The gut mycobiome of a cross-sectional Northern German population

Principal Investigator

Prof. Dr. rer. nat.

Associated Doctoral Researcher

Associated Principal Investigator

Background and current state of research

The gut mycobiome, i.e. the sum of all fungi, is an integral part of the human gastrointestinal (GI) tract microbiome community. The size of the mycobiome amounts up to 106 microorganisms per gram of faeces.1 While the diversity and function of the colonic bacterial microbiota have been broadly characterized, little is known about the composition and function of the commensal fungal microbiome in health and disease. Evidence from human epidemiological and animal studies implicates not only a role for GI commensal fungal microbiota but also for the invasion of host niches by pathogenic fungi as well as a contribution of fungal metabolites in chronic and malignant GI disorders (e.g. inflammatory bowel diseases, irritable bowel syndrome, liver cancer, oesophagogastric cancer etc.). However, the potential mechanisms of infection and important causative cofactors still remain unclear.2

Recent reports using Next Generation Sequencing (NGS) technology suggest a high diversity of commensal fungal communities in humans.3-5 However, little data is available on the fungal population composition in the large intestine and faeces. Moreover, data that has been generated to this end was derived from rather small study populations and sample sets. We here propose that in order to properly evaluate and understand the importance of the mycobiome in human GI health that large-scale and systematic studies are needed. At first it will also be important to understand the role in the general population and in healthy populations. In a next step, more disease-oriented research is necessary.


1. Huffnagle GB, Noverr MC. Trends Microbiol. 2013;21(7):334-41.

2. Wang ZK, Yang YS, Stefka AT, et al. Aliment Pharmacol Ther. 2014;39(8):751-66.

3. Hamad I, Sokhna C, Raoult D, et al. PLoS One 2012;7: e40888.

4. Iliev ID, Funari VA, Taylor KD, et al. Science 2012;336(6086):1314-7.

5. Ott SJ, Kuhbacher T, Musfeldt M, et al. Scand J Gastroenterol 2008;43:831–41.

Our goals

We have set up a semi-automated pipeline for generating and analyzing microbial high-throughput data. Here we aim to establish the necessary infrastructure for high-throughput mycobiome analyses and interaction studies. Using this resource we will then examine the faecal fungal composition and the function of the mycobiome in a large representative German population sample (provided by the local biobank PopGen). Metabolic, genetic and microbial data is already available for the same individuals and will be employed to understand the function of the mycobiome and its interaction with the host and its gut bacteria in more detail.