Cohort 1: Subjects who had a Clostridioides difficile infection (CDI) recurrence in study SERES-012 within 8 weeks of receipt of study drug will be eligible. The purpose of this cohort is to assess safety and efficacy of SER-109 in reducing recurrence of CDI in adults who had a CDI recurrence within 8 weeks after receipt of SER-109 or Placebo in study SERES-012.

Cohort 2: Cohort 2 is an open-label program for subjects who were not part of SERES-012. The purpose of this cohort is to describe safety and tolerability of SER-109 in subjects 18 years of age or older with at least a first recurrence of CDI.

Cohort 1 is an open-label extension of study SERES-012. Subjects who had a CDI recurrence in study SERES-012 within 8 weeks of receipt of study drug, have responded to a course of standard of care (SOC) antibiotic treatment, will receive an oral dose of SER-109. A treatment regimen of SER-109 is defined as an oral dose of SER-109 (4 capsules once daily) for 3 consecutive days.

Approximately 30 eligible subjects with recurrent CDI disease from study SERES-012 are expected to enroll. Screening for this study will begin at the Recurrence Visit of Study SERES-012.

Cohort 2 is an open-label program for subjects who were not part of SERES-012. Subjects 18 years of age or older who had one or more CDI recurrence and have responded to a course of antibiotic treatment will receive an oral dose of SER-109. The CDI recurrence must be confirmed by a positive C. difficile stool toxin or polymerase chain reaction (PCR) assay to confirm eligibility. A treatment regimen of SER-109 is defined as an oral dose of SER-109 (4 capsules once daily) for 3 consecutive days.

Approximately 200 eligible subjects with recurrent CDI disease are expected to enroll.

Cohort 1 Main Inclusion Criteria:

1. Previously enrolled in Study SERES-012, had CDI recurrence within 8 weeks after receipt of a treatment regimen of SER-109 or placebo
2. Signed informed consent prior to initiation of any study-specific procedure or treatment. The subject, or their legally authorized representative, must be able to provide written informed consent and understand the potential risks and benefits from study enrollment and treatment.
3. The CDI recurrence in Study SERES-012 must have met the protocol definition of ≥ 3 unformed stools per day over 2 consecutive days, a positive C. difficile stool toxin assay, and the requirement of CDI SOC antibiotic therapy, and an adequate clinical response following antibiotic therapy (<3 unformed stools in 24 hours for 2 or more consecutive days).

Cohort 1 Main Exclusion Criteria:

1. Female subjects who are pregnant, breastfeeding, lactating, or planning to become pregnant during the study.
2. Known or suspected toxic megacolon and/or known small bowel ileus.
3. Admitted to or expected to be admitted to an intensive care unit for medical reasons (not just boarding). Note: nursing homes, rehabilitation, assisted living centers and acute care hospitals are acceptable.
4. Absolute neutrophil count of <500 cells/mm^3.
5. Major gastrointestinal surgery (e.g. significant bowel resection or diversion) within 3 months before enrollment (this does not include appendectomy or cholecystectomy), or any history of total colectomy or bariatric surgery (bariatric surgery which does not disrupt the gastrointestinal lumen, i.e., restrictive procedures such as banding, are permitted).
6. History of active inflammatory bowel disease (ulcerative colitis, Crohn's disease, microscopic colitis) with diarrhea believed to be caused by active inflammatory bowel disease in the past 3 months.
7. Concurrent intensive induction chemotherapy, radiotherapy, or biologic treatment for active malignancy (subjects on maintenance chemotherapy may only be enrolled after consultation with the study medical monitor).
8. Any history of fecal microbiota transplantation (FMT) in the past 3 months.

Cohort 2 Main Inclusion Criteria:

1. Subjects 18 years of age or older who had one or more CDI recurrence (as confirmed by a C. difficile stool toxin or PCR test) and have responded to a course of antibiotic treatment.
2. Signed informed consent prior to initiation of any study-specific procedure or treatment. The subject, or their legally authorized representative, must be able to provide written informed consent and understand the potential risks and benefits from study enrollment and treatment.

Cohort 2 Main Exclusion Criteria:

(all Cohort 1 exclusion criteria [#1-8 above] plus the below addition criterion)

9. Previously enrolled in a Seres Therapeutics clinical study. An exception is made for subjects who screened in SERES-012 who did not receive SER-109 and did not previously roll-over to SERES-013.