sequencing applications for clinical microbiology diagnostics at the University hospital of Linköping.


Daniel Lundin (Postdoc). Presently at Linnaeus University.

Brynjar Smári Bjarnason (Graduate Student). Presently at Spotify.

Ino de Bruijn (Graduate Student, Bioinformatician). Presently at Memorial Sloan Kettering Cancer Center.

Hussein Shokry (Graduate Student).

Florian Heigwer (Erasmus Student). Presently at German Cancer research Center.

Nasir Abbasi (Project Student).

Hugo Wefer (Project Student). Presently at Clinical Genomics/Scilifelab.

Press Releases

Check out our projects on GitHub:

Where we share our bioinformatic software and lab protocols.