Team Microbiota-Inflammation

The driving question of my research team is the role of the microbiome in chronic infections like HIV /HCV and Mycobacterium tuberculosis. Additionally we investigate the mechanisms behind success of microbiome modulation in the clinic – faecal microbial transplantation - which has very good outcome in treating recurrent Clostridium difficile infections.

Our group has previously shown that changes of gut microbiota are extensive during HIV infection and contribute to the inflammation that is pathognomonic for HIV infection. Furthermore, we have recently reported that Elite controllers (rare individuals that can control HIV-1 infection without antiviral treatment) have a gut microbiome that is more like healthy individuals concerning the bacterial composition and functional metabolic potential.

My studies aim to elucidate the complexity of interactions between microbiome and immune system that leads to disease control mechanisms. The research is of translational nature and is highly patient-orientated and we apply the novel knowledge of omics in solving important clinical questions. Besides patient-orientated studies my research interest also include in vitro studies on models of gut inflammation/microbial translocation.

Research Team Leader

Piotr Nowak

Team Leader, Senior Researcher

I have obtained MD degree at Warsaw Medical University, Poland and PhD at Karolinska Institute /Division of Virology (2007). Since 2014 I am an Infectious Disease Specialist and currently hold the award of Clinical Research Fellow (2016-) SLL/KI.

Team members

Jan Vesterbacka


I am specialist in infectious diseases and senior consultant at the Department of Infectious Diseases, Karolinska University Hospital with special assignment at the HIV unit. Presently a PhD student with focus on microbial translocation and alterations in the gut microbiota in HIV infected patients and their changes during antiretroviral therapy.

Anoop T Ambikan

Research Assistant (Bioinformatics)

I got my Master’s Degree in Bioinformatics from Amrita School of Biotechnology, India in 2012. I have more than two years experience as Bioinformatics Programmer, at SciGenome Pvt ltd with advanced level skill in programming with interpreted language Perl and statistical software R. I am well versed with open-source bioinformatics tools for NGS analyzing like de-novo whole genome and transcriptome analysis, reference based analysis and microbiome analysis including the commercial NGS data analysis software CLC genomics workbench. In my present research group I am dealing with bioinformatics analysis of various kinds of "omics data" viz, transcriptome, proteome, microbiome and metabolome data related to HIV research. I am working to develop a simplified and efficient pipeline to integrate multi-omics data to draw a clinically relevant inference with reduced manual effort.


High throughput sequencing, metabolomics, integrated system biology, cell cultures


  • Roger Paredes, Microbial Genomics Group at the IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain.
  • Marius Troseid, University of Oslo
  • Lars Engstrand, Karolinska Institutet

Research support

  • Stockholm County Council
  • Swedish Physicians Against AIDS Foundation
  • Karolinska Institutet Research Foundation Grants