Studies conducted at the Microbiome Research Center

Our various studies conducted at the Microbiome Research Center at Shamir Medical Center (Assaf Harofeh) may be divided into 2 types:

  1. Diagnostic studies dealing in analysis and characterization of the human microbiome composition in various health and illness states.
  2. Conducting fecal microbiota transplantation for various medical indications and testing the effect of this treatment on subjects.

Diagnostic studies:

  • Characterization of the composition of the microbiome in various populations and the connection to Clostridium difficile infection

The bacterium Clostridium difficile is acquired by humans by feco-oral transmission and through contact with the environment. Certain strains of this bacterium produce toxins and may cause severe gastrointestinal symptoms such as diarrhea, fever and abdominal pain and even severe infectious intestinal diseases. The main risk factor for the onset of the disease is lengthy antibiotic therapy that disturbs the balance of the intestinal bacteria population, meaning that this infection is common in hospitals and nursing homes. At the Microbiome Research Center we are conducting a number of studies in various population groups:

(*) Children who are carriers and non-carriers of CD – most carriers of the bacterium are children under the age of two and most have no disease symptoms, so they may be a source of infection in high risk populations. Our main goal is to characterize the composition of the bacteria population in the gastrointestinal tract of children who are CD carriers and non-carriers with the aim of increasing our understanding of the factors affecting CD colonization and the tendency for infection/

For this study we enroll healthy infants and toddlers up to two years of age, without:

- Gastrointestinal symptoms such as vomiting, diarrhea, reflux, etc.

- Previously documented disease caused by Clostridium difficile.

- Chronic diseases or regular medication.

(*) Patients suffering from recurrent CD infection and treated by fecal microbiota transplantation – in the last decade, microbiome transplantation or fecal microbiota transplantation has been gaining momentum around the world and in hospitals in Israel. In this procedure, bacteria are taken from the stool of a screened, healthy individual and are inserted into the gastrointestinal tract of a patient suffering from CD, thus treating the pathogenic bacterium and allowing proliferation of the normal intestinal bacteria environment to prevent recurrence of Clostridium once the antibiotic therapy is over. The transplantation is done using capsules based on stool samples from healthy donors, like ordinary fecal microbiota transplantations.

In these studies, we wish to characterize the microbiome of patients who have been diagnosed with recurrent CD infection and identify the specific bacterial strain. We also wish to identify the connection between the variety of bacteria in patients reporting success of treatment and those reporting failure, and the connection between the bacterial population composition in transplant recipients compared to that of donors.

  • Comparison of the microbiome of men with infertility to men with normal fertility:

The common definition of “infertility” is inability to become pregnant after sexual intercourse during ovulation for a year. The frequency of infertility in Israel is 18%-20% of couples of childbearing age, and in 30% of those applying for an investigation due to infertility, the cause is the male partner. Abnormal sperm is caused by many reasons, including genetic, hormonal and anatomical disorders, but is also affected by lifestyle, including physical activity, nutrition and environmental exposure.

In a number of studies, a connection has been found between the intestinal microbiome and nutrition and lifestyle and pathological conditions such as obesity, diabetes, autoimmune diseases, allergy and more. Our goal in this study is to examine the relationship between intestinal microbiome and male infertility and sperm question, and comparing the microbiome composition in fertile men to those of infertile ones due to abnormal sperm.

  • The effect of hyperbaric oxygen therapy on the composition of the human microbiome:

Hyperbaric oxygen therapy is treatment involving breathing oxygen in which the patient is in a pressure chamber that has a pressure higher than atmospheric pressure and breathes 100% oxygen at ambient pressure. Under these conditions, the oxygen passes from the lungs to the bloodstream, in which it becomes dissolved and makes its way to tissues in greater quantities that the hemoglobin in red blood cells can carry (up to 20 times the normal, ordinary quantity in the blood). Using this method, body tissues are enriched with very large quantities of oxygen, which cause faster natural healing and various physiological processes, such as wound healing and edema treatment, angiogenesis (formation of blood vessels), building of tissues and improvement in the immune system’s response. The purpose of this trial is to test for hyperbaric oxygen therapy’s effect on the composition of intestinal bacteria (the microbiome) in humans. We hypothesize that hyperbaric oxygen therapy changes the composition of intestinal bacteria in favor of oxygen tolerant ones. This change has potential health effects and some of the beneficial effects of hyperbaric therapy may be due to this change.

  • The connection between antibiotic therapy in newborns, the microbiome composition and the body’s response to vaccines:

The fetal gastrointestinal tract is sterile and is rapidly populated by various bacterial populations immediately after delivery. The composition of bacteria has a vital functioning in shaping inflammatory responses and in the normal development of the immune system. A lot of research has been conducted in recent years to examine how the microbiome changes in the course of various diseases, and one may find changes in inflammatory bowel diseases, asthma and other diseases. There are various factors that can affect the way in which bacteria populate the gastrointestinal tract, including delivery type (vaginal versus cesarean section), nutrition and exposure to antibiotics. Various studies on mice have demonstrated that exposure to antibiotics at a young age can affect the normal development of the immune system. In addition to this it is known that antibiotics at a young age increase the risk of developing inflammatory bowel disease.

Many newborns receive antibiotic treatment after delivery due to maternal risk factors (such as maternal fever), clinical or laboratory findings of the newborn. In most cases, antibiotics are discontinued after a few days, but the long term effects of this treatment are unknown. In this study, we are examining the connection between use of antibiotics in infancy and changes in the microbiome and the body’s reactions to vaccinations. To this end we enroll healthy neonates who have been born at full term (week 37-42) and of normal birth weight and follow up the change in the microbiome composition (by collecting stool samples) for 9 months from the day of birth and taking a single blood sample for research purposes.

Fecal microbiota transplantation study

  • Fecal transplantation in children with autism and gastrointestinal disorders:

Many studies show that 50% of children on the autistic spectrum suffer from at least one gastrointestinal disorder (constipation / diarrhea / distension / pain and discomfort / reflux / incontinence / nausea), and that the severity of their autism is affected by this. There are a range of hypothesized causes of the connection between autism and gastrointestinal disorders, and the

central nervous system may reciprocally interact with the bacteria in the gastrointestinal tract. Many researchers believe that there is a connecting axis between microbiota, the gastrointestinal tract and the brain, and studies in mice have shown that gastrointestinal bacteria affect their central nervous system and behavior. In addition to this, they demonstrated a difference in microbiome composition in the gastrointestinal tracts of children with autism compared to neurotypical children, meaning that a change in the intestinal bacteria composition in children on the autistic spectrum may result in a change in gastrointestinal symptoms and possibly have benefit for their autism. The purpose of the study is to examine the safety and efficacy of fecal microbiota transplantation 3 weeks after treatment of gastrointestinal symptoms in children with autism and gastrointestinal disorders. In addition to this, we are interested in examining whether fecal microbiota transplantation from a healthy individual may affect the microbiome composition and whether this change will positively correlate with gastrointestinal and autism symptoms.

For this study, we are enrolling children aged 7-20 on the autistic spectrum who are experiencing at least one gastrointestinal symptom that impairs their life routine, are not taking antibiotics or anti-inflammatory drugs and are capable of swallowing capsules.

  • Fecal microbiota transplantation in patients suffering from irritable bowel syndrome:

Irritable bowel syndrome (IBS) is a syndrome that involves chronic abdominal pain, discomfort and feeling of fullness of the gastrointestinal tract and changes in bowel movements. This is a functional syndrome, i.e. there are no signs of inflammatory disease in the intestine or other explanations that can be proved by various tests, such as celiac, lactose intolerance or various infections. Changes in bowel movements can include diarrhea or constipation, and the syndrome is diagnosed by criteria known as ROME. The main cause of this syndrome is unknown, but there are a number of theories, the major one stating that there is a problem in the interaction of the brain with the gastrointestinal tract. It is known that intestinal bacteria have an important functioning in maintaining the normal activity of the gastrointestinal tract, and disturbing the microbial balance may cause the onset of various gastrointestinal syndromes. Therefore we believe that the effect of intestinal bacteria through fecal microbiota transplantation may lead to an improvement in the health condition in irritable bowel syndrome patients. Men and women aged 18-60 diagnosed as having irritable bowel syndrome according to the ROME IV criteria will participate in this study.

  • Fecal microbiota transplantation in patients suffering from ulcerative colitis:

Ulcerative colitis is a chronic inflammatory disease that usually affects the rectum region and spreads proximally along the entire colon through an increased immune system response. This disease affects two main age groups: the younger group aged 15-30, and a 60-80 year old age group. The most common symptoms of ulcerative colitis are: bloody diarrhea, convulsive abdominal pain and discomfort during defecation, and possible weight loss, fever and anemia. In addition to this, in 10 to 20 percent of cases, symptoms that are not directly related to the gastrointestinal tract may appear, such as: skin rashes, joint pain or swelling and liver disease. This disease is more common in people who have relatives with ulcerative colitis, which indicates the involvement of genetic factors in the disease. In recent years, more evidence has accumulated to show that the colitis patient’s intestinal bacteria profile differs from that of healthy individuals, so we hypothesize that fecal microbiota transplantation in colitis patients from healthy individuals will restore the bacterial balance to the normal state, which may help improve their disease symptoms. At the microbiome research center at Shamir Medical Center, studies are underway in 2 different population groups:

(*) Naïve patients suffering from mild-moderate ulcerative colitis – this patient group includes the adult population group aged 18-70 diagnosed in recent months and not treated with anti-inflammatory or immunomodulatory drugs. The disease symptoms in naïve patients are not expressed because the disease is in remission.

(*) Children suffering from mild-moderate ulcerative colitis – this patient group includes the young population aged 12-18 diagnosed in recent months and not treated with anti-inflammatory or immunomodulatory drugs.

  • Autologous fecal microbiota transplantation in patients suffering from inflammatory joint diseases:

Arthritis is a general name for a group of diseases in which inflammation develops in the joints, leading to pain and structural damage. This is a common group of diseases and its main symptoms include: pain, stiffness, restriction of joint movement and inflammatory reactions manifesting in pain, heat and redness of the skin in the joint area. The two most common types of arthritis are: generative joint disease (osteoarthritis) and rheumatoid arthritis (RA). Inflammatory joint diseases are characterized by spontaneous eruptions and remissions. In sates in which the arthritis is active and prolonged, medication often achieves low inflammatory activity and even remission. Many studies have shown that the intestinal bacteria composition is different in patients with inflammatory joint diseases than healthy individuals. Recently, a number of studies have also shown evidence that medication for these diseases results in a change in the intestinal microbiome after an improvement in patients’ conditions. We estimate that maintaining the new bacterial flora that is formed after medication by performing autologous fecal microbiota transplantation may lead to a low disease activity level, thus reducing the need for chronic medication.