Re: [biocurious] sequence your microbiome for only $49!

[Bryan Bishop]

On Fri, Feb 1, 2013 at 1:14 PM, Patrik D'haeseleer <pat...@gmail.com> wrote:
> Eri has a nice comparison between American Gut and uBiome up on Quora

Can someone repost the actual content for those of us who don't want
to register with Quora?

- Bryan
http://heybryan.org/
1 512 203 0507

[Patrik D'haeseleer]

Here ya go:

What is the difference between American Gut and uBiome?

And which should people participate in?


Eri Gentry, Health. I wants it

I posed the same question within this thread on the BioCurious Google Group, where one of the collaborators of American Gut, Jason Bobe, spoke up to help explain the project. Independently, I chatted with Jessica Richman, one of the founders of uBiome, about her project and the difference between it and American Gut. I'll share what they had to say and then describe some differences between the two, both my own anthropological views, and measurable differences.

American Gut

Quoting Jason Bobe (Executive Director at Personal Genome Project)

The thing I like most about the American Gut team is that they have a deep bench of scientists who have a proven track record of producing great microbiome work. Some actually worked on the Human Microbiome Project, or wrote the data analysis tools (e.g. QIIME) that everyone uses, or optimized the DNA extraction protocols, or helped set-up high-throughput infrastructure for managing thousands of samples, etc.  I'm always worried about people actually delivering what they say they will deliver when it comes to crowdfunding projects.  I don't have those sorts of concerns with the American Gut project.  I've worked with several of the scientists on a few microbiome projects (I've known Rob Knight for 10 years and have 2 other microbiome studies underway with him, including one study characterizing the microbiomes of 5 body sites for PGP participants).

uBiome

From talking to Jessica Richman, I took home the message that the important difference is not in how testing is done (the techniques are nearly identical) but in how the data are managed. For uBiome, the emphasis is on crowdsourcing data that is analyzed by uBiome, then delivered right back to the community, with raw data also made available for personal analysis. I also learned that uBiome offers more testing sites than American Gut.

Sampling sites | Price per test site

uBiome: GI, mouth, skin, nose, genitalia | $79
American Gut: stool, skin, oral | $99

American Gut has put a few spins on their sampling:

• extensive microbiome analysis for $15,000
• they will look at dog and cat microbiomes
• they have plans to compare what they find in the typical U.S. gut with a few hundred people in rural Namibia, who eat what's described as hunter-gatherer fare

Both projects quote the NIH’s $173 million dollar Human Microbiome Project as the standard for microbiome testing. Notably, the Human Microbiome Project looked at data from only 250 participants. The crowdfunded projects have much higher expectations for participation.

American Gut wants to enroll 10,000 people from around the country (national). uBiome hopes to enroll 2,000 people from across the globe (international).

As of today (January 28, 2012), American Gut has raised $245,470 of its $400,000 goal. Their campaign ends on February 2nd. uBiome has raised $199,238 of its $100,000 goal. The campaign ends on January 31st. Both projects are raising money are IndieGoGo, where projects keep all the money they raised, whether the goal is met. American Gut has not met its goal and it is not clear whether this will impede progress or diminish the benefits to existing donors.

My thoughts: uBiome is a Silicon Valley startup run by ex- and current academics and entrepreneurs. American Gut seems to be a largely academic and East coast influenced endeavor. (The project itself is based in New Orleans, LA.) If you've lived on both coasts, you've probably noticed a geographic/cultural difference in the way entrepreneurs do business. One is more excited and focused on growth in the early stage -- I'm not saying this is the case here, but a lot of companies in Silicon Valley start without the founders having any idea what they're doing. This is not necessarily a bad thing, but it gives a certain feel to the experience of the consumer. East coast ventures tend to be more buttoned-up, more thought out before the first step is taken, and less willing to take risks. Academic ventures are like East coast ventures but with a much longer outlook and, often, timeline (read: it can take a long time before results are available.)

Although I was initially on the fence, I decided to go for uBiome's campaign simply because, when I donated, its crowdfunding campaign was doing better and because it was $20 cheaper for roughly the same thing. In the end, all else held equal, what matters is against how many people you are able to compare yourself. Both of these projects have been able to attract over 1,000 participants, which is a pretty good start regardless. I believe both projects are going to do well. It will be fun to be an early adopter in this analysis and watch what new findings arise about the global microbiome. We are trying to take the learning a step further with a potential Human Microbiome Class at BioCurious. (https://groups.google.com/forum/...)

Update, February 1st: American Gut is offering an additional test site for $49 (it must be added to an existing order). uBiome has extended their campaign to February 18.

[Patrik D'haeseleer]

For what it's worth, I decided to go with 3 American Gut samples, and one uBiome for comparison.

Like Jason, I know the people involved in American Gut, and I think they're probably the top team in the world to run this kind of project. Don't really know the uBiome team, but as I understand they're a for-profit startup - make of that what you will.

Note that American Gut now also does international samples (they had to wait for approval from their IRB), and they've added the ability to add *any* kind of body site or surfaces in your home.

Patrik