Tools for microbiota profiling
Accumulating evidence indicates that perturbation of intestinal microbiota is associated with intestinal disease and other conditions such as metabolic syndrome, non-alcoholic fatty liver disease and diabetes. Identification of intestinal microflora diversity traditionally relied on a strategy that detects the 16S ribosomal DNA. This gene is universally present and has been employed for distinguishing between taxa. However, this approach has not been tested clinically or for distinguishing among yeasts and parasites. The scope of the EU-funded project GUT18S (Comprehensive molecular analysis and differentiation of the eukaryotic microbiota in faecal samples from human cohorts to establish the role of intestinal eukaryotes in health and disease) was to develop DNA-based tools for the exhaustive detection and differentiation of prokaryotic and eukaryotic organisms in human samples. Towards this goal, researchers developed a highly standardised diagnostic tool of unprecedented sensitivity and resolution with high applicability. This tool relies on the identification of the 18S ribosomal DNA initially by polymerase chain reaction followed by next generation sequencing. This approach avoids amplification of human DNA but can detect eukaryotic DNA from parasites capable of colonising the human intestine for years without causing any symptoms. Data analysis was performed by a sophisticated bioinformatics tool, the BION software. Using these tools, scientists showed that single-celled intestinal parasites, such as Blastocystis and Dientamoeba, are common in the healthy background population. Albeit of unclear health significance, colonisation with Blastocystis was found to be chronic especially in healthy individuals compared to patients suffering from inflammatory bowel disease or irritable bowel syndrome. Furthermore, they discovered Blastocystis to be associated with certain microbial communities. The GUT18S approach was implemented in clinical microbiology laboratories as a new diagnostic service, facilitating the comprehensive detection and differentiation of bacteria, fungi and parasites in patient samples. Partners expect the service will gain immediate momentum, becoming an indispensable tool in gut microbiota profiling.
Keywords
Microbiota, parasites, GUT18S, 18S ribosomal DNA, Blastocystis
