uBiome co-founder and co-CEO Jessica Richman, who was placed on administrative leave in May 2019 pending an board investigation into the start-ups billing practices.

Marc Harris, a South Carolina resident, started getting bombarded with ads from a health start-up called uBiome last year. Harris, who's in his mid-50s, has a rare gastrointestinal disorder, so he often searches for new information related to his disease. He figured the company targeted him based on his search history or other info he was looking for.

Harris ordered the SmartGut test from uBiome, which promised to provide new insights into the bacterial makeup of his gut so that he could make improvements to his health. Harris thought he'd receive one test. Instead uBiome sent six kits in the mail, with an email noting the company would track his "microbiome changes over time."

After that, he said, uBiome sent him more than three emails every week pushing him to send back the samples. He ended up returning two, and received an Amazon gift card in return. He didn't finish the full six. His doctor didn't see the value in the test, and he didn't learn anything new.

So Harris was surprised to see the test billed to his insurance five times, with the cost amounting to $2,970 per test. He shared with CNBC a copy of his insurance claims history, as well as multiple email communications from uBiome.

This was a common practice at uBiome, a health-care start-up raided by the FBI last week, according to company insiders. uBiome was routinely billing patients such as Harris multiple times without their consent, prompting insurance plans to start rejecting these claims. The company also pressured its doctors to approve tests with minimal oversight, according to insiders and internal documents seen by CNBC. The practices were in service of an aggressive growth plan that focused on increasing the number of billable tests served.

Venture-funded direct-to-consumer health companies such as uBiome have come under fire for failing to provide sufficient support to patients before prescribing medical testing. Many health experts are concerned about so-called "doc in a box" practices, where companies approve medical tests without communicating with patients outside of a checklist-style survey. Critics say this practice means patients are less likely to get diagnosed with underlying conditions, and say that some of these companies are cutting corners with regulations that are designed to protect their users. Prescribing tests without sufficient medical oversight can also lead to unnecessary tests that burden an already overtaxed health system.

Proponents argue that most patients don't spend more than a few minutes with a doctor even in person, and many lack access to a medical clinic, so these services can help underserved patients. uBiome says its tests bring unprecedented health information to consumers and help them "take greater control over their health."

uBiome's billing practices came to a head last week when the FBI searched the company's San Francisco offices and seized employees' computers. An FBI spokesperson confirmed that the raid at the company's 360 Langton St. offices was part of "court-authorized law enforcement activity."

On Wednesday, uBiome said that its co-CEOs and founders Jessica Richman and Zac Apte are on "administrative leave" and that the board would launch an independent investigation into uBiome's billing practices. John Rakow, the company's general counsel, has taken on the role of interim CEO.

uBiome declined to comment, beyond pointing to the press release announcing the investigation and Rakow's appointment. Rakow did not respond to requests for comment.