Larry Smarr: Where There Is Data There Is Hope

“I never thought I would be getting into this business.”

This is the first sentence in a mind-expanding talk by Larry Smarr about his self-tracking journey.

In 1999 Larry moved from Illinois to La Jolla, CA to take a position at the University of California, San Diego (UCSD). Like most Southern California transplants he quickly adapted to the local norms and began looking for ways to improve his fitness and health.


Tracking his weight and then his physical activity with a few different devices led him to become more curious about nutrition and he began tracking his diet. When he discovered that he was pre-diabetic and wanted to more closely monitor his inflammation he decided he wasn’t going to just trust the diet books, but “actually measure.” So he enlisted a personal blood testing service to track his ratio of Omega-6/Omega-3 fatty acids.

Slide05The beauty of the blood tests Larry was doing were the vast amounts of data that that he could see and think about over time. He noticed that one variable, C-Reactive Protein, was consistently out of normal range.  What other tests could give him more information about what was going on? He tried a stool test, a comprehensive panel that tests samples for the presence of inflammatory markers as well as the abundance of good and bad bacteria.

From his stool test Larry was able to see that his lactoferrin levels were consistently higher than normal. Some research into lactoferrin led him to find that is was associated with IBD. He didn’t feel any worse, but his data was starting to tell him a different story and he decided to trust the data and continue exploring.

“This idea that you can just feel what is going on inside of you, that is just so epistemologically false. You just can’t do it.”

Through 23&Me, Larry learned that he had a marker that was associated with greater risk for Crohn’s disease. From reading scientific literature, he found that immune system dysfunction and microbial factors are both associated with Crohn’s disease. What did his stool sample say?


Immune system dysfunction? Turns out his lysozyme levels were in an “episodic war” trying to control bacteria levels. Additional tests found that his good bacteria levels weren’t up to par. Unfortunately these stool test were only able to give him insight into a small window of his microbial ecosystem. Thanks to his relationships in the scientific community and his access to computing resources at UCSD he began the process of whole genome sequencing of his stool samples. This process of data collection, testing, researching, reading, and the re-testing has given something more than just knowledge. It’s given him hope. And even joy.

I’m learning more as a scientist, and I’m doing more hands-on research than I have in 25 years.”

If you’re interested in Larry’s process of self-tracking and health testing I highly suggest reading his excellent article, Quantifying your body: A how-to guide from a systems biology perspective


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14 Responses to Larry Smarr: Where There Is Data There Is Hope

  1. Alexandra Carmichael says:

    I admire Larry’s dedication to understanding his health!! I’m curious though, what he hopes to learn from stool microbial genome sequencing – will this be able to predict illness before it happens, or is there any other known direct benefit? And wouldn’t this need to be done regularly, like every day, to be able to detect subtle changes? If anyone has any knowledge on this, please share! :)

  2. Gary Wolf says:

    Is there any firm knowledge even of the # of different species of bacteria that typically inhabit the human gut?

    (According the abstract, this paper argues that a typical bacterial “species” is actually more what we think of as a genus when we are talking about fungus, plants and animals: in other words, there is lots of genetic diversity here:

  3. Eri says:

    I get such a kick out of Larry’s quest to find out more about the inner workings of his body. He’s like the Gut MacGyver, taking all the diagnostics available to him and trying to come up with a conclusion. But I’m reminded that we are at such an early stage in understanding our personal microbiome (let alone how we compare to the average so-and-so) that making correlations requires a fair amount of hacking.

    The future of knowing what’s kicking around your and your friends’ guts looks ready for a shift, with projects like uBiome and American Gut shooting for sequencing the microbial life of 2,000-10,000 people around the globe. Kits are well under $100 and data will be open source. American Gut just ended their IndieGoGo campaign and uBiome has a few days before their campaign ends.

    I think if enough of us opt into getting and sharing our data, we can draw conclusions like Larry’s. But there is some work that needs to be done after collecting microbiome data, including establishing a common data infrastructure and creating systems that help the average guy know what an NIH study means in light of his gut bacteria. Perhaps a 23andMe for guts?

  4. Larry Smarr says:

    Alexandra-In June Science and Nature had special issues with papers from the NIH Human Microbiome Project which for the first time established “healthy” ecological distribution of microbial phyla and species. Researchers like me are now trying to determine how dysbiotic the ecological distribution becomes with different disease states. Eventually, we may be able, by tracking the beginnings of disequilibrium in the microbial profiles, to adjust the microbes back into a good stable equilibrium, perhaps avoiding the onset of disease.

  5. Larry Smarr says:

    Gary-while the concept of “species” is a challenging one for microbes, NIH has am ID for each species and substrain that have been sequenced. In our work we look for shifts across phyla, between species, and even within a species (like E. coli where there are over 100 genetically sequenced strains).

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  7. Eri says:

    A related topic I’m following is the success of fecal transplants, and more so the reasons why they work. A recent paper may be of interest:

    Fecal Transplant Boosts Drug Tx for C. Diff

    ” In a small, open-label, randomized controlled trial, 81 percent of patients treated with fecal infusion following a short-course of vancomycin had resolution of C. difficile-related diarrhea compared with 21 percent of patients treated with a longer course of vancomycin with bowel lavage and 31 percent who received vancomycin alone (P<0.001 for both), according to Josbert Keller, PhD, of the University of Amsterdam, and colleagues. "

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  12. katrina z says:

    Dr Smarr
    I along with many members of Ulcerative colits and Crohn’s forums have followed your work. Yes, our gut ecologies are out of balance- the question is: how do we return them back to a healthier state? Personally, what are YOU trying to do in regards to this? [ It’s OK if you prefer not to answer in a public forum. ]FT seems to be the answer for many and now that the US and insurance companies have approved this for treatment of C. diff, how can we get it approved for IBD treatment?
    thank you

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