Current guidelines mandate Helicobacter pylori (H. Pylori) eradication with 2-3 antibiotics for 14 days ,This may result in multiple side effects and in eradication of important bacterial species to human health, exposing humans to multiple disease conditions.

Preservation of fecal microbiome prior to antibiotic therapy and auto-transplantation of the microbes post H. pylori eradication, will enable avoiding eradication of beneficial microbial populations and perhaps protect from consequent disease conditions.

This is a pilot study. Prior to antibiotics therapy for their baseline H.Pylori infection, patients will be asked to deliver at least 50 grams of fresh stool to the Tel Aviv Medical Center (TLVMC) Bacteriotherapy Clinic. All patients will receive therapy to eradicate H. Pylori according to current guidelines (14 days) and physician's discretion, and will be tested to validate H. pylori eradication, at least 21 days post therapy (according to guidelines: Kyoto/ ACG/ Maastricht). For patients that H. pylori was not eradicated- a second line therapy will be administered according to guidelines, and stool will be retrieved at an additional time point, before FMT and after successful H. pylori eradication.

Patients will be allocated into one of three groups:

1. Intervention group- patients will undergo Auto-FMT through capsules.
2. Intervention group-patients will undergo Auto-FMT through enema.
3. Control Group-patients will receive FMT through placebo capsules.

Patients in Intervention group will undergo an additional breath test for H. Pylori, 14-28 days post FMT, to exclude H. pylori-self infection, by the FMT. This concern is related to the capsules therapy, although the fecal filtrate is double packaged in two capsules (one inside another) which are designed to dissolve only in the duodenum at a basic pH.

If patients are found to be re-infected, they will undergo an additional antibiotics course and post eradication will receive FMT through an enema according to the above specified protocol.

FMT capsules will be generated at the laboratory of the Gastrointestinal department at the Tel Aviv Medical Center. The same procedure for FMT generation will be used in this study as in other studies of the IBD unit and in the clinical Bacteriotherapy setting.

FMT administration:

1. FMT through capsules (FMT/placebo)- patients will evacuate the bowel with 1 liter of Meroken solution 12 hours prior to the procedure and will fast from food for 12 hours prior to the procedure. Patients will swallow 30 frozen capsules on two consecutive days.
2. FMT through enema- patients will evacuate the bowel prior to the procedure and will fast for 3 hours prior to the procedure . Patients will receive 80 ml of enema. Enemas will be administered with the assistance of the study nurse. Patients will be asked to hold the enema content for at least 15 minutes.

At the post-FMT visit and follow -up visits, patients will be examined by a physician who will record clinical symptoms (abdominal pain, nausea, vomiting, weight change), adverse events (fever, abdominal pain, bloating, changes in bowel habits) and general well-being (quality of life and patient reported outcomes questionnaires).

Inclusion Criteria:

• Age 18-70 years old
• Positive H. pylori on either breath test or gastric biopsy
• Patient is intended to receive antibiotics therapy for H. pylori eradication

Exclusion Criteria:

• Severe systemic disease that may impact the microbiome. For example: heart disease, type two diabetes, chronic liver or kidney failure
• Antibiotics therapy during the prior 2 months to enrollment
• Planned to receive antibiotics within the upcoming 2 months (surgery etc) for reasons other than H. Pylori
• Inability to complete the study protocol (swallow capsules or to hold enema content for at least 15 minutes)
• Pregnancy
• Inability to give informed consent

Capsules will be either with FMT or placebo. Same appearance. Patients will be randomized to either arm.