No poop required: Researchers devise blood test for gut microbiome diversity using data from defunct startup Arivale

No poop required: Researchers devise blood test for gut microbiome diversity using data from defunct startup Arivale

5:08am, 3rd September, 2019
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 (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 , are selling microbiome insights directly to consumers for overall health. Given the relatively early stage of microbiome research, 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, who worked with 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: 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. 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.
Salesforce CEO Marc Benioff invests in $25M round for Naveen Jain’s microbiome startup Viome

Salesforce CEO Marc Benioff invests in $25M round for Naveen Jain’s microbiome startup Viome

2:19pm, 17th April, 2019
(Viome Photo) , a wellness startup from entrepreneur , has raised $25 million in funding from a crop of investors that includes Salesforce CEO Marc Benioff. Jain said the new cash, which brings the Seattle-area startup’s total funding to $45 million, would be used to fund research into the link between the human microbiome and chronic diseases including diabetes, autoimmune disorders and Parkinson’s, as well as cancers. Naveen Jain. (Viome Photo) “We are now doing a bunch of clinical studies with 15 or so separate diseases,” said Jain. The aim of the studies, which are looking at diseases as wide-ranging as insomnia and pancreatic cancer, is to “understand exactly what’s happening inside the human body so that we can predict, prevent and reverse chronic diseases,” he said. Viome analyzes its customers’ microbiomes through stool samples in order to make food recommendations for health or weight loss. The idea is to foster health through microbes, which make up more than half of the cells in the human body. The funding round included return investor Bold Capital as well as Physician Partners, Hambrecht Healthcare Growth Venture Fund, and Matthew Harris of Global Infrastructure Partners. Viome said the financing was part of a series B round in which the company aims to raise $100 million. “People are investing because we’re solving a massive problem,” Jain said. “[Benioff] is a very happy customer and he said, ‘I want to be part of it.'” The Salesforce CEO has shown an interest in mental health and wellness, adding meditation rooms to the Salesforce offices and investing in Thrive Global, a wellness startup founded by Arianna Huffington. A spokesperson for Benioff declined to comment when contacted by GeekWire. Jain says the company’s competitive edge lies in its RNA sequencing technology, which emerged from defense work at the Los Alamos National Laboratory. Viome uses machine learning algorithms with the aim of predicting the body’s response to certain foods based on the composition of an individual’s microbiome. Researchers cast doubt These claims have drawn criticism. Jonathan Eisen, a professor at UC Davis, the “Theranos of the microbiome world” on Twitter last year, referencing Elizabeth Holmes’ blood testing startup that became infamous for false claims about its technology. “My issue with Viome was overstating the state of the science,” Eisen told GeekWire. “There’s no scientific support for any of their tools.” The Viome material on Amazon is filled with completely misleading overselling snake oil – e.g. they claim they can tell you "exactly which foods to eat and which to avoid in order to support your wellness" — Jonathan Eisen (@phylogenomics) In the early 2000s, Jain for claims he made about InfoSpace, a high-flying internet business that fell to earth during the dot-com bust. Jain later went on to co-found public records firm Intelius as well as Moon Express, which aims to . (Viome Screenshot) Jain responded to the criticism by saying that Viome’s underlying technology is superior to the microbiome sequencing technology used by other companies. Eisen once served as an advisor to Viome competitor uBiome. Several startups have set out to give health insights based on an analysis of gut bacteria, including and . And the promise of the microbiome has caught the attention of investors. Cowboy Ventures founder Aileen Lee, famous for coining the term “Unicorn” to describe billion-dollar startups, recently about the brain-gut connection and her own dietary experiments. “Changes in diet can modulate the microbiome and have an effect on health,” said Sean Gibbons, an assistant professor at the Institute for Systems Biology in Seattle. But Gibbons said it’s too early to draw conclusions about the specific effect of individual foods on a person’s health. “For anyone to claim that there’s a general purpose algorithm that can predict health from the microbiome is sort of a sci-fi, weird claim to make this point,” he said. Prominent endorsements for Viome That’s not to say that tinkering with the microbiome doesn’t have potential. Fecal transplants, which insert gut bacteria from healthy people into sick patients, have proven to be , a bacteria that infects nearly 500,000 Americans each year. Viome has received endorsements from health and wellness celebrities like , as well as . The startup recently partnered with Helomics, a precision medicine company, to study the link between the gut microbiome and ovarian cancer. Viome from Campbell Soup earlier this year for an undisclosed sum. The company has nearly 150 employees across six locations, including its headquarters in Bellevue, Wash. and offices in San Diego, Santa Clara, Calif., New York, Bangalore and Los Alamos, N.M. Viome is Jain’s seventh venture and the first to come out of his Bellevue-based innovation factory. BlueDot looks for market opportunities for technology developed at leading research labs, with a focus on the health and energy sectors.