Researchers at the Institute for Systems Biology in Seattle developed a way to test for microbiome diversity from a blood sample. (Artist rendering courtesy of ISB)
If you want to know what’s going on in your gut microbiome, the community of bacteria in our intestines that are tied to overall health, there are plenty of companies willing to help. You just have to pay them — and send in a poop sample.
But it turns out that bottling feces isn’t the only way to gain insights into the gut. Researchers at the Institute for Systems Biology (ISB) in Seattle have devised a new way to look into the state of your microbiome with a blood test.
Microbiome startups have proliferated in recent years. Some are going after drug discovery for specific diseases, such as Finch Therapeutics and Maat Pharma. Others, including Seattle-based Viome, are selling microbiome insights directly to consumers for overall health.
Given the relatively early stage of microbiome research, critics have questioned how useful insights from the gut can be. That’s why ISB researchers decided to focus on the diversity of microbes.
“There’s not a good correlation between diversity in and of itself and clinical health. But there are specific cases in which it does seem to be a huge risk factor,” said Dr. Sean Gibbons, who worked with Dr. Nathan Price on the study, which was published today in Nature Biotechnology.
Low microbiome diversity is a strong risk factor for patients with recurring Clostridium difficile (C. diff), Gibbons said. C. diff is a potentially life-threatening bacterium that comes back in nearly a third of patients following antibiotic treatment.
ISB researchers Dr. Nathan Price and Dr. Sean Gibbons. (ISB Photos)
“Getting these recurrent infections is super hard on patients,” Gibbons said. “If you could avoid that cycle, you could not only decrease the cost of healthcare, you would actually be saving lives and producing a lot less suffering.”
Patients with C. diff can be treated with a fecal transplant, but those are only administered after antibiotics have failed. Gibbons thinks that a blood test could pre-screen patients at risk of recurring C. diff and avoid the painful cycle.
Related: Why Arivale failed: Inside the surprise closure of an ambitious ‘scientific wellness’ startup
To create the test, researchers leaned heavily on data compiled by Arivale, a Seattle startup that aimed to help people become healthier and avoid disease through wellness.
Arivale shut down in April after it failed to find a market for its pricey service. But Dr. Lee Hood, who co-founded both Arivale and ISB, rescued much of the data and technology from the startup and brought it to ISB.
That resource gave Price and Gibbons extensive data on hundreds of former Arivale customers who had their microbiomes sequenced and their blood tested, among other tests. The researchers were able to train a model to predict which individuals are likely to have very low microbiome diversity by looking at 11 blood metabolites. Arivale customers gave permission for their data to be used for research, and the information was anonymized.
The ISB study is a “beautiful example” of how personal data clouds can give new insights into biology and disease, Hood told GeekWire in an email.
They also found what they believe to be a “Goldilocks zone” of gut diversity. People with low diversity tended to have diarrhea and inflammation, whereas those with very high diversity tended to be constipated or have toxins in the blood.
With the help of Arivale’s data, ISB researchers think more microbiome-related insights can be found. “We’re trying to build a real map that can lead to actionable insights of how to manipulate the microbiome,” Gibbons said.
One disadvantage of the dataset is that it skewed toward white, health-conscious people, who were more likely to be Arivale’s customers. “It is a bit of a biased sampling,” said Gibbons.
In the future, ISB intends to partner with Providence St. Joseph Health, which would give researchers access to a more representative population.
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