Microbiome Research

The microbiome consists of the totality of all microbial species in a human host. It includes a combination of bacteria (bacteriome), viruses (virome) and fungi (fungome). Recent advancements in sequencing technologies and bioinformatics techniques have allowed for the large-scale characterisation of the microbiome in both healthy individuals and diseased patients. This research has shown that the microbiome (in particular the gut microbiome) plays in important role in the regulation of the host immune system, with a healthy microbiome being an essential element of good health. However, our understanding of the role of the microbiome in the context of patients with immune dysfunction is limited. It is particularly unclear how the microbiome influences the risk of downstream complications of therapies linked to immune dysfunction (e.g. stem cell transplant, steroids, antibiotics etc).


The aim is to improve our understanding of this critical area of research with the following goals:
1. To describe the make-up of the microbiome (including the bacteriome, virome and fungome) in participants with immune dysfunction
2. To understand the interaction of the microbiome and the host immune system in the context of clinical outcomes in persons with immune dysfunction
3. To assess the clinical benefit of microbiome-based interventions on clinical outcomes in persons with immune dysfunction

To achieve these goals, PERSIMUNE has developed an extensive clinical biobank of faecal and other biological samples from persons with immune dysfunction. Samples from this biobank are being used to characterise the microbiome using whole genome shotgun sequencing. To analyse these samples, PERSIMUNE researchers have developed expertise in the bioinformatics and statistical analyses of microbiome data.


  • Emma Elizabeth Ilett
  • Daniel D Murray
  • Joanne Reekie
  • Jens Christian Nørgaard
  • Cameron MacPherson
  • Mette Jørgensen
  • Ramtin Zargari Marandi
  • Preston Yui Sum Leung
  • Kirstine Krøyer Rasmussen
  • Tereza Faitová
  • Jens Lundgren
  • Henrik Sengeløv
  • Marie Helleberg
  • Susanne Dam Poulsen
  • Gedske Daugaard
  • Carsten Utoft Niemann
  • Søren Schwartz Sørensen
  • Therese Katzenstein
  • Hanne Ravn
Microbial Genomics Research Group at IrsiCaixa, Badalona, Spain
  • Roger Paredes
  • Marc Noguera
  • Mariona Parera


  1. Incidence Rates and Risk Factors of Clostridioides difficile Infection in Solid Organ and Hematopoietic Stem Cell Transplant Recipients.  Ilett, E. E., M. Helleberg, J. Reekie, D. D. Murray, S. M. Wulff, M. P. Khurana, A. Mocroft, G. Daugaard, M. Perch, A. Rasmussen, S. S. Sorensen, F. Gustafsson, N. Frimodt-Moller, H. Sengelov and J. Lundgren
    Open Forum Infect Dis. 2019; 6(4):ofz086. Abstract
  2. Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing.Ilett, E. E., M. Jorgensen, M. Noguera-Julian, G. Daugaard, D. D. Murray, M. Helleberg, R. Paredes, J. Lundgren, H. Sengelov and C. MacPherson
    Sci Rep. 2019; 9(1):13351. Abstract