Pr Soumelis is a medical doctor specialized in hematology. He received his medical training in Paris, followed by a residency in clinical hematology in Lyon, and a PhD in immunology in the USA (DNAX Research Institute). Since 2011, he has coordinated with Dr. Mechta-Grigoriou the "tumor micro-environment" Program of the Curie Institute. He obtained a grant for a European project to study the role of the skin microbiome in cutaneous inflammatory diseases for which he coordinated the data analysis and their bioinformatics modelization. He has also developed an analytic platform at the interface between immunology, bioinformatics, and systems biology. He is the coordinator of the ImmunAID consortium that includes microbiome analysis, being involved in data integration. Pr Soumelis is now starting a new Inserm research Unit at the Hôpital Saint Louis in Paris.
Pr Soumelis, what is your point of view on the biggest challenges and opportunities in microbiome biomarker discovery? (especially scientific insight and evidence-based medicine)
I am interested in all “omics” and data integration to look at the global response of immune cells to their environment. I am currently an investigator in the immuno-oncology field where I study inflammation. I have no research project yet in microbiome in cancer patients, but in the light of the growing literature on the subject, I am certainly very interested in that field.
I see a lot of potential, but microbiome research is relatively young and yet mature for clinical application. One big challenge is technical because microbiome studies are not robust enough yet. We need a better knowledge of what a ‘normal microbiome’ is. We should have a precise anatomical and subanatomical cartography of microbiome communities as it is starting to be done in the gut and in the skin. We also need to know which factors affect these ‘normal microbiomes’ (e.g. age, geographical location, life habit), and how fast microbial communities recover from these possible disruptions.
To collect this information in a robust manner, we need prospective cross-sectional studies in large international cohorts. To date, the predictive value of microbiome biomarkers has not been assessed in sufficiently powered clinical studies. It might be critical to restrict microbiome sequencing to well-selected populations in robustly designed studies that include bioinformatics experts. Eventually, microbiome could become part of biomarker panels used by clinicians to measure the risk for or diagnose a cancer, as well as predict the efficacy and the toxicity of anticancer therapy. Additionally, it would be very interesting to develop products or diets that can accurately, effectively, and safely modulate the microbiome because these products are usually well accepted by the patients. However, before attempting to manipulate a patient’s microbiome, one will need to accurately define ‘dysbiosis’ in this category of patients.
To conclude, the biggest challenge will be the complexity of exploiting microbiome data because it cannot be analyzed without precise information on diet and environmental factors that can significantly impact the microbiome and represent important sources of confounding factors. In the future, we will therefore require a close collaboration between academic researchers, clinicians, and the biopharma industry. There are already several initiatives at the local, national, and international levels and this will definitely be important in order to foster innovation in the field of the microbiome
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