Nonprofit infrastructure · Microbiome

OpenBiome

The first public stool bank in the United States. For eleven years it shipped investigational fecal microbiota material to more than 1,300 hospitals and clinics under an FDA enforcement policy. In December 2024 it shipped its last clinical treatment and became a foundation.

A friend of a friend, and a year and a half

In 2011 Mark Smith was working on a PhD in microbiology at MIT when a friend’s cousin was diagnosed with Clostridioides difficile, one of the most common infections people pick up in American hospitals. Antibiotics did not hold it. The man had read about fecal microbiota transplantation, then investigational, and could not find a physician willing to arrange it. Donors had to be screened for infectious disease, and physicians were reluctant to order tests for someone who was not sick.

“I felt like I was part of a system that was failing,” Smith told Mother Jones by email in 2014. “We had a serious public health problem and we already knew the solution to it. Yet somehow the solution wasn’t getting out to patients.”

The man eventually received a transplant, after a year and a half of recurring infection, and recovered. Smith kept thinking about the logistics rather than the biology. “It seemed obvious that we needed to set up a stool bank to make this work,” he told MIT Spectrum.

The gap

C. difficile infection is one of the most common healthcare associated infections in the United States and is associated with 15,000 to 30,000 deaths a year, according to the FDA. Most people clear it after one course of antibiotics. A minority relapse.

Screening was the expensive part, repeated from scratch for every patient who found a willing doctor. A bank inverts that arithmetic: screen a few donors carefully, then use their material many times. OpenBiome described 107 screening questions, testing for 26 infectious agents, a 60 day quarantine and a second round of testing. Smith’s summary of it in 2014: it “basically excludes you if you’ve done anything too interesting in your life.”

Two classmates who chose not to make money

Smith and James Burgess were Princeton classmates, both class of 2009. Smith was finishing his doctorate in Eric Alm’s lab at MIT; Burgess was starting an MBA at MIT Sloan. Burgess looked at the idea as a business first and passed: the intellectual property was largely in the public domain, so he saw little potential for profit, Princeton Alumni Weekly reported. They built a nonprofit instead, in a corner of Alm’s lab. The IRS granted exemption in November 2013 to Microbiome Health Research Institute, Inc., doing business as OpenBiome.

By late 2014, a year after the first patient, OpenBiome was working with more than 130 hospitals in 34 states. The 2016 Form 990 shows how lean the top of the house was: Burgess, executive director and clerk, $112,132; Smith, president and director, $69,832.

The policy the whole thing rested on

In July 2013 the FDA said it intended to exercise enforcement discretion over investigational new drug requirements for fecal microbiota for transplantation to treat C. difficile infection not responding to standard therapies, provided the treating physician obtained consent stating the use was investigational and discussing its risks. That policy is what OpenBiome shipped under for its entire operating life.

A draft revision came in March 2016. The final guidance, November 2022, carried the sentence that ended the arrangement: “This policy does not apply to FMT that is obtained from a stool bank.” Hospital laboratories working under their own clinicians stayed outside the definition.

2019, then 2020

On June 13, 2019 the FDA issued a safety alert after two immunocompromised adults in two independent trials developed bacteremia from extended spectrum beta lactamase producing Escherichia coli, linked by sequencing to the same donor. One died. The case report ran in the New England Journal of Medicine that November. That material did not come from OpenBiome.

The alert that did came on March 12, 2020: six patients who had received product from an unnamed US stool bank developed infections caused by enteropathogenic or Shiga toxin producing E. coli, four of them hospitalized. The company had also told the agency of two patients who died after receiving product from the donor linked to the Shiga toxin cases. The FDA was careful: “It is not known if STEC infection contributed to these deaths.” On April 6, 2020 it named the bank as OpenBiome and ordered nucleic acid testing of donors. Product from three donors was recalled.

Then the pandemic stopped the line. In a typical year OpenBiome shipped thousands of treatments; in 2020 it shipped a little more than 200, STAT reported. The Form 990 registers the hit as a negative: net inventory sales of minus $1,508,279 in 2020, against $9,610,021 in 2019.

Approved products, then the end of the bank

On November 30, 2022 the FDA approved Rebyota, from Ferring, the first approved fecal microbiota product. On April 26, 2023 it approved Vowst, from Seres. Both are for prevention of recurrence in adults 18 and older after antibacterial treatment. Neither is indicated for children or severe disease.

OpenBiome told providers its material would stop after October 31, 2024. Physician and patient groups wrote to the FDA on October 8. The agency extended distribution to December 31 on condition that OpenBiome file an investigational new drug protocol by November 30. It filed on November 29. The last treatment went out in December. The running total, by the organization’s own count, was 72,507.

What is proven, and what is still claimed

Read plainly: the regulatory and safety history is documented, and it cuts both ways. OpenBiome built screening and logistics that a scattered practice lacked, published its own operating data, and was named by the FDA when its material was implicated in infections. What stays company-stated is the headline number, 72,507, and the partner counts. What does not match the record is the framing of 2022 as an action aimed at OpenBiome.

What to watch

• Whether the investigational new drug protocol filed on November 29, 2024 ever supports renewed distribution. No later regulatory record was found.
• The fiscal 2025 Form 990, the first covering a full year with no distribution.
• Whether the grant program and the biobank, including a library of 7,758 bacterial isolates with 3,632 paired genomes, become the main output.
• Who fills the gap the approved products leave: children, and severe or fulminant disease.

In their words

OpenBiome funding profile on HVCFHealthcare Venture Capital Fund

Related companies

• Evolvere BioSciences: Also in Therapeutics. An Oxford spinout designing protein based antibiotics meant to stay ahead of bacterial resistance instead of losing to it
• HepaTx: Also in Therapeutics. A Stanford spinout turning liposuction fat into liver cells, aiming to replace a transplant with an infusion
• SFA Therapeutics: Also in Therapeutics. A Temple University spinout turning short chain fatty acids from the human gut into oral pills
• Persephone Biosciences: Also in Therapeutics. It mapped the gut microbiomes of hundreds of American babies, published the findings, then built a supplement out of them

Sources

1. Public recordEnforcement policy on IND requirements for FMT, final guidanceFDA CBER · Nov 2022
2. Public recordSafety alert on transmission of pathogenic organismsFDA · Mar 12, 2020
3. Public recordDonor testing for EPEC and STEC, naming OpenBiomeFDA · Apr 6, 2020
4. Public recordFDA approves first fecal microbiota product, RebyotaFDA · Nov 30, 2022
5. Public recordFDA approves Vowst, first oral fecal microbiota productFDA · Apr 26, 2023
6. Public recordDrug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota TransplantNEJM · Nov 21, 2019
7. Public recordForm 990 series, EIN 46-1681862, fiscal 2013 to 2024IRS via ProPublica · Sep 2026
8. IndependentOpenBiome to wind down stool bank operationsSTAT · Feb 23, 2021
9. IndependentEasy Access to Conventional FMT Continues, for NowMedscape · 2024
10. PartnerUniversity of Minnesota collaboration with OpenBiomeUniv. of Minnesota · Jan 20, 2022
11. CompanyOur Story, Our Work, Our Impact, grant programOpenBiome · Sep 2026