The human microbiome data collection race is in full force, with everyone from academic researchers to start-up companies looking to find answers and treatments from what is considered “golden stool.” However, in collecting, preserving, and studying material that comes from the human microbiome, will the people whose samples are taken from genuinely benefit? Who will control and profit from the genetic data they generate? What are the privacy risks involved in this type of data collection?
Join us as we tackle these questions and take an honest look into the world of human microbiome data collection. This article breaks down the different types of collection and research, including Fecal Microbiota Transplantation (FMT) and “biobanking,” and discusses the stigma and controversies surrounding them. We also examine studies that are changing a legacy of exploitation in conducting microbiome data collection and using its data to better the communities that need help the most.
Fecal Microbiota Transplantation: The Ins and Outs
Fecal Microbiota Transplantation is front and center when discussing the world of human microbiome data collection. The FMT procedure transfers fecal matter from healthy donors into the colon of sick patients. The procedure is proving to be an effective treatment for many patients, and researchers see massive potential for using these organisms to treat diseases from diabetes, gut disorders, and depression to obesity and cancer. Additionally, newer types of fecal transplants come in capsule form or through an enema. So, where is the controversy behind FMTs – besides the “ick” factor? It starts with the FDA.
The FDA & the “Poop Drug Cartel”
One report in Gastroenterology and Hepatology states that the controversy surrounding FMTs began in 2013 when the US Food and Drug Administration (FDA) noted that an investigational new drug (IND) application would be required to perform FMTs. However, in a bold move, the FDA quickly reversed its stance on requiring an IND a month later to allow the use of FMT in cases of recurrent or refractory Clostridium difficile infection (rCDI). Clostridioides difficile is a debilitating bacterial infection that affects 500,000 Americans a year. Today, the FDA does not approve FMT for any use, and according to an investigative piece in the New York Times, at the heart of the controversy surrounding FMTs is a question of classification. The article asks, “Are the fecal microbiota that cure diseases like C. diff a drug, or are they more akin to tissues, organs, and blood products transferred from the healthy to treat the sick?” The answer to this question will determine how the FDA regulates the procedure, how much it costs, and who will profit. However, these questions will remain unanswered until the agency gives its decision.
Even though FMT is not FDA-approved, the agency does play a role in supporting product development while assessing the risks and benefits to patients of unapproved therapies. Under this guidance, OpenBiome, a centralized stool bank in the US, opened its doors and supplied clinicians with rigorously screened donor stool. Unfortunately, it had to shut down due to an FDA safety alert and other issues (primarily financial) stemming from the pandemic. Though OpenBiome has an extensive inventory expected to last through 2022, most clinicians realize their stool supply is – or will be – gone or may be too expensive to utilize. According to Healio, several companies have been conducting clinical trials on oral alternatives to address this issue. However, even with these breakthroughs, controversies surround these alternatives. Dr. Alexander Khoruts, a gastroenterologist at the University of Minnesota, tells the New York Times he fears the FDA is favoring the interests of what he calls the “poop drug cartel,” a group of companies seeking approval for new ways to deliver the active ingredients in transplanted feces. Several of these companies have raised millions of dollars from investors and recently formed an association to advance their interests with the FDA. Khoruts also states, “I don’t think there are clear villains here, but I worry that the regulators are not caught up on the latest science and that the interests of investors may be exceeding those of patients.”
Bio Banks
According to Inverse, scientists are worried the world is at risk of losing certain microbial species, which may be the most helpful for treating disease. This loss includes the diverse microbiomes of humans. Competing efforts are underway to collect and preserve samples of these microbiomes found within stools in banks like the Microbiota Vault. This “vault” is intended to house the diverse microbiomes of the world’s human population. Plans for the Microbiota Vault are still underway, but a recent feasibility study gives a solid picture of its vast storage procedures. These methods will include two copies of every sample, and local communities can choose whether or not they’d like to deposit one copy to be stored in the Vault and genetically sequenced. However, creating these biobanks spur questions that have long plagued this kind of research:
- In collecting, preserving, and studying material that comes from people’s bodies, namely poop, will the people from whom the samples are taken really benefit?
- Who will control and profit from the genetic data they generate?
- Are there privacy risks involved in this type of data collection?
The reason for all of these questions? They are primarily a byproduct of a historical practice called bioprospecting.
Bioprospecting
Bioprospecting is a systematic and organized search for useful products derived from bioresources, including plants, microorganisms, and animals, that can be developed further for commercialization and the overall benefits of society. However, there is a dark side to this type of investigation. Bioprospecting has a history of academics from wealthy nations using biological material and data from non-white and Indigenous communities without consent or approval in ways that align with belief systems and cultural values. With this history, many of these communities are deeply skeptical about participating in any kind of biological material-collecting research. However, the tides are changing.
Katya Moniz, the executive director of the Global Microbiome Conservancy, tells Inverse, “We don’t want to follow the traditional model of science or bioprospecting.” So how will they achieve this? Moniz explains, “By supporting local collaborators and scientists so that they can do the work that serves their local populations and their health concerns.” The bank also allows donors to own their own stool samples.
Inverse underscoresthat although Moniz emphasizes this point, there does not seem to be a standardized approach yet, at least regarding monetary gain. The article states, “Legal safeguards would, at a minimum, prevent companies from profiting from the biological data of people who gave it up for free.” So what would the biobank do if the genetic data is used to develop a profitable therapeutic? Moniz tells Inverse, “We are building a benefit-sharing strategy in communication with other nonprofits who already do this. And we’re seeking guidance from them on the best way to do this because it’s very complicated.”
Privacy and Regulation Issues
Other stigmas and risks surrounding human microbiome data collecting involve privacy and regulatory issues. In terms of regulation, Inverse states, “There’s no consensus on how research on the microbiome should be done, and the legal status of microbiota samples is also unclear. It’s something scientists say mostly hinges on informed consent.” However, the idea of informed consent also carries a stigma. For example, in 2003, members of the Havasupai tribe learned that blood samples they had given to researchers at the Arizona State University, which they believed would be used for diabetes research, were used in several other unrelated studies. Members of the tribe said they would not have consented had they been informed of the other research. As a result, they filed a lawsuit against the Arizona Board of Regents and Arizona State University. Regarding privacy, there are multiple avenues by which an adversary could obtain microbiome samples, including public databases and cyberattacks against healthcare facilities and research organizations. However, companies and academic research institutions are taking strong measures to protect participant privacy and strengthen the informed-consent process.
The Good News
Biobanks, like the Global Microbiome Conservancy, are working harder to break down the stigma surrounding microbiome data collecting by having participants own their own stool samples and supporting local collaborators and scientists so that they can do the work that serves their local populations and their health concerns. Today, most microbiome data collection companies and organizations ensure access to data only for people who need it (like a designated clinician). Many also promise the ability to destroy the sample upon customer request and never to sell data to third parties. Academic researchers and companies also tackle privacy issues by establishing well-known anonymization techniques to protect participants’ data. Data anonymization protects sensitive information by erasing or encrypting identifiers that connect an individual to stored data.
We at Endominance also go to great lengths to protect our study participants. Case in point, we have launched a meaningful Microbiome, Anxiety, and Cognitive Orientation (MACO) study to understand better the effects of human gut microbiome metabolites on anxiety behavior and the role cognitive orientation has in connection to anxiety. This study follows all necessary data compliance rules regarding participants’ privacy, including ensuring all data is completely anonymized. Our informed consent process also follows strict guidelines that allow the participant to ask questions and consider whether to join the study. Additionally, we are committed to using our data to further mental health research initiatives and organizations, giving back to those needing help the most. Please visit our research page for more information on all of our studies.
