Microbiota

Ultra-processed food (UPF) intake has been related to negative health effects and incresed energy intake in previous intervention studies. Thus, previous studies have seen weight gain from higher UPF intake which obscures the potentital to see effects on cardiometabolic biomarkers, independent of weight changes. The overall aim of this project is to study the causal effects of a high UPF diet, compared to a nutrient-matched low UPF diet, on appetite and cardiometabolic health in a weight-stable context.

The prevalence of aortic valve disease is increasing, with these valvulopathies present in half of individuals over the age of 65. Oberbach A. et al (1) demonstrated the presence of microbiota in 52% of cases of explanted aortic valves. One current hypothesis is the role of this microbiota in the pathophysiology of these degenerative valve diseases. This microbiota is probably not completely eradicated after resection of the native valve and implantation of a conventional prosthesis; it is even left in place during percutaneous aortic valve implantation, during which the prosthesis is deployed within the native valve. It could therefore also play a role in the occurrence of postoperative complications and the degeneration or thrombosis of a bioprosthesis. Furthermore, recent clinical and epidemiological studies have shown a link between oral infections and cardiovascular diseases. As recommended by the HAS, these patients require multidisciplinary care, involving cardiologists, cardiac surgeons and general practitioners, as well as careful oral and dental care and monitoring provided by specialists in oral pathologies and oral care. The accumulation of bacterial plaque on the surface of the tooth and certain oral bacteria causes the development of periodontal pockets which are characteristic of periodontitis. Bacteria, microbial products and inflammatory mediators produced locally can then enter the bloodstream and affect distant organs such as the cardiovascular system. The recommendations of the European Society of Cardiology are therefore to carry out regular oral and dental consultations to prevent the risk of infection. Therefore, within the Toulouse University Hospital, a care network has been set up for patients with cardiovascular pathologies, in order to improve their access to dental care, screening and management of oral diseases. For the past year, patients hospitalized in the cardiology departments have been seen in consultation in the dental department of the Toulouse University Hospital.

This study aims to evaluate the effect of probiotics 7 days before cesarean section (CS) on postoperative recovery and the change of gut microbiota in pregnant women. Samples were obtained from a total of 202 pregnant individuals, divided into control group and probiotics group. Anal exhaust time and first defecating time were set as the primary outcome of recovery of CS.

This randomized clinical trial evaluates the effect of a mango and chia-based beverage on gut microbiota modulation in 100 Paraguayan children aged 8-16 years with obesity. Participants will consume the intervention beverage for 6 weeks. Fecal samples will be collected before and after each intervention to analyze microbiota composition using 16S rRNA sequencing. This study aims to characterize the gut microbiota of Paraguayan children for the first time and assess whether this functional beverage can positively modulate intestinal bacteria as a potential strategy to address childhood obesity, which affects 1 in 3 school-age children in Paraguay.

The consumption of plant-based foods, particularly berries, has been associated with improved health due to their high content of bioactive compounds. Among these, polyphenols-especially proanthocyanidins (PACs)-may offer protective effects against chronic diseases related to overweight and obesity. Cranberries are naturally rich in PACs and may positively influence metabolic health by modulating the gut microbiota. However, their specific effects on intestinal integrity and broader metabolic outcomes remain underexplored. The primary aim of this study is to assess the effects of cranberry supplementation on glucose metabolism, insulin sensitivity, blood lipid levels, and the composition and function of the gut microbiota in overweight and obese individuals. This randomized, double-blind, placebo-controlled, crossover clinical trial will include two 12-week intervention periods-one with a cranberry beverage and one with a placebo-separated by a 4-week washout period and preceded by a 2-week lifestyle stabilization phase. Participants will undergo comprehensive metabolic assessments (glucose control, insulin sensitivity, lipid profile), body composition analysis, gut microbiota profiling, and liver fat imaging (MRI in a subsample of female participants). Additional evaluations will include markers of inflammation, appetite regulation, intestinal health, and lifestyle factors.

Idiopathic nephrotic syndrome (NIS) is a clinical entity defined by the association of selective albuminuria, hypoalbuminemia, and nonspecific glomerular lesions (lesions minimal glomerular (LGM) or segmental and focal hyalinosis (HSF). The complication of this kidney disease is the progression towards chronic renal failure and in case of kidney transplantation, its immediate recurrence on the graft . The origin of this syndrome is unknown but a number of clinical observations tend to show an involvement of immune system. A link has been highlighted between atopy, diet and nephrotic flare-ups. The speed of recurrence of this initial disease on the graft and the observation of remissions obtained after treatment by plasma exchange or immunoadsorptions support the presence of a pathogenic plasma factor. Anti-CD20 treatments depleting B lymphocytes has made it possible to favorably treat a number of patients. Dysfunction of regulatory T cells has also been shown in SNI patients. This modification seems linked to allergies and could be due to an aberrant microbiota. The hypothesis of causality between dysbiosis, alteration lymphocyte and triggering of an SNI was mentioned recently. Two studies have shown intestinal dysbiosis in pediatric SNI/LGM, with reduction of T circulating regulators

The goal of this clinical trial is to learn whether microbiome analysis, education, and personalized recommendations can improve gut health and reduce early markers of immune-related conditions in infants aged 0-3 months delivered via Cesarean section. The study aims to determine whether these interventions can increase beneficial bacteria, decrease C-section-associated microbiome signatures, reduce opportunistic pathogens, and improve functional potential for HMO digestion and SCFA production. The study also seeks to assess whether improvements in microbiome composition are associated with a reduced prevalence of early atopic symptoms. Researchers will compare three groups: a full intervention arm that receives microbiome reports, coaching, personalized recommendations, and educational materials; a limited intervention arm that receives simplified reports and basic recommendations; and a control arm that receives no results until study completion. This design allows evaluation of both a comprehensive intervention and a more scalable, minimal-results model. Participants will: 1. Provide six microbiome stool samples over a 24-month period. 2. Provide additional small stool samples at two timepoints for exploratory metabolomic analysis. 3. Receive microbiome reports and guidance according to their assigned study arm. 4. Complete surveys on infant health history, symptoms, diet, and environmental exposures. 5. Participate in standardized eczema assessment(s) administered by a Nurse Practitioner and evaluated by a Pediatric Allergy Specialist if any symptoms are reported. This study seeks to demonstrate that targeted microbiome support can positively shift gut microbial development in C-section infants and may reduce risks linked to the early stages of the atopic march. Findings may inform scalable strategies for delivering microbiome-based support in early life and improve long-term health outcomes for this high-risk population.

This randomized controlled clinical trial aims to evaluate the effectiveness of adjunctive coenzyme Q10 and probiotic supplementation (Limosilactobacillus reuteri Prodentis®) in improving periodontal health in pregnant women undergoing non-surgical periodontal therapy. Forty participants will be randomly assigned to two groups: the test group will receive professional oral hygiene every three months along with a coenzyme Q10-based toothpaste and daily probiotic supplementation; the control group will follow the same protocol without probiotics. The primary outcome is the reduction of the Plaque Index (PI), while secondary outcomes include Bleeding on Probing (BoP), Probing Pocket Depth (PPD), Clinical Attachment Level (CAL), gingival inflammation (MGI, PMGI), plaque distribution (PCR%, API), and gingival recession (R). The study duration is 6 months. The goal is to assess whether this combined therapy can promote a balanced oral microbiota and enhance periodontal health during pregnancy.

Acute coronary syndrome (ACS) remains one of the leading causes of morbidity and mortality worldwide despite major advances in acute management and secondary prevention. Gut dysbiosis has been described as linked to cardiovascular events. Modulating the gut microbiota through symbiotics-a combination of probiotics and prebiotics-represents a promising, low-risk and widely accessible strategy to influence these pathways and contribute to the enhancement of cardiovascular prevention, with regards to the global burden as well as health costs. The SYMBIO-ACS study is therefore designed to assess the effects of a symbiotic intervention on TMAO levels and identify new cardiometabolic biomarkers in patients following ACS, providing essential pilot data for future larger-scale preventive trials.

In recent years, there has been growing interest in the human gut microbiota, whose health is characterised by high microbial diversity. Through the gut-brain axis, the microbiota influences the homeostasis of the central nervous system by regulating neurological, immune and epigenetic functions. Intestinal dysbiosis is associated with various neurological and oncological diseases, including paediatric diseases and colorectal cancer. Recent studies highlight a significant link between microbiota and brain tumours: cancer patients show reduced microbial richness and altered bacterial composition. In addition, an intratumoural microbial population has been identified that can influence tumour initiation, progression and response to therapies by modulating tumour cells and the immune system. The aim of this study is to analyse stool samples to study the microbiota in children suspected CNS brain tumor as there are currently no studies of this kind reported in the literature to assess whether microbial changes can be detected at diagnosis, can be found during the course of the disease or are associated with tumour progression.

The small intestine is an understudied frontier of microbiome research. While aspiration during endoscopy is considered the gold standard to assess small bowel bacteria, the tools for sterile retrieval are primitive and poorly validated. Endoscopic aspiration is time-consuming and prone to contamination. Inspired by plants' ability to draw water by capillary action, a novel multi-capillary sterile system was designed which is a modified version of the conventional aspiration catheter. The purpose of this study is to examine the time and volume capabilities of this catheter in suctioning various liquids compared to conventional aspiration catheter, in two groups, each includes 23 patients that going under endoscopy at GI lab at Cedars Sinai Medical Center. The investigator will collect up to 2 ml fluid from Duodenum- in first group by using the conventional catheter and in second group by using the capillary catheter. The time collection and the volume of samples in 2 groups will be compared.

Colorectal cancer (CRC) is one of the most common and deadly cancers worldwide. About 1 in 4 people with CRC already have cancer spread (metastasis) when first diagnosed, and about half develop spread during their illness. Recent research shows that bacteria living in the gut and even within tumors might play an important role in how cancer spreads. The goal of this study is to better understand how bacteria might influence the spread of colorectal cancer. The main questions the investigators aim to answer are: Are there differences in bacteria between people whose cancer has spread and those whose cancer has not spread? Could certain bacteria help predict which cancers might spread? To answer these questions, the investigators will: Collect different types of samples from participants: Tumor tissue Normal tissue near the tumor Tissue from where cancer has spread Stool samples before surgery Study the bacteria in these samples using advanced testing methods Compare bacterial patterns between different groups People can take part in this study if they: Are between 18 and 75 years old Have colorectal cancer confirmed by doctors Have not taken antibiotics recently Do not have immune system problems This research may help us: Understand why some colorectal cancers spread Find new ways to predict which cancers might spread Develop better treatments for colorectal cancer

The goal of this observational study is to learn how the bacteria in the gut and mouth (called the microbiota) are linked to different types of epilepsy and how they may affect how well seizure medicines work. Researchers want to answer two main questions: Are certain types of epilepsy linked to changes in the gut or mouth microbiota? Do the bacteria in the gut change how seizure medicines work for each person? Epilepsy is a brain condition that causes seizures. Even though there are many medicines for epilepsy, some people still have seizures or side effects. Studies in animals show that gut bacteria can raise or lower the chance of seizures. Smaller studies in people suggest the same thing, but they have been limited in size and scope. In this study, researchers will collect biological samples from people who have newly diagnosed epilepsy and from people without epilepsy (called healthy controls). The samples will be tested to learn which bacteria are present. The researchers will then look for patterns that may explain which types of epilepsy are linked to changes in the microbiota. The study will also look at whether the bacteria in the gut and mouth affect how well anti-seizure medicines (ASMs) work. For example, the researchers will explore if certain bacteria make medicines work better or worse. Patients will provide blood, stool and saliva samples. If collected for medical reasons, cerebrospinal fluid (CSF) - the clear liquid that surrounds the brain and spinal cord -will also be used. Healthy controls will provide stool and saliva samples only All participants will be asked to fill an online questionnaire to share health and lifestyle information. Patients also allow researchers to confidentially access data from medical records related to diagnosis and treatment. By comparing data from many participants across Sweden, researchers hope to understand how gut and mouth bacteria influence epilepsy and seizure control. This research may help doctors in the future to use a person's microbiota profile to choose the best seizure medicine. The long-term goal is to improve seizure control, reduce side effects, and raise the quality of life for people living with epilepsy.

The goal of this clinical trial is to test the ability of different bacterial products in restoring natural gut microbiota in C-section born infants. The main question it aims to answer is: Do maternally derived strains of bacteria perform better than commercially available probiotic strains in restoring the gut microbiota of C-section born infants? Researchers will compare the gut microbiota of treated infants to that of untreated C-section born infants and untreated vaginally born infants to see if the bacterial treatments cause the microbiota to resemble that of vaginally born infants. Participants will be given a bacterial product orally once daily for either one or four weeks and be asked to collect faecal, urine and saliva samples.

The FLORA-ACS study aims to evaluate the relationship between dysbiosis and high platelet reactivity during treatment with ticagrelor in patients with a history of acute coronary syndromes and investigate the use of rifaximin to eliminate dysbiosis and thus provide effective antiplatelet treatment.

Endometriosis is a chronic inflammatory, polygenic, and multifactorial disease affecting approximately 10% of women of reproductive age, corresponding to over one million women in France. Endometriosis profoundly impairs the health and quality of life of affected individuals and carries a significant socio-economic burden, making it a major public health concern. To date, the pathogenesis and prognostic factors of disease progression remain poorly understood. Despite current treatment options, which are based on hormonal therapy or surgery, resistance and recurrence are frequent, underscoring the urgent need for innovative therapeutic strategies. The hypothesis of retrograde menstruation of endometrial cells, among other proposed theories, appears insufficient to fully explain the development of the disease. Immunological factors may be implicated. Endometriosis is characterized by the presence of endometriotic tissue outside the uterine cavity- within the peritoneal cavity or at distant sites-forming lesions that, like eutopic endometrium, contain infiltrating immune cells, with varying compositions across menstrual cycle phases. Although data remain scarce, the literature points to several key mechanisms: Inflammation and innate immunity with the dendritic cells, that initiate and orchestrate immune responses, appear to be present in different proportions and exhibit altered phenotypes in endometriotic tissue compared to healthy tissue. Macrophages, essential for phagocytosis, tissue repair, and the resolution of inflammation, also show functional and phenotypic modulation. In particular, efferocytosis-their ability to clear apoptotic cells-is impaired, and an imbalance in M1/M2 polarization has been described, potentially facilitating menstrual cell escape. The local microenvironment is characterized by altered cytokine and chemokine profiles. Natural Killer cells exhibit disrupted expression patterns of activating and degranulation capacity. Microbiota: Many studies suggest a potential role for the intestinal microbiota in the initiation and/or promotion of endometriosis. Patients frequently exhibit gut dysbiosis, marked by reduced microbial diversity. Resolution of Inflammation: Endometriosis may be associated with defective resolution of inflammation. Resolutive pharmacology involves the use of pro-resolving factors to exert a therapeutic effect by accelerating or stimulating the resolution of inflammation. The interplay between local inflammation, the gut microbiota, and disease progression remains incompletely elucidated. A comprehensive phenotypic and functional characterization of immune cells-particularly innate immune cells (dendritic cells, macrophages, Natural Killer cells) - in parallel with microbiome profiling and clinical outcome data, may yield novel insights into disease mechanisms and support the development of pro-resolutive therapeutic strategies that may be of interest in endometriosis. Study Design This will be a monocentric (at Grenoble University Hospital), open-label, prospective experimental study with a control arm. The primary objective is to identify immune biomarkers associated with endometriosis. Secondary objectives include: 1. Identification of immune biomarkers associated with clinical outcomes in endometriosis. 2. Characterization of the immunogenetic KIR/HLA (Killer Immunoglobulin-like Receptors / Human Leukocyte Antigen) system in both study groups. 3. Analysis of stromal cells, apoptosis, macrophage efferocytosis, and their responsiveness to pro-resolutive factors in both groups. 4. Identification of a characteristic bacterial gut microbiota profile at diagnosis in women with endometriosis versus controls, and/or profiles associated with one-year clinical outcomes (favorable vs unfavorable), as well as temporal microbiota trajectories over one year in relation to clinical response. Study Population: The study will include women undergoing surgery for endometriosis versus control women undergoing benign gynecological surgery with no known history or intraoperative evidence of endometriosis, aged 18 to 42. Study Procedures: Women in the endometriosis group will undergo collection of endometriotic lesions, adjacent tissue, eutopic endometrium, and peritoneal lavage during surgery. Controls will provide biopsies of eutopic endometrium, unaffected peritoneum, and peritoneal lavage. For both groups, peripheral blood samples will be collected during routine care and stool samples obtained at baseline (Day 0). For the endometriosis group, a second stool sample will be collected at 12 months (M12). A clinical evaluation will be performed at inclusion for all participants and repeated at one year for the endometriosis group. Participation for control group subjects is limited to the day of surgery, whereas endometriosis group subjects will be followed for 12 months.

The goal of this observational study is to learn about intestinal microbiome structure and function in individuals who have undergone a pancreatoduodenectomy and compare to healthy matched controls. The primary objectives of the study are: 1. To explore and describe any differences in the gut microbiota especially Shannon diversity index 2. To conduct functional profiling by exploring and describing any differences in functional metabolites produced in the gut in people having had pancreatoduodenectomy greater than 6 months ago compared to healthy matched controls. Participants will be asked to complete the following: * Three-day food, bowel and medication diary (see Protocol appendix 5) * Gastrointestinal Symptom Rating Scale (see Protocol appendix 6) * Quality of life questionnaire (see Protocol appendix 7) * Stool sample test using Microba Insight TradeMark (a small swab is taken from soiled toilet paper, sealed in a room-temperature storage capsule and mailed to the testing laboratory)

The goal of this clinical trial is to ascertain whether oropharyngeal administration of colostrum contributes to postnatal growth in very preterm infants (those born before 32 weeks of gestation). The main questions it aims to answer are: Can Oropharyngeal administration of colostrum effectively lower the incidence rate of extrauterine growth restriction (EUGR) in participants? Does oropharyngeal colostrum intervention bring about changes in the early gut microbiota of participants? Researchers will conduct a comparative analysis between colostrum and a placebo (normal saline) to investigate whether oropharyngeal administration of colostrum has a beneficial effect on the postnatal growth of participants. Participants will: Initiation of oropharyngeal colostrum administration will take place within 48 - 72 hours after birth, and the treatment will be administered continuously for a period of 5 days. Stool samples will be collected from the participants both before and after the intervention. Participants will be required to maintain a diary to document their basic characteristics and clinical outcomes.

Neonates delivered by scheduled Cesarean Section will be randomized to receive vaginal seeding (exposing the infant to Mother's vaginal flora) or sham. Infants will be followed for three years to examine health outcomes including microbiome development, immune development, metabolic outcomes, and any adverse events.

Anorexia nervosa (AN) is a serious mental disorder occurring mainly in women. AN is characterized by severely restricted food-intake and subsequent low weight. The disease burden for the individual is high with medical complications and psychiatric comorbidities. Despite decades of research, there are large gaps in the understanding of the biological aspects of AN and lack of effective interventions. Current clinical treatment is associated with gastrointestinal problems, high rates of relapse and poor outcome causing long-term sickness absence and disability. During the COVID19 pandemic the prevalence and severity of AN has spiked. Therefore, there is great need of novel strategies for AN treatment, that can be easily implemented in the clinic without adding complexity to the standard care of treatment. During the resent years it has been proposed that mental disorders might be treated via manipulating the composition and function of the microbes that live in the gut (the microbiota) by adding or restricting fermentable nutrients (prebiotics) in the diet. However, in order to use prebiotics to treat the microbiota in AN patients, more knowledge is needed on how the AN microbiota is affected by the current standard care treatment. Whether prebiotics can be useful for normalizing AN microbiota remains to be established. The overall aim of the "Norwegian study of Microbiota in Anorexia Nervosa" (NORMA) is to join forces of researchers, clinical health care services and voluntary sector in a transdiciplinary approach to improve the understanding of the role of the gut microbiota in AN patients. The current project will include a clinical trial in AN patients and experimental studies to screen novel prebiotics for their ability to modify and normalize AN derived microbiota. The long-term goal of the project is to pave the way for a targeted and clinically feasible individualized treatment for better tolerable weight-restoration and improved health in AN patients.

Cirrhosis is a common digestive system disease and represents the final stage of the progression of various chronic liver diseases. During cirrhosis, the intestinal microenvironment is affected due to liver damage and increased portal venous pressure. Displacement of gut microbiota is closely related to the occurrence and development of cirrhosis. Disruption of the gut microbiota is associated with changes in the levels of nitric oxide (NO), hydrogen (H₂), methane (CH₄), and hydrogen sulfide (H₂S). Breath testing is an emerging method for assessing gut microbiota. This project aims to investigate the characteristics and prognosis of patients with chronic liver disease by detecting exhaled breath markers such as nitric oxide (NO), hydrogen (H₂), methane (CH₄), and hydrogen sulfide (H₂S), in conjunction with results from serological tests, gut microbiota analysis, and radiomics. The goal is to identify new diagnostic biomarkers and therapeutic targets, to recognize high-risk patients at an early stage, and to improve patient survival rates and quality of life.

Colorectal cancer is the third most common cancer worldwide, yet it was the second leading cause of cancer-related deaths in 2020. The average French population faces a colorectal cancer risk partly linked to lifestyle factors. The majority of colorectal cancer cases (approximately 85%) are not caused by hereditary mutations. Environmental factors, such as lifestyle or diet (notably through endocrine disruptors), can affect the gut microbiota (a collection of microorganisms - bacteria, viruses, parasites, and fungi - residing in the intestinal environment) and lead to disturbances in its composition, referred to as dysbiosis. While the mechanisms underlying dysbiosis associated with colorectal cancer remain poorly understood, the involvement of certain ingested substances, known as xenobiotics, is increasingly suspected, including endocrine disruptors. Among the most common endocrine disruptors found in water and food are parabens and phthalates, which will be examined in detail in this study. These substances may be directly involved in the development of colorectal cancer and in response to its treatment. The main objective of this studie is to characterize the relationship between colorectal cancer diagnosis, activity/composition of the gut microbiota, and patients' exposure to selected endocrine disruptors, particularly parabens and phthalates.

The human body inhabits a complex consortium of different microbes which together form the microbiota. Virtually every surface of the human body is colonized by a distinct microbiota, forming complex communities. An increasing number of research results indicates that changes in the microbiota can have vast effects on the health of its host. Most studies investigating the microbiota were conducted on animals, as many interventions and investigations cannot be performed on humans due to ethical considerations. This raises the question if findings from experimental studies are translational and can benefit patients. That becomes especially apparent when trying to dissect molecular mechanisms involved in this fine-tuned interplay between nutrients, the microbiota, and its host. By establishing human organoid cultures from the large and small intestine that can be exposed to microbes and/or microbial products with subsequent transcriptomic, epigenetic and immunological analysis, the investigators aim to generate findings with high translational potential with new insights into the complex interaction of the microbiota, the host and its immune system.

This monocentric study aims at evaluating the effects of fecal microbiota transplantation from newly diagnosed cachectic and non-cachectic pancreatic cancer patients, and healthy volunteers on several cachexia-related parameters of germ-free mice.

The study aims to investigate the effects of sleep deprivation on women's health across different phases of the menstrual cycle.