The human microbiota: A long ignored ecosystem that today is revolutionizing medicine, science and nutrition.
Our microbiota, with their complex structures and multiple roles in human physiology, form our second genome. This ecosystem, present throughout our lives, now appears as a source of biomarkers useful for diagnosis and prognosis in many pathologies as well as responses to certain treatments. Since 2017, the iBiote team has dedicated its efforts through research and development (R&D) to make a specialized routine test available to physicians and their patients.
Our research projects
The iBiote team is actively involved in research on human microbiotes. Thanks to our collaboration with numerous clinicians and hospital structures, we are now involved in numerous research projects studying microbiotes in relation to human health.
Faced with this booming theme which is revolutionizing the medical environment today, we have set up the MEDIBIOTE studies. The studies in which we participate are carried out with the collaboration of clinicians with various medical specialists on cohorts recruited through our hospital network.
Standardization work
The lack of standardization in metagenomics is a recurring problem in the study of microbiota. Among the many steps in which biases can be introduced, the iBiote team has focused on sample collection, sample stabilization and extraction, and data analysis.
MEDIBIOTE studies
MEDIBIOTE studies aim to characterize human microbiota and identify microbiotic signatures in many pathologies. These studies aim to advance our knowledge of microbiota in order to use them as a diagnostic and prognostic tool, but also in the prevention of diseases, thus contributing to the improvement of patient management by clinicians.
MEDIBIOTE 1 study: Microbiotic imprint of a pathology: IBD and Parkinson's disease
Today many chronic diseases are associated with an imbalance in the intestinal microbiota called dysbiosis. Among these chronic diseases are IBD (Inflammatory Bowel Diseases) and Parkinson’s disease for which the involvement of the microbiota in the onset and progression of symptoms seems to be a key element in their physiopathology. These pathologies are often associated with an inflammation and hyperpermeability of the digestive mucosa, thus generating a passage of intestinal bacteria into the bloodstream (phenomenon of bacterial translocation).
Today, through the MEDIBIOTE 1 study, our laboratory aims to identify the microbiotic signatures of these pathologies as well as a possible correlation between digestive and blood microbiota according to the progress of the disease.
This study has started recently.
MEDIBIOTE 2 Study: Microbiotic imprint of a pathology: Systemic Scleroderma
Systemic scleroderma (SSc) is a rare autoimmune disease that has no cure to date. Its pathophysiology may be characterized by fibrosis and more or less severe vascular obstruction of the skin and other organs (particularly the digestive tract). This disease is multifactorial, involving both genetic and environmental factors, including the intestinal microbiota, which has been identified as an essential element in the occurrence and initiation of this pathology.
The aim of the MEDIBIOTE 2 study is to define an intestinal microbiotic signature characteristic of SSc. Its longitudinal nature will also make it possible to evaluate the dynamics of this signature’s evolution through the progression of the disease in patients.
The study will start in 2019.
MEDIBIOTE 3 Study: Microbiotic imprint of a pathology: Ankylosing spondylitis
Ankylosing spondylitis (AS) is a chronic inflammatory joint disease characterized by a slow progression with periods of relapses and remissions. This disease mainly affects the spine and pelvis, with a high cardiovascular risk if not properly managed. Studies have shown, on the one hand, the involvement of certain intestinal bacteria in the onset and progression of this disease and, on the other hand, the role of the intestinal microbiota in predicting the response to treatment (anti TNF α and anti-IL17).
The aim of the MEDIBIOTE 3 study is to longitudinally study the faecal microbiota of AS patients before and after 3 months of treatment in order to identify the microbiotic signature of the pathology and to highlight any changes in the microbiota following treatment.
The study will start in 2019.
MEDIBIOTE 4 Study: Microbiotic imprint of a pathology: NAFLD and NASH
Non-Alcoholic Fatty Liver Disease (NAFLD) is a chronic liver disease that can progress to Non-Alcoholic Steatoheaptitis (NASH). NASH dramatically increases the risk of cirrhosis, liver failure and hepatocellular carcinoma (HCC). This disease has no characteristic symptoms, making it difficult to diagnose and manage. Studies have shown that the presence of dysbiosis in the intestinal microbiota as well as bacterial metabolism may be involved in the pathogenesis of NASH. This pathology is often associated with an increase in intestinal permeability facilitating the passage of bacteria from the intestine to the bloodstream (bacterial translocation phenomenon).
Today, our MEDIBIOTE 4 study aims to study the correlation between blood and faecal microbiota and their variability in patients with NAFLD and NASH. In addition, this study will also identify the evolution of possible microbiotic changes during the different stages of this chronic liver disease.
The study will start in 2019.
Clinical studies in which one of the components is the study of microbiotes
Lupus Living Lab (3L1) study and salivary and faecal microbiota
Systemic lupus erythematosus (SLE) is a rare autoimmune disease. It can affect the whole body with clinical manifestations varying from one patient to another, ranging from mild symptoms (skin involvement) to more severe symptoms (kidney and heart involvement). The diversity of symptoms thus makes diagnosis and patient management difficult. Studies have shown the involvement of the intestinal microbiota not only in the onset of the pathology but also in the progression of its symptoms. In addition, recent data have highlighted the involvement of the oral microbiota in this disease. Today, the 3L1 project aims to explore in a comprehensive and longitudinal manner a cohort of lupus patients whose goal is to define and follow the evolution of the microbiotic signatures at the intestinal and oral levels through the progression of the disease.
This study also investigates other parameters, other than the microbiota, that are important in the understanding of the pathology, however they are not mentioned in this paragraph.
Prove study and pulmonary microbiota
• Prove study and pulmonary microbiota
This study also investigates other parameters, other than the microbiota, that are important in understanding the pathology, however they are not mentioned in this paragraph.
Study started in 2018.
Upcoming studies
- Papillomavirus (HPV) and vaginal microbiota
- Cancer and fecal microbiota
- Endometriosis and faecal microbiota
Our publications
- Standardization on sample stabilization – in progress
- A first study showed a variation in the microbial profile in the absence of stool stabilization. This variation is random and cannot be predicted by an algorithm.
- Since a stool stabilisation step is essential to obtain a reliable microbial profile, a second study was carried out to test all the stabilising solutions available on the market. It was shown that the stabilization efficiency differed from one solution to another, highlighting biases, with overestimation and underestimation of certain bacterial populations that may be significant. It is therefore important to be aware of the limits that may be encountered and this highlights that the pre-analytical stage is a crucial step in the microbiota analysis protocol.
Our congress participations
- Importance de l’expertise bioinformatique lors de l’analyse du microbiote intestinal. A. Plauzolles, G. Penaranda, E. Toumi, H. Khiri, C. Camus, L. Chiche, F. Retornaz, J. Allardet-Servent et P. Halfon. RICAI, 2017.
- Microbiote intestinal : Importance de la conservation des selles au cours du temps. A. Plauzolles, E. Toumi, G. Penaranda, H. Khiri, C. Camus, L. Chiche, F. Retornaz, J. Allardet-Servent, P. Halfon. RICAI, 2017.
- La stabilisation d’un microbiote fécal est fortement influencée par le choix de la solution stabilisante ainsi que la composition bactérienne du microbiote analysé. A. Plauzolles, E. Toumi, B. Goutorbe, G. Penaranda, G. Bidaut, H. Khiri, C. Camus, L. Bruot, M. Bonnet et P. Halfon. MBIO 2018.
- Microbiota & health: impact of new pipelines in targeted metagenomics. B. Goutorbe, A. Plauzolles, G. Bidaut et P. Halfon. JOBIM, 2018.