Microbiome Resource Center

Microbiome Resource Center

Disclosures: The study was supported by Crohn’s and Colitis Foundation, African American Success Foundation, National Institutes of Health Grants (NIDDK DK112978 and a SUCCESS philanthropic award. Faith reports being on the scientific advisory board of Vedanta Biosciences, receiving research grants from Janssen Pharmaceuticals and receiving consulting fees from Innovation Pharmaceuticals, Janssen Pharmaceuticals, BiomX and Vedanta Biosciences; Grinspan reports no relevant financial disclosures. Please see the study for all other authors’ relevant financial disclosures.
September 27, 2021
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Potential alternative to FMT in bacteria may restore gut microbiome

Disclosures: The study was supported by Crohn’s and Colitis Foundation, African American Success Foundation, National Institutes of Health Grants (NIDDK DK112978 and a SUCCESS philanthropic award. Faith reports being on the scientific advisory board of Vedanta Biosciences, receiving research grants from Janssen Pharmaceuticals and receiving consulting fees from Innovation Pharmaceuticals, Janssen Pharmaceuticals, BiomX and Vedanta Biosciences; Grinspan reports no relevant financial disclosures. Please see the study for all other authors’ relevant financial disclosures.
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Researchers discovered a group of bacterial species and strains that may be used as an alternative to fecal microbiota transplantation to restore a patient’s gut microbiome, according to a study in Nature Microbiology.

“This study is another step in the evolution of FMT. The field is moving away from FMT and toward defined consortium of microbes that can restore a function of the gut microbiome that was lost — either from an antibiotic or from some disease state,” Ari Grinspan, MD, associate professor of medicine, division of gastroenterology, Icahn School of Medicine at Mount Sinai, told Healio Gastroenterology. “Engraftment of donor microbes into the recipient appears to be an important factor in determining whether or not the therapy will be effective. This study shows that long-term engraftment is achievable with a single dose of FMT.”

Jeremiah Faith, PhD, Grinspan and colleagues collected 1,008 bacterial strains that were cultured from fecal samples of 22 FMT donors and recipients. They developed Strainer, a statistical approach to detect and track bacterial strains from metagenomic sequencing data using strain collection combined with metagenomic sequencing data from these samples. Strainer was applied to a cohort of 13 recurrent Clostridium difficile infection FMT recipients and used to detect stable engraftment of 71% of donor microbiota strains in recipients up to 5 years after FMT.

Results showed FMT eliminated 80% of recipient gut bacterial strains before FMT. Grinspan and colleagues noted post-FMT strains persisted up to 5 years later, along with environmentally acquired strains.

After the initial and repeat FMT, researchers noted the qualification of donor bacterial strain engraftment in recipients independently explain clinical outcomes.

“The next step in our research is to see if a defined cocktail of the bacteria that transferred most frequently by fecal microbiota transplantation can be manufactured in the laboratory and used to treat recurrent C. difficile infection as a replacement to the costly, time-consuming job of finding human donors whose stool passes numerous safety screens, and an alternative to the messy process of blending their stool into a slurry,” Faith, associate professor, Precision Immunology Institute and Icahn School of Medicine at Mount Sinai, department of genetics and genomic sciences, told Healio Gastroenterology.