Gina M. Mendolia, BA1, Haixin S. Bi, BS2, Zain Kassam, MD, MPH3, Nathaniel Chu, PhD2, Mark Smith, PhD3, Eric Alm, PhD2, Jessica R. Allegretti, MD, MPH4
1OpenBiome, Somerville, MA; 2Massachusetts Institute of Technology, Cambridge, MA; 3FInch Therapeutics, Somerville, MA; 4Brigham and Women's Hospital, Boston, MA
Introduction: Fecal microbiota transplantation (FMT) capsules have emerged as a therapeutic option for recurrent C.difficile infection (rCDI). Standard FMT capsules are prepared under aerobic conditions; however, anaerobic processing limits oxygen’s impact on healthy anaerobic microbes, may enhance microbial community viability, improve engraftment, and may in turn increase efficacy. Thus, we compared the engraftment profiles of FMT capsules prepared by aerobic (AER) versus an anaerobic process (ANA) in rCDI patients. We applied a novel DNA-sequencing method (PMA-seq) to differentiate living and dead microbes.
Methods: We conducted a prospective cohort study of rCDI patients (3 or more confirmed episodes within 1 year) eligible for standard of care FMT. Subjects were enrolled sequentially to receive either a single administration of 30 capsules of standard AER or ANA. 3 healthy donors were use and stool donation was split; half prepared under anaerobic and half under aerobic conditions. This technique was used to address donor and stool specific confounding effects. All measures were taken to manage oxygen exposure, otherwise the split stool samples were treated identically. ANA preparations occurred inside an anaerobic chamber. Patients were assessed, and stool samples collected at 72 hours, 10 days, 4 weeks and 8 weeks post-FMT. Gut microbial communities were profiled via shotgun metagenomic and 16S sequencing. Additionally, PMA-seq, a novel species-specific live-dead assay was conducted. Pre and post treatment microbiome engraftment outcomes were analyzed. Assessment for clinical cure was done at week 8 [testing via (GDH/EIA)].
Results: A total of 10 recurrent CDI patients were enrolled (5 AER and 5 ANA). Relevant characteristics were similar between the AER [mean age: 73 (SD=15.9), mean recurrence 3.4] and ANA groups [mean age: 67.1 years (SD=18.7), mean recurrence 3.0]. Overall, gut microbial community outcomes from ANA and AER, including alpha diversity, beta diversity and relative abundances, did not vary substantially by 16S, shotgun metagenomic sequencing or PMA-seq (Fig 1 and 2). Clinical cure at week 8 for AER and ANA was 100% (5/5 in each group). Both formulations were safe and well-tolerated.
To our knowledge, this is the first study to compare aerobically versus anaerobically prepared FMT capsules, including assessment of live and dead specific-microbial profiles. This pilot study suggested there were no significant differences in engraftment profiles in rCDI.
Citation: Gina M. Mendolia, BA; Haixin S. Bi, BS; Zain Kassam, MD, MPH; Nathaniel Chu, PhD; Mark Smith, PhD; Eric Alm, PhD; Jessica R. Allegretti, MD, MPH. P1036 - ANAEROBIC VERSUS AEROBICALLY PREPARED FECAL MICROBIOTA TRANSPLANTATION CAPSULES: A PILOT COMPARATIVE COHORT ANALYSIS USING A NOVEL SEQUENCING APPROACH. Program No. P1036. ACG 2019 Annual Scientific Meeting Abstracts. San Antonio, Texas: American College of Gastroenterology.