The composition of the human gut microbiome is considered playing a modulating role on the health status of individuals. Relationships between several organs and the gut microbiome are suggested as well as an impact on the onset or development of some diseases such as acne, asthma, autism, autoimmune diseases, depression, diabetes, inflammatory bowel disease and obesity. Therefore, the gut microbiome is extensively studied. Microbiome-based biomarkers and particular gut microbiota profiles are identified for early diagnosis and monitoring linked to specific risks. In the future, knowledge on human microbiome is expected to play a key role in personalised health and precision medicine. Many companies already offer microbiome-testing services to citizens, for instance, analysing a stool sample sent by post, based on which diagnosis and treatments are proposed. However, this requires understanding the mechanisms of the bidirectional microorganism-host interactions and reliable measurements to ensure data quality and comparability of results. Aware of this situation, several companies have recently put on the market different materials based on human faecal material, individual or mixture of microbial DNA or microbial whole cells to be used as reference. These materials allow validating different steps of the microbiome analysis, from the sample storage to the DNA extraction and quantification to demonstrate reproducibility (or the lack of it) across laboratories. Different quantification methods, relative or absolute, can also be used, in a complementary manner. Besides, there is an on-going debate about the need for a single standardised methodology. As the most appropriate method for one microbiome might not be the most appropriate for another microbial community, a single methodology might not be desirable. Moreover, different methods and platforms might be useful to better elucidate interaction mechanisms with the host. Nevertheless, there is a need for quality control and for adequately detailed analytical protocols specifically designed for the complexity of microbiome analysis. The current international collaborations and efforts of the Human Microbiome project (HMP), Microbiome Quality Control (MBQC) project and International Human Microbiome Coordination and Support Action (IHMCSA) are essential for the development of guidelines for method validation and for the value assignment of reference materials to support method validation. These will increase reproducibility and comparability of microbiome studies. This report provides an overview on the different challenges of microbiome analysis and the on-going efforts in the field.
TOUSSAINT Brigitte;
MUNOZ PINEIRO Amalia;
RODRIGUEZ ALONSO Raquel;
2024-09-18
Publications Office of the European Union
JRC139121
978-92-68-20629-4 (online),
1831-9424 (online),
EUR 40029,
OP KJ-01-24-025-EN-N (online),
https://publications.jrc.ec.europa.eu/repository/handle/JRC139121,
10.2760/8748720 (online),
