uBiome

uBiome was a biotechnology company based in San Francisco that has developed technology to sequence the human microbiomes.

uBiome, Inc.
Private
IndustryBiotechnology
Founded2012 October
FounderZachary Apte, Jessica Richman
Headquarters
San Francisco, California
,
United States
Products
  • SmartGutTM
  • SmartJaneTM
  • ExplorerTM
Websitewww.ubiome.com

History

The company was founded by Jessica Richman, Zachary Apte, and Will Ludington who were scientists in the California Institute for Quantitative Biosciences.[1] In November 2012, uBiome generated $350,000 through a crowdfunding campaign.[2] The founders received mentoring and funding from Y Combinator and further funding from Andreessen Horowitz and 8VC.[3][4][5]

As of 2015, uBiome offered a $1 million grant program to researchers and citizen scientists for microbiome sampling and related analysis.[6] One winner of the first round of such grants was the Centers for Disease Control and Prevention.[7]

Products and services

Customers purchase kits to sample one or more parts of their body, including the gut, genitals, mouth, nose, or skin. After swabbing, a participant takes a survey which is used to make correlations with microbiome data. The participant sends the kit to the company in the mail and receives data in a few weeks; he or she can compare their data with that of uBiome’s data set.[8][9] In 2015 uBiome received Clinical Laboratory Improvement Amendments (CLIA) certification from the State of California.[10] In 2016, uBiome received accreditation from the College of American Pathologists.[11]

Technology

As of 2015, the company first amplifies a portion of the bacterial gene that encodes 16S ribosomal RNA using PCR, then sequences the amplified 16S ribosomal RNA gene, in order to categorize the bacteria at the genus level.[12] The company has proprietary machine learning algorithms that analyze the sequence data and compare it with the company's proprietary database of microbiomes, built from the samples that partners and single customers send to them, and web-based software that allows individuals to view their microbiome and make certain comparisons.[13][14] A 2014 report in Xconomy said the company outsources the sequencing.[14] The sequencing is done on the Illumina NextSeq500 sequencer.[15][16]

In October 2015 the company introduced an app on iOS using ResearchKit that allowed customers to view their results on mobile devices.[17]

uBiome has been compared with Theranos and 23andMe, each of which are also biotechnology companies influenced by Silicon Valley.[7][18]

Controversies

Amy Dockser Marcus noted in a 2014 essay in The Wall Street Journal that when Ubiome raised its initial round of crowdfunding in early 2013, many questions were raised by bioethicists about the company's citizen science business model - namely whether it had actually obtained informed consent from its customers, and whether direct to consumer genetic testing initiatives could be ethically conducted at all, and its lack of Institutional review board (IRB) approval.[19][20][21] The Wall Street Journal essay also noted that questions were raised about the quality of data obtained in citizen science initiatives, with regard to self-selection and other issues.[19][22]

The company obtained IRB approval in July 2013.[19][23][24]

In 2014, people experienced in biotechnology entrepreneurship also raised questions about the ethics of crowdfunding a biotech company, as the risks of such ventures are high even for people with scientific and business sophistication.[19][25]

In April 2019, FBI agents raided the UBiome office in an investigation over possible insurance fraud.[26][27] Cofounders Apte and Richman were put on administrative leave pending an investigation by the company's board.[28]The company filed for bankruptcy on September 4, 2019 amidst the investigation.[29]


Awards and recognition

In March 2018, uBiome made Fast Company's list for The World's Most Innovative Companies in Data Science, acknowledging uBiome's work collecting data to develop tests for HPV and STIs.[30]

gollark: You're entirely missing the point.
gollark: Presumably they still use Java 8.
gollark: Yes, that.
gollark: No, that's silly, those would be handled by Java or something.
gollark: Maybe it's an issue with newer HTTPS certificate authorities?

References
  1. Lee, Teresa (April 22, 2013). "Swabbing for Science". The Berkeley Science Review.
  2. Vachelard, J; Gambarra-Soares, T; Augustini, G; Riul, P; Maracaja-Coutinho, V (17 February 2016). "A Guide to Scientific Crowdfunding". PLOS Biology. 14 (2): e1002373. doi:10.1371/journal.pbio.1002373. PMC 4757556. PMID 26886064.
  3. Chokkattu, Julian. "uBiome Raises $4.5M From Angel Investors, Andreessen Horowitz To Crowdsource Microbiome Research". TechCrunch.
  4. Dillet, Romain. "Andreessen Horowitz Raises Massive New $1.5 Billion Fund". TechCrunch.
  5. Buhr, Sarah. "Gut health startup uBiome has raised $15.5 million and is launching a DNA test for your poop". TechCrunch.
  6. "FACT SHEET: Announcing the National Microbiome Initiative" (PDF). obamawhitehouse.archives.gov. The White House. May 13, 2016.
  7. Zhang, Sarah. “Microbiome Startup uBiome Will Sequence Poop for the CDC.” Wired. Nov. 30, 2015 Quote: "Recent controversy over the blood testing company Theranos has highlighted the sometimes loose regulations, and the Food and Drug Administration has it wants to regulate lab tests more strictly"
  8. Gertner, Jon (January 7, 2015). "What's Lurking In Your Microbiome? Possibly, A Cure For Disease". Fast Company.
  9. Almalki, M; Gray, K; Sanchez, FM (February 24, 2015). "The use of self-quantification systems for personal health information: big data management activities and prospects". Health information science and systems. 3 (Suppl 1 HISA Big Data in Biomedicine and Healthcare 2013 Con): S1. doi:10.1186/2047-2501-3-S1-S1. PMC 4437547. PMID 26019809.
  10. "uBiome Launches CLIA Lab". genomeweb. April 28, 2015.
  11. Taylor, Julie (October 4, 2016). "uBiome's Laboratory Receives Accreditation by College of American Pathologists (CAP)". PRWeb.
  12. Scoles, Sarah (7 October 2015). "I Sent a Sample of My Poop to uBiome -". The Crux @ Discover Magazine.
  13. Khamsi, Roxanne (17 July 2014). "Can Gut DNA Sequencing Actually Tell You Anything About Your Health?". Newsweek. Retrieved 21 March 2015.
  14. Tansey, Bernadette (18 August 2014). "Glowing Plants To Nanodiamonds: Y Combinator's Biotechs Debut". Xconomy.
  15. "ubiome 0.5.8 : Python Package Index". testpypi.python.org. Retrieved 29 October 2016.
  16. Mac, Tracy (June 2, 2015). "Interview with Jessica Richman of uBiome". The Power of Poop.
  17. Taylor, Nick Paul (Oct 11, 2015). "UBiome taps Apple ecosystem to broaden microbiome data-gathering drive". FierceBiotech.
  18. Leonard, Andrew (December 22, 2015). "Silicon Valley Will See You Now". Modern Luxury: Silicon Valley. But a healthy dose of skepticism is also in order, not least because of the difficulties faced by the two most-celebrated digital-health startups, 23andMe and Theranos....In 2013, the FDA banned 23andMe from marketing its Personal Genome Service. The FDA, which had yet to fully sign off on the technology, was concerned “about the public health consequences of inaccurate results from the PGS devices.” The lesson for the rest of the digital-health industry was clear: Unless they’re expressly permitted by the FDA, companies should not encourage consumers to make medical decisions based on the health data the companies provide. ...Theranos came out of the gate with an unprecedented bang.....Then, in mid-October, an earthquake hit that rocked not just Theranos but the entire digital-health community.
  19. Marcus, Amy Dockser (24 October 2014). "The Ethics of Experimenting on Yourself". Wall Street Journal.
  20. DNLee (February 22, 2013). "On Ethics and Self-Policing in (Citizen) Science". Scientific American Blog Network.
  21. Chorost, Michael (23 September 2013). "Crowdsourced Research Delves, Uncertainly, Into the Human Microbiome". The Chronicle of Higher Education.
  22. Hall, Harriet (June 25, 2013). "Meet Your Microbes: uBiome Offers New Service". Science-Based Medicine.
  23. Stone, Judy. "uBiome: Ethical Lapse or Not?". Scientific American. Retrieved 9 February 2015.
  24. Jessica, Richman; Apte, Zachary (July 22, 2013). "Crowdfunding and IRBs: The Case of uBiome". Scientific American Blog.
  25. Lee, Stephanie M. (February 15, 2014). "Biotech startup turns to crowdfunding". San Francisco Chronicle.
  26. Shin, Sally (2019-04-26). "uBiome office in San Francisco getting raided by FBI San Francisco division special agents Video from @ltbatch on the ground pic.twitter.com/GO4Sb2LFMO". @sallyshin. Retrieved 2019-04-26.
  27. Mathews, Anna Wilde; Marcus, Amy Dockser (2019-04-26). "FBI Searches Microbiome Testing Startup in Billing Probe". Wall Street Journal. ISSN 0099-9660. Retrieved 2019-04-26.
  28. Farr, Christina (6 May 2019). "Health tech start-up uBiome suspends clinical operations following FBI raid". CNBC. Retrieved 18 June 2019.
  29. "Everything we know about uBiome, the startup that convinced Silicon Valley that testing poop was worth $600 million, and then filed for bankruptcy amid an FBI investigation". Business Insider. Retrieved 2020-05-10.
  30. "The 2018 Top 10 Most Innovative Companies by Sector: Data Science | Fast Company". Fast Company. Retrieved 2018-03-26.

See also
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