CDC taps uBiome for large-scale microbiome sequencing initiative

The Centers for Disease Control and Prevention (CDC) has hooked up with microbiome sequencing startup uBiome to study hospital-associated infections. At the heart of the collaboration is a major data generation and analysis initiative, for which uBiome will sequence 10,000 stool samples before sifting through the data to learn how the makeup of gut bacteria changes during hospital stays.

The CDC has initiated the collaboration to further its ambition to develop Microbiome Disruption Indices (MDIs), diagnostic tools that it sees coming to play a central role in infection control and prevention of multidrug-resistant organisms. By turning to uBiome for help with the sequencing and analysis aspects of the initiative, the CDC has delivered a major boost to the visibility and credibility of the three-year old microbiome startup, while also providing it with a new source of samples to sequence. In the past, uBiome has claimed to have the largest microbiome database in the world.

San Francisco, CA-based uBiome built the database by selling gut sequencing kits, initially through a crowdfunding campaign. Like 23andMe, a company it resembles in respects, uBiome has moved to broaden the scope of its operation as it has grown. The collaboration with the CDC is one aspect of this process. Another component took shape this week when uBiome unveiled Dr. Alan Greene as its first chief medical officer. UBiome made the hire to support preparations for the introduction of its clinical tests, the most advanced of which are now in the final stages of development.

UBiome has also worked to put in place an operation it thinks can support the rollout of the clinical tests without incurring the wrath of FDA. "We assume we're in good standing because the CLIA requirements are already met," Daniel Almonacid, a senior scientist at uBiome, told Wired.

- read the CDC release
- here's Wired's take
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