Project Acronym:

Project Reference:

Duration: 52 months

Contract Type:
Small or medium-scale
focused research project

Project Funding:
6 million euros

Research area:
HEALTH.2012.2.4.5-2 Biomarkers and diagnostics for chronic inflammatory diseases of the joint and/or digestive system

This project has received funding from the European Union's Seventh Framework Program for research, technological development and demonstration under grant agreement #305676

Microbial profiling

The GA-map allows screening of many samples using a panel tailor-made for IBD analysis

It is now well recognized that understanding microbial content of the gut is relevant for inflammatory bowel diseases .  However little is known about the aetiology – if changes in microbial content of the gut are causative or an effect of disease progression. Furthermore there are lacking large collaborative studies coupling knowledge about gut microbial content and host genetic factors as well as identification of differences in gut microbiota early on in the IBD. Therefore, a comprehensive study of the gut microbiota will be important for this project. In order to allow screening of large numbers of patients for presence of many different microbes, we will develop an IBD-relevant microbe bead-array (called GA-map™). By performing 16S rRNA amplicon pyro-sequencing of collected samples from IBD patients and healthy controls, a catalogue of microbes of interest in IBD will be established. This in combination with other public projects for microbe cataloguing, e.g. and the Human Microbiome project  and MetaHIT , partner GA will design unique and specific DNA probes for the GA-map platform, capable of reporting the presence of the various selected microbes. Based on the observations that there is high intra-individual variation of intestinal microbiomes in the human population, we hypothesize that characterizing IBD microbiomes could disclose bacterial and fungal species implicated in IBD aetiology. To better understand how microbiomes relate to human disease, we will undertake a comparative sequencing survey of the microbiomes present in faces in 40 IBD patients and 40 unaffected individuals using whole metagenomic sequencing in order to verify data from GA-map and look for additional microbial markers outside the 16sRNA amplicon.

Currently pyro-sequencing of the 16S rRNA gene is the most commonly used method for studying diversity in the gut microbiota . Although the method is useful as a discovery tool, the output of the sequence analysis requires several complex computational steps, as well as some subjective decisions as to sequence identity. Reducing the number of samples in each run will reduce the complexity of analysis, but this will drastically increase the cost per sample. Therefore, in order to be able to do a quality comparison of all samples, a novel technology (GA-map™) will be adapted that utilizes a combination of specific DNA probes to profile the gut microbiota. The GA-map™ technology platform is also included in another ongoing FP7 project (KBBE.2011.2.2-01, grant no 289517), and will here be further developed and tailor-made for IBD analysis. To our knowledge, this will be the first time a microbial profile will be obtained and compared from this many clinical samples. In addition, whole genome metagenomic sequencing of a sub-set of samples is expected to give additional information on biological markers and phenotypic traits of important bacteria contributing to disease. These various microbial profiling approaches will be performed on a unique sample material, namely from patients just diagnosed with IBD and before any treatment has commenced. Using this unique material will help us to understand the mechanism of initiation of disease, as well as identify markers or microbial profiles that can be used for early diagnosis of disease.

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