uBiome's underlying data tainted with samples from infants, pets: report

A white box with the SmartGut sample collection kit in it
Some samples used to develop uBiome's clinical SmartGut sequencing test included high levels of microbes linked to breast milk, while others showed bacterial results not found in humans. (Image: uBiome)

Following an FBI raid on its San Francisco headquarters and the ensuing replacement of its leadership, it’s now come to light that the data underpinning uBiome’s flagship microbiome test may be contaminated with flaws.

A report from Business Insider details how deficiencies in the company’s database—including the presence of data from dozens of minors, infants and at least one animal in its analysis of collected fecal samples—could make the results of its clinical tests unreliable.

uBiome has confirmed the issue, and its recently installed executives have said it is conducting an internal review. The journal PLOS One, which previously published the company’s data in a 2017 paper, is also investigating.

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According to the report, the primary dataset used to build uBiome’s first clinical test, SmartGut, was populated by samples volunteered by employees and participants in an online fundraiser.

The collection was originally designed for its wellness-focused offering, the direct-to-consumer Explorer test, which was not intended to diagnose any disease. Customers mailed in their own samples, which were checked against the volunteer database for deviations that may indicate poor health. However, experts doubted that a one-time sampling of the microbiome compared to a limited database of volunteers would provide useful information.

RELATED: Turmoil persists at uBiome with new management overhaul amid FBI probe

In addition, uBiome also used that database to help develop its top-selling SmartGut test, which aims to use microbial sequencing to inform people of their risks of diseases ranging from cardiovascular conditions to kidney disease to irritable bowel syndrome. The company also offers several treatment guides to physicians based on the test’s results. 

Those volunteered fecal samples—collected unobserved and mailed in using the same commercial test kits offered to customers—were tainted by a number of specimens most likely taken from infants and pets, the report said. Some included high levels of microbes linked to breast milk while others showed bacterial results not found in humans.

RELATED: CEOs of uBiome take administrative leave following FBI raid

uBiome was forced to halt sample testing early last month for its sole remaining test, Explorer, after a round of layoffs claimed its laboratory director and other key staff, in addition to half of its employees across its locations in California and Latin America. 

The company had previously stopped its physician-ordered tests for the gut and women’s health after the FBI raided its headquarters in April, as part of an investigation into the company’s billing practices. A number of large insurers, as well as the California state insurance regulator, have also been looking into the company, which reportedly double-billed when using the same sample and may have had financial connections to doctors prescribing the tests.

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