The availability of cheap culture-free sequencing approaches in microbiology, such as 16S rDNA sequencing, revealed the existence of trillions of microorganisms in the human intestine forming a complex ecological community [1, 2]. Most of the gut microorganisms are not only crucially involved in digestion and fermentation processes, but also exhibit protective and structural functions within the human intestine [1, 3]. On the other hand, imbalances within the normal human gut microbiota, termed dysbiosis, have been associated with numerous human diseases such as inflammatory bowel disease, cancer and obesity [3, 4]. Hence, one current research focus regarding microbial composition in health and disease is to understand how signals from human gut microorganisms may influence the human immune system.
Since 2014, Prof. Franke has been active in microbiome research and established a microbiome laboratory at IKMB that currently has 1 leader, 2.5 technicians, and 3 bioinformaticians (3 postdocs, 1 PhD student). During this time, the microbiome laboratory has been involved in more than 150 different microbiome sequencing projects (internally and in collaboration with numerous external partners) focusing mainly on microbiota changes in different diseases including IBD, but also liver, lung and skin diseases with undefined aetiology. Within these projects, semi-automated DNA/RNA-extraction form diverse sample types (stool, swabs, biopsies) was set up. To determine microbial richness and ASVs in a given sample (Who is there?), the microbiome laboratory has established high-throughput amplicon sequencing not only specific for bacteria, but most recently also for the reliable detection of fungi and archaea. Overall, more than 60.000 samples have been amplicon sequenced in the past years. In addition, whole-metagenome (Who is there and what are they doing?) and whole-metatranscriptome (What are they doing and who is alive?) sequencing have been established on Illumina NovaSeq instruments.
Within miTarget, the microbiome laboratory serves as the main point of entry for all miTarget-related sample extraction and sequencing projects and will thus help unravelling the metabolic and immunological importance of the gut microbiome in the course of IBD.
- Macpherson, A.J. and N.L. Harris, Interactions between commensal intestinal bacteria and the immune system. Nature Reviews. Immunology, 2004. 4(6): p. 478-85
- Artis, D., Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut. Nature Reviews. Immunology, 2008. 8(6): p. 411-20
- Hill, D.A. and D. Artis, Intestinal bacteria and the regulation of immune cell homeostasis. Annual Review of Immunology, 2010. 28: p. 623-67
- Moore, W.E. and L.H. Moore, Intestinal floras of populations that have a high risk of colon cancer. Applied and Environmental Microbiology, 1995. 61(9): p. 3202-7