Clinical Research Directory

REMBRANDT: REcovery of the MicroBiome fRom Antibiotics for Dental implanTs

Antimicrobial therapy can lead to disruption of the gut microbiome and infection with Clostridioides difficile, a disease associated with high morbidity and mortality, particularly among the elderly. Drawing on observations that pet ownership and close contact with pets are protective against colonization with C. difficile and recurrence of C. difficile infection, the proposed study will test the hypothesis that microbiota that provide colonization resistance against C. difficile are shared between patients and their pets and that pet contact can mitigate antimicrobial-associated gut dysbiosis and the risk of C. difficile infection. This study will further define epidemiologic and pathophysiologic characteristics of C. difficile infection and gut microbiome dysbiosis that could enhance therapeutic options for these conditions, potentially through non-invasive interventions involving animal contact.

Determination of Vaginal Colonization and the Effect of an Oral Probiotic (PROSALVAG)

The aim of this study is to determine the efficacy of an oral nutraceutical with probiotics in restore vaginal health.

Effect of Bioflor on Gut Microbiota in Proton-Pump Inhibitor Users

Proton-pump inhibitors (PPIs) are widely used to treat acid-related stomach problems, such as heartburn and acid reflux. Long-term use of PPIs has been linked to changes in the gut bacteria and fungi (called the gut microbiota), which may contribute to digestive side effects. Bioflor® is a probiotic product containing a yeast called Saccharomyces boulardii, which has been used to help with various digestive problems. However, little is known about how Bioflor affects the gut microbiota in people who are taking PPIs. This study enrolled three groups of adults at four hospitals/research centers in Korea: a control group without digestive symptoms who were not taking a PPI, a group of patients with reflux symptoms who started taking a PPI alone, and a group of patients who started taking a PPI together with Bioflor for 8 weeks. Participants completed symptom questionnaires and provided stool samples before and after treatment, which were analyzed to study changes in gut bacteria and fungi. The purpose of this study was to compare gut microbiota composition and digestive symptoms between PPI users who did and did not take Bioflor, in order to better understand the role of Bioflor in people taking PPIs.

Effects of Synbiotic Supplementation on Gastrointestinal Symptoms, Appetite, and Nutritional Recovery in Patients After Autologous Bone Marrow Transplant

Patients undergoing autologous bone marrow transplantation (ABMT) receive high-dose chemotherapy and routine prophylactic antibiotics, which often disrupt the gut microbiome (dysbiosis). This imbalance can lead to debilitating gastrointestinal complications, loss of appetite, decreased dietary intake, and malnutrition, impairing recovery. The purpose of this randomized controlled trial is to evaluate whether daily supplementation with a tri-component synbiotic (combining multispecies probiotics, xylo-oligosaccharide prebiotics, and a tributyrin postbiotic) can improve gastrointestinal symptoms, appetite, and nutritional status in adult hematological cancer patients following autologous bone marrow transplantation. Participants will be randomly assigned (1:1 ratio) to either: 1. Control Group: Receiving standard post-transplant nutritional care based on clinical guidelines. 2. Intervention Group: Receiving the same standard nutritional care plus a daily oral synbiotic capsule for 3 months. Participants will be followed during the 3-month intervention period and for an additional 1-month post-intervention follow-up phase to assess the sustainability of benefits. The study will evaluate digestive symptoms, self-reported appetite, dietary intake, body weight, inflammatory markers (fecal calprotectin), and protein status (serum albumin), while closely monitoring participant safety.

FMT for 90-Day Outcome of Clinical Use in ICU Sepsis

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection, representing one of the leading causes of death in intensive care units (ICUs) worldwide. Gut microbiota disruption is increasingly recognized as a key driver of persistent inflammation and multiple organ dysfunction in septic patients. Fecal microbiota transplantation (FMT) has emerged as a promising approach to restore gut microbial homeostasis. This study hypothesizes that FMT acts not through long-term engraftment of donor microbes, but via a "functional pulse" - a potent, transient biological intervention that delivers high-dose microbial metabolites (e.g., short-chain fatty acids), competitively inhibits pathogens, and rapidly modulates intestinal immune cell functions. This is a single-center, open-label, randomized controlled trial conducted in the ICU of Union Hospital, Tongji Medical College, Huazhong University of Science and Technology. A total of 60 adult patients diagnosed with sepsis according to Sepsis-3 criteria within 24 hours of ICU admission will be randomized in a 1:1 ratio to receive either ICU standard care alone (control group) or ICU standard care plus FMT administered via a nasojejunal tube for three consecutive days (intervention group). The primary endpoint is all-cause mortality at 90 days. Secondary endpoints include ICU mortality, in-hospital mortality, 28-day mortality, changes in gut microbiota composition and metabolites, serum citrulline levels as a marker of intestinal barrier function, Sequential Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation II (APACHE II) scores, vasopressor requirements, C-reactive protein and procalcitonin levels, fluid balance, incidence of ICU delirium and feeding intolerance, and 90-day hospital readmission rate. Safety outcomes include gastrointestinal symptoms and transient fever.

Gut Microbiome in Gynecological Cancer Patients With Pelvic Toxicity: Controls Versus Ozone Treatment. (MicrOzoGineTox)

Patients treated for gynecological tumors with radiotherapy (RT) and/or chemotherapy (CT) frequently develop pelvic toxicity (TPIRQT), a condition that can become persistent, progressive, and refractory to standard treatments. This toxicity, affecting the rectum (proctitis), bladder (cystitis), and vagina (mucositis), severely deteriorates quality of life. Standard options for refractory cases are limited; at our center, rectal ozone therapy is used with high rates of symptomatic improvement (66-75%). Emerging evidence suggests a link between gut microbiota and the development of TPIRQT. However, it is unknown how rectal ozone therapy may influence the gut microbiome or if this modulation is part of its therapeutic mechanism. This prospective observational study will investigate the potential relationship between gut microbiome profiles (composition and diversity), the presence and severity of TPIRQT, and the response to rectal ozone therapy.

Assessment of the Impact of Type of Probiotic, Delivery Type and Feeding Type on Baby's Microbiota After Dysbiotic Delivery

This study aims to determine the effect of three factors (delivery type, feeding type and the use of two different dietary supplements) on rebiosis after disbiotic delivery. This is a randomized, single-blinded study with two parallel arms. Group 1 will receive L. reuteri (10\^8 CFU) once a day, group 2 will receive B. longum and P. Pentosaceus (10\^9 CFU) once a day. The total duration of intervention will be 3 months.

My Baby Biome: Infant Stool Samples for Microbiome Health (MBB)

My Baby Biome is an observational study that will use 600 infant stool samples to determine the biomarkers associated with a healthy infant gut. Biomarkers identified in this study will be used to develop precision probiotics and LBPs for improving infant gut health outcomes to the benefit of all infants. Parents will be asked to submit follow-up questionnaires regarding infant immune health to improve insights obtained from the data.

Effect of Agave Consumption on Performance and Gut Microbiota in Adults Undergoing Physical Training

The purpose of this study is to analyze changes in the gut microbiota of healthy adult athletes, both men and women, before and after supplementation with a dietary fiber (agavins). Each participant will be their own control, so the design will allow us to identify whether the intervention generates changes in bacterial composition and whether these changes are related to variations in physical performance. The study will determine changes in the gut microbiota, athletic performance, and markers of metabolic stress such as lactate and creatine kinase. Volunteers will be required to take 10g of agavins in warm water for 6 weeks. The gut microbiota will be evaluated through a stool sample, while athletic performance will be measured through direct calorimetry, determining VO2max. Lactate will be determined by finger prick using Accutrend Plus equipment, while creatine kinase will be measured using a blood sample taken by staff from the biomarker measurement laboratory of the Department of Nutrition and Functional Foods.

Fecal Microbiota Transplantation by Oral Capsules for Hepatic Encephalopathy Treatment

This interventional study aims to evaluate the safety and efficacy of oral capsule fecal microbiota transplantation (FMT) for treating hepatic encephalopathy refractory to conventional rifaximin and lactulose therapy in patients with liver cirrhosis. Patients diagnosed with hepatic encephalopathy refractory to rifaximin and lactulose therapy will be randomized into three groups. While continuing conventional therapy, the first group receives FMT via colonoscopy and oral capsule administration, the second group receives only oral capsule administration, and the third group serves as a control, receiving only conventional therapy. The aims of the study are: To evaluate the efficacy and safety of FMT by oral capsules in cirrhotic patients with hepatic encephalopathy refractory to standard therapy. To evaluate changes in the gut microbiota composition and in the intestinal and systemic inflammatory condition occurring after FMT and if they can be associated with clinical improvement. To evaluate metabolic modifications occurring after FMT and if they can be associated with clinical improvement.

Metabolic and Functional Study of γδ T Cells in Critically Ill Patients

This prospective observational cohort study investigates the subset-specific metabolic adaptation and functional remodeling of cytotoxic γδT cells in critically ill patients with and without sepsis. Emerging evidence indicates that γδT cells, as a bridge between innate and adaptive immunity, play a critical role in early anti-infection defense during sepsis. However, the functional status and underlying regulatory mechanisms of cytotoxic γδT cells in septic patients remain incompletely understood. Our preliminary single-cell transcriptomic analysis revealed that cytotoxic γδT cells from septic patients exhibit significant alterations in cytotoxicity-associated molecules (GZMB, PRF1, GNLY) and mitochondrial oxidative phosphorylation (OXPHOS) pathway genes, particularly COX6C, which correlates with cytotoxic effector molecule expression. This study aims to systematically characterize the proportion, cytotoxicity, and mitochondrial metabolic function of circulating cytotoxic γδT cells across three cohorts: healthy controls, critically ill non-septic patients, and critically ill septic patients. By integrating flow cytometry, mitochondrial function assays, and functional validation experiments, we seek to elucidate the role of COX6C-mediated mitochondrial metabolic abnormalities in cytotoxic γδT cell dysfunction, providing theoretical basis for understanding immune dysregulation in sepsis and identifying novel therapeutic targets.

Almonds, Gut Microbiome and Kids

This 8-week parallel-arm randomized controlled trial (N=70; ages 6-13) will determine the impact of daily almond butter consumption on gut microbiome composition and function, intestinal barrier integrity, and cardiometabolic health in school-aged children. Participants will be randomized to either a once-daily snack of personalized-portion almond butter (ALB; 16g, Creamy Natural Almond Butter) or an isocaloric nut-free chocolate spread control (CTL; 16g, Cadbury Milk Chocolate), each served on two plain unsalted saltine crackers, added to their habitual diet. The primary outcomes include oro-gut microbial composition and diversity, gut microbial functional capacity and metabolomics (SCFAs, bile acids, amino acid metabolites), and intestinal barrier integrity. Secondary outcomes include fasting cardiometabolic markers, systemic inflammation, appetite-regulatory and metabolic hormones, and sleep-related biomarkers. Feasibility, adherence (weekly logs; serum α-tocopherol), and precision nutrition potential will also be assessed, with stratified analyses by age, sex, BMI, ethnicity, and pubertal stage. This pilot trial will generate the first multi-omics characterization of almond butter's effects on the gut-immune-metabolic axis in children.

Pulse Education and Children

This parallel-arm, randomized controlled trial will evaluate the effectiveness of a 6-week pulse-focused nutrition intervention in school-aged children (6-13 years). The study aims to assess adherence to a pulse-based diet providing 1.5 cups of pulses per week and to examine the effects of whole-cooked pulse consumption on gut health, including gut microbiome composition, metabolomic profiles, and gut barrier function. Secondary objectives include evaluating the impact of pulse consumption on markers of metabolic health and inflammation. Forty participants will be randomized to either a pulse-focused nutrition education program with weekly provision of pre-measured pulses (black beans, lentils, and chickpeas) or a pulse-focused nutrition education program in which participants independently procure their own pulses. Participants will follow the assigned intervention for 6 weeks.

Microbiome Metabolites and Alcohol in HIV to Reduce CVD RCT

Among people living with HIV, heavy drinking increases the risk of heart disease and death. Studies suggest that alcohol changes the number and kind of bacteria in your gut and these changes increase the risk of heart disease and death. This randomized controlled trial will determine whether a pill containing healthy gut bacteria can increase the number good bacteria in the gut, lower levels of inflammation, and lower the risk of heart disease and death.

Probiotics in the Prevention of Recurrent Prosthetic Joint Infection of the Hip and Knee

Prosthetic joint infection (PJI) is one of the most devastating complications following total joint arthroplasty (TJA) of the hip and knee. Standard of care (SOC) treatment includes surgery and antimicrobials. Morbidity and mortality remain high despite contemporary treatments. The human body is colonized by billions of organisms, collectively, the microbiome, which is central to healthy immune function. Microbiome disruption, dysbiosis, can impair the immune response to infection. Despite recent evidence that suggests dysbiosis may be implicated in PJI, the role of probiotics in the treatment of PJI is unknown. Perioperative probiotics have been demonstrated to be safe and effective for infection prevention in abdominal surgery. The investigators hypothesize that perioperative probiotics will reduce re-infection in patients treated for PJI. A multi-centered, randomized controlled trial (RCT) at two academic, tertiary care centers will be conducted to determine the impact of probiotics on recurrent infection following treatment for PJI. Controls will receive SOC; study patients will receive a probiotic, started shortly after the initiation of and for the duration of their antibiotic therapy + 7 days, in addition to SOC. Primary outcome is re-operation for recurrent infection within 1 year.

Fecal Microbiota Transplantation in Axial Spondyloarthritis

Although biologic therapy have revolutionized the treatment of Spondyloarthrtitis (SpA), many patients do not experience complete relief of SpA related complaints. It has been established that patients with SpA have an altered composition of microorganisms (microbiota) in the gut compared to healthy controls, and that this correlates to disease activity and respons to therapy. The goal of this randomized double-blind study is to evaluate the efficacy of fecal microbiota transplantation (FMT) in patients with axial SpA with a suboptimal effect of biologic therapy. The main questions it aims to answer are: * Can FMT reduce disease activity in axial SpA? * Can FMT alleviate pain and reduce fatigue in axial SpA? * Is the composition of microorganisms restored to normal in patients with SpA after a treatment with FMT? Participants will receive a single treatment in the form of an enema with either donor FMT or placebo at baseline. The primary endpoint will be evaluated after 90 days, but efficacy and safety will be monitored from baseline until 365 days.

Dietary Pattern Intervention for Neurodevelopment in Preterm Infants

The purpose of this randomized controlled trial is to evaluate the effect of a structured, high-prebiotic dietary pattern on the neurodevelopmental outcomes of preterm infants. The intervention lasts for 6 months and aims to promote the growth of endogenous beneficial gut bacteria through targeted complementary feeding. The primary outcome is assessed by the Gesell Developmental Schedules or the Ages \& Stages Questionnaires (ASQ-3). Secondary outcomes include longitudinal changes in gut microbiota composition,targeted metabolomics (such as short-chain fatty acids and tryptophan metabolites), and systemic inflammatory markers.

A Study of Healthy Microbiome, Healthy Mind

Researchers are doing this study to find out if a high fermented food diet is tolerable, and if it will help improve quality of life after surviving a critical illness, including severe COVID-19, by promoting gut health recovery and decreasing gut inflammation.

Probiotics Supplementation for Neurodevelopment in Preterm Infants

The purpose of this randomized controlled trial is to evaluate the effect of daily supplementation with a probiotic mixture on the neurodevelopmental outcomes of preterm infants with a history of neonatal antibiotic exposure. The intervention lasts for 6 months. The study hypothesizes that early gut microbiota remodeling via exogenous probiotics can improve neurodevelopment. The primary outcome is assessed by the Gesell Developmental Schedules or the Ages \& Stages Questionnaires (ASQ-3). Secondary outcomes include longitudinal changes in gut microbiota composition,targeted metabolomics (such as short-chain fatty acids \[SCFAs\], and systemic inflammatory markers.

Association Between Fecal Microbiota Composition, Metabolite Concentrations, and Indoxyl Sulfate Levels

Gut dysbiosis is frequently characterized by decreased microbial diversity and alterations in the abundance of certain microbial species. In individuals with chronic kidney disease (CKD), dysbiosis and metabolic imbalances are prevalent, contributing to the buildup of gut-derived retention solutes and metabolites in the bloodstream. Research has consistently shown that CKD patients exhibit lower levels of beneficial gut bacteria. However, the specific functional changes in gut microbiota and their interactions with levels of uremic toxins in hemodialysis (HD) patients remain incompletely understood. This study seeks to explore the association of fecal metagenomics and targeted metabolomics in a cohort of 60 patients with different levels of to characterize the complex interplay between the gut microbiome and fecal and serum metabolites.

Impact of TAVI on the Gut Microbiota and Its Metabolites

Aortic stenosis is a common heart valve disease in older adults. It occurs when the aortic valve becomes narrowed, making it harder for blood to flow from the heart to the rest of the body. Without treatment, this condition can lead to serious complications and reduced survival. A widely used treatment is transcatheter aortic valve implantation (TAVI), a minimally invasive procedure that replaces the diseased valve and improves blood flow. Recent research suggests that heart diseases, including aortic stenosis, may affect the gut (intestinal) environment. The gut contains trillions of microorganisms (called the gut microbiota) that play an important role in digestion, immunity, and overall health. In patients with heart conditions, reduced blood flow may impair the intestinal barrier and alter the balance of these microorganisms. This imbalance may contribute to inflammation and other complications. This study aims to better understand how aortic stenosis and its treatment with TAVI influence the gut microbiota and intestinal health. Researchers will measure specific substances produced by gut bacteria (called metabolites) in blood and stool samples. These include bile acids, trimethylamine N-oxide (TMAO), tryptophan-related compounds, and short-chain fatty acids. Samples will be collected before and three months after the TAVI procedure. In addition, genetic analysis of stool samples will be performed to identify and compare the types of bacteria present before and after treatment. The goal is to determine whether improving heart function with TAVI can restore a healthier gut environment. This may help identify new ways to improve outcomes and reduce complications in patients with aortic stenosis.

Almonds to Improve Gut Health and Decrease Inflammation

Almonds are a good source of beneficial compounds. This study will investigate if eating almonds everyday for 12 weeks can affect gut health and inflammation in persons with metabolic syndrome. Investigators will measure changes in metabolism, heart health, and the levels of vitamins and other compounds from almonds.

Effect of Lentils and Chickpeas on Gut Microbiome and Metabolic Health

The primary goal of this research is to evaluate the effect of daily whole-cooked chickpea and lentil consumption for 8-weeks on gut health, including microbiome-metabolome arrays and gut epithelial/barrier function, in healthy young adults. Secondary Objectives include: * To examine the effect of daily whole-cooked chickpea and lentil consumption for 8-weeks on the measures of metabolic health and inflammation in healthy young adults. * To determine the feasibility of healthy young adults to successfully incorporate and sustain the recommended daily intake of pulses into their diets for eight consecutive weeks Research Interventions: Participants will be asked to consume a normal diet supplemented daily with either A) whole-cooked canned lentils, or B) whole-cooked canned chickpeas. The control condition will be instructed to consume a normal diet while restricting all pulse intake throughout the study.

Prebiotic Effects of California Grapes on Gut Health and Cardiometabolic Health in Overweight Men and Women

The goal of this clinical trial is to assess the impact of table grape consumption on gut microbiome, intestinal permeability, systemic inflammation, and vascular function in healthy overweight men and women aged 45-70 years. The main questions it aims to answer are: * Does daily grape intake alter intestinal microbiome composition and intestinal permeability? * Are changes in gut microbiota and intestinal permeability correlated with changes in cardiometabolic risk factors (inflammation, vascular function, lipid profiles)? * Does response to grape intake on gut microbiota, intestinal permeability, cardiometabolic and inflammatory markers differ between men and women? * Are metabolic pathways modified by grape consumption able to explain the link between gut health and cardiometabolic factors? Researchers will compare freeze-dried grape powder to placebo powder to see if grape powder improves cardiometabolic risk factors. Participants will * Consume the powder dissolved in water twice daily for 3 weeks * Follow their usual diet, modified to limit polyphenol-rich foods * Visit the clinic at the beginning and end of the intervention for vascular measurements and blood sample collection * Complete a 3-day 24-hour dietary recall and collect stool sample before each visit