Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome… (#54)

By popular demand, an entire episode dedicated to exploring the human microbiome!

Are you really 90% bacteria and 10% human? How can you manage or optimize your own microbiome? Should we do fecal-matter transplants from “untouched” indigenous tribes to reverse chronic illness? We tackle all this and much more…

Ep 54: The Promises and Perils of the Microbiome - Dr. Jonathan Eisen and Jessica Richman

Jessica Richman is co-founder and CEO of uBiome, a startup backed by Y Combinator and Andreessen Horowitz, which uses citizen science to understand the human microbiome.

Jonathan Eisen is a Full Professor at the University of California, Davis with appointments in the School of Medicine and the College of Biological Sciences. Dr. Eisen’s research focuses on the evolution, ecology and function of communities of microorganisms.

You can find the transcript of this episode here. Transcripts of all episodes can be found here.

This podcast is brought to you by 99Designs, the world’s largest marketplace of graphic designers. Did you know I used 99Designs to rapid prototype the cover for The 4-Hour Body? Here are some of the impressive results.

QUESTION(S) OF THE DAY:  What’s the most interesting or helpful thing you’ve ever learned from a medical or biological test? Please share in the comments.

Scroll below for links and show notes…


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Selected Links from the Episode

uBiome’s Twitter | Jessica Richman Twitter | Indiegogo

  • Connect with Jonathan Eisen:

Twitter | Personal Blog | The Tree of Life | TED

Show Notes

  • Interesting answers to boring questions… [1:00]
  • Defining “microbiology” [2:30]
  • What is “phylogenomics”? [4:00]
  • Microbiome misconceptions [6:40]
  • Defining citizen science [9:30]
  • Gut | Mood | Behavior [11:30]
  • Scaling microbiome research using the public [21:30]
  • How experts think about probiotics [34:30]
  • A new perspective on probiotic solutions [42:20]
  • The idea of a fecal bank, and the scientific feasibility of actually doing it [52:00]
  • Exploring vegetarianism [1:04:45]
  • Rules that stifle vs. constraints that enable [1:07:10]
  • Jessica’s founding story of uBiome [1:13:40]
  • Long-term goals of uBiome [1:17:00]
  • Rapid-fire questions for Jonathan [1:19:55]
  • Rapid-fire questions for Jessica [1:29:55]
  • Many more rapid-fire questions…

People Mentioned

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65 Replies to “Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome… (#54)”

  1. I contribute my microbes to uBiome. I would love to participate in this discussion.

    I can’t.

    Because I have no idea what the podcast is all about.


    I am deaf hence the podcast is inaccessible.

    As you promised a transcript and I have yet see a transcript.

  2. Tim, at a certain point, Jonathan mentions about the study that we’d be 50% microbial cells and 50% normal smashing the myth of 90% – 10%. could you please point out to the study?

    I tried finding it, but I got no luck. Thanks!

  3. YES! I’ve been waiting for this. One of the most fascinating subjects in todays science frontiers. Thanks Tim!

  4. Tim, you have very interesting guests on your podcast.. I’d really like a outline tree with a summary (pref. with hyperlinks that refer to the specific piece in the podcast) so I don’t have to skim the audio and can actually see what the actions are. I like to start with the decisions I might want to take and get information from there, not the other way around.

  5. This made me think of the “Bill Gates drinks faeces water” story of this week. It looks like this bacteria stuff is really our medical and biological future.

    1. Tom, it’s also one of the main interest of current science. It’s fascinating. If you wanna become more knowledgeable on the subject you could take one of these coursera courses on the microbiome. They’re held by professor from top universities.

  6. I used to work on cell towers after being stuck in front of live antennas for years I was not feeling well I got my blood test and it revealed I had the testosterone level of a 78 year old man I was only 30 at the time! after leaving the industry and taking supplements I have brought everything back around to normal. I have also utilized Tim’s triple your testosterone from the four hour work week that cod liver oil is good stuff. that much high level of extended RF exposure is no good. I also only carry my cell phone in an armband or for quick times in my back pocket. gents don’t cook your boys!

  7. Ive been hearing and reading much about bacteria these days. Thanks for giving another post on this. i enjoyed it.

  8. I have experienced that I’m a spiritual beeing and I have seen miracles in kung fu no scientist will ever be able to explane. I have cured illnesses by telling people think specific thoughts. A friend waked up a koma patient deserted by medicine. Are we biological? TimnFerris I would have expected this from every body but not from you. i would love to challange you and your scientiests let me know if you are interested.

  9. I don’t know if it was the MOST helpful but it really changed some of my eating habits. I found out I was neither gluten sensitive nor lactose intolerant. Now I can have cinnamon toast and a glass of milk. Very helpful!

  10. Scientist are just scratching the surface in their understanding what our microbiome can do to make us hale or ill.

    So far, it’s pretty clear that the bacteria in our gastrointestinal tract have a profound influence on our cardiovascular system, chronic inflammation, body composition,and even depression.

    Startling to realize how powerful are these microscopic critters.

    I’ve read and written quite a bit on the subject, and have followed the progress of uBiome since they were on a crowd funding platform (Kickstarter?). Very impressive.



  11. HI Tim, I was bit by Lyme in 2007 after traveling to Africa, Ecuador and China, I came back to the US for my friend’s wedding in PA and I was bit by this life altering disease. Amazing how I didn’t get anything until I came back to US soil. Just awesome!.. (sarcasm). I’d love to know what diet & treatments you have found that works for you. My brain fog has gotten the best of me lately.



    (Newport Bch CA)

    1. Hey Tim and Lauren,

      I am also a Lyme patient and have done extensive research on the subject because of the extreme brain fog. As far as diet goes the best thing I have found is to go with a low carb high health fat diet such as the Bulletproof, Paleo, or Ketogenic diet (avoiding sugar, gluten, corn and processed foods). The purpose of these diets is to reduce inflammation caused by the Lyme that is more than likely attributing to your brain fog. With this i really found the key to the diet was completely eliminating sugars to be able to kill the Candida in my gut which was not allowing my medications (both natural and antibiotics) to work as well as they could. Although the antibiotics obviously work in killing off Lyme I think that if I were to go back with the knowledge I have now I would not have taken that path due to the deteriorating effects they have on your gut and your micro biome.

      Alternative natural paths could include using different oils such as Samento oil or Cats Claw which both help to lift brain fog. Also I’ve began to take an all natural Colostrum supplement which has been shown to help work almost as an antibiotic in killing of Lyme while also rebuilding your gut at the same time (also gives you great energy). On top of the treatments I think that you MUST supplement with a good multivitamin and high doses of Vitamin D, Magnesium, and CoQ10. Thorne FX is by far the best brand out there, and you will not find better quality on the market.

      After you have nutrition and supplementation taken care of its time to use some of the “woo woo methods”. Methods such as meditation, tapping, and quigong are great for opening up the mind and the body to staying positive and de-stressing. Other things that may work but are a little more on the pricey side are Rife Machines, and Ozone therapy. Rife uses certain vibration frequencies to match the frequency of the Lyme to kill it. I am not as knowledgable on on Ozone therapy but it seems to be very effective in killing infectious and autoimmune diseases.

      The best thing you can do for yourself is find a Lyme literate doctor, ask questions, and keep doing research for your self because even a lot of Lyme docs are not up on all the best forms of treatment. Lyme effects each person differently and we need to all learn how to stay positive in fighting this disease because from personal experience I know that it is possible to beat!

      Good Luck in your pursuit of health!


  12. Hi Tim

    During the interview you commented on donating sperm and getting past your “best before date” (I’m paraphrasing). Recently…within the last year…

    I was reading or listening to something on stem cell research and it said that the only two cells that don’t age are cancer cells and sperm cells. I just turn 47 and gave up on having kids long ago. After hearing that I am considering having kids again. I would be interested hearing any further information regarding this and the risks (to the child) of having kids after a certain age for men. Thanks! Really enjoy your stuff.

  13. With particular reference to crowdsourcing anecdotal data, how can web and mobile developers get involved in building [custom] apps to help with the data collection?

  14. I’ve learnt that a physical prostate test with my local fat fingered GP is far less pleasurable than from the new twenty something female trainee 😁

  15. Great topic! Thanks for bringing it.

    Best medical / biological test:

    1. Has to be the wonderful (and frightening) tests available that let us know our twin embryos were healthy (healthy = free from the diseases they were screened for); and that we were having a boy and a girl. JACKPOT! : )

    (They are 5 now and life is full…)

    2. I was surprised and grateful to learn back in 2006 that a blood test could help diagnosis and catch potentially serious medical problems.

    I suddenly felt sicker than ever and almost immobilized one night in 2006. The next day I went in and blood tests were ordered. I didn’t have the flu as suspected, I had pancreatitus. This led to more tests to find the cause and turns out I had gall stones. I got treatment and became well again. (Thankfully, this was all taken care of before becomming pregnant with the twins. ) I learned a lot about my whole digestive system in the process.

  16. Really interesting stuff as I have had Crohn’s for 10 years. I’m able to control it with the paleo diet (no immunosuppressants) however cheat days are a no-go for me.

    You’ve probably already done this Tim but it’s worth having a Skype consultation with Glenn Taylor from He is one of the leading FMT researchers and I found him through Chris Kresser’s podcast.

  17. In regards to the honey before bed. Two other substances that would be interesting to see work, IF someone has access to them. Or if someone knows where to get access to them let me know.

    I wonder if Peter Attia’s synthetic keytones would perform similarly to honey or not? Assuming one can choke it down.

    The other would be if C7 Oil (Triheptanoin)?

    Mainly to see if it is actually glucose/fructose involved or the fact that some sort of high performance energy source is supplied right before bed.

  18. In regards to the honey before bed… I’m curious if it is the glucose/fructose specifically or other substances in the honey or if it is the energy it supplies to the brain. If it is the energy it supplies to the brain during sleep, then it is possible the following two substances could also work.

    1. Peter Attia’s synthetic keytones, assuming one can choke them down.

    2. C7 Oil (Triheptanoin) – I’m assuming this is easier for the body to use as an energy source than regular MCT oil.

    I don’t have access to these, but if someone does it would be nice to see if it does work. Then we’d know it was the supplementation of energy right before bed and not some other substance in the honey.

    1. No chance you could sleep after using synthetic keytones. Tried them several times and its pure energy. And wow…most awful tasting thing ever.

  19. Thanks, Tim. Great show. Here are a few things you might like. I’ve been getting Bik’s Picks, a micro biome digest put out by Elisabeth Bik at Stanford. See, e.g., last Friday’s:

    Warning: you can go down the rabbit hole for hours every week day!

    Also, Martin Blaser’s recent “Missing Microbes” is really interesting. [That’s a book, but I don’t know how to underline or italicize in these comments.]

    Finally, Robynne Chutkan’s talk at Mind, Body, Green is fun:


  20. Oh, and the most interesting thing I’ve learned in a medical/bio test was that I needed to put together a DIY FMT capsule protocol to cure a decade of annoying mutherfucking illnesses!

    Fact is, knowing what bacteria are in your gut and how your small intestine works (or doesn’t) will change your life. There’s lots of hope out there for many inflammatory and neurological illness sufferers but, unfortunately, most of us find it impossible to even maintain a suitable diet to ‘feed’ our good bacteria.

    As for tests: uBiome is a good start. But it drops you into the proverbial rabbit hole … which is where everyone gets lost.

    Also… Got auto-immune issues? Then eating paleo isn’t going to be your friend.

  21. Quite the exotic concept to say the least … but that’s what you specialize in Tim 😉 Love the podcast, keep it up man!

  22. The point Jonathan made about spending the money on experiments reminded me of your question to Ed Cooke about if he’d rather have one guy spending an incredible sum, or many others spending relatively large sums. While Bill Gates is nice to have around, there are millions of little projects that could see great returns. In that case you are dependent on a single person or group recognizing them and funding it.

  23. You say you are in a less productive period, yeah but you are producing amazing podcasts.

    This topic interests me because if one is paying attention to one’s health then their digestive system is important. In 1979 I started experimenting with eating a lot of fiber (the so called “save your life diet”…if you didn’t blast a bran storm diet really). High fiber diets are healthy, but too much bran is not good for the colon. The amount of water consumed can affect stools significantly.

    My wife is an expert at propagating pathogenic bacteria. It is true that there are no ideal probiotics. My wife says that one of survivable ones is Dr. Ohhira’s. It seems to work well for me. Eating raw foods like a locally grown apple is a good source of probiotics. If you live in an urban area you are living in a sea of enteric bacteria (due to the 1000s of gallons flowing in sewers and people and pets crapping everywhere) so there is no need for probiotics. More likely in urban areas people can get incompatible or strains of E. Coli. I am fortunate to beach it in Mexico every year. I get something every year after a week. I take pep-to Bismol which kills gut E. Coli. When I get home the normal flora comes back.

  24. Love the Edge…lol not a great plot synopsis.. They are in Alaska for his supermodel wife’s photoshoot… Anywho… I have a crazy question… There has been a lot of discussion around skin and GI flora and how they have been evolving to the anti-septic and antibacterial drugs/soaps… I was wondering how about our mouths? What has the impact been of mouth wash and brushing teeth… Touth decay is related to diet eg sugar and acid exposure… This sounds crazy but are we going to use probiotic toothpaste soon?

  25. Great information. I think there is a strong link in gut bacteria and autism and other neurodevelopmental disorders. It’s great to see this information becoming main stream. Natasha Campbell has some interesting points on this topic as well.

  26. This is actually very interesting. We are basically 100% human, everything else is a matter of perspective, or so they say.

  27. Hey Tim! Happy New Year mate. A quick note if you’ve got a minute: I want to start moving on my long-term goal of raising the funds to build a school in Vietnam.

    My business is repairing Guitars and Amplifiers and building electric and acoustic guitars in Melbourne, Australia.

    I could use clarification from you as to what might prove most effective:

    I plan to a) use everyday customer flow to generate funds based on a percentage of their normal fee – average spend per customer per visit = $180

    b) when i build a guitar, ask the customer to donate a percentage of the guitar’s costs AND offer to match that donation myself – electric is $3300, acoustic is $5000

    c) every six months or so build an artistic guitar to auction online, all proceeds going to this cause. – purposefully lavish and unique with a starting bid of $6000

    Do you think the a) option should be optional or compulsory?

    How do people respond to what is effectively a tax on their services? As in, what is their threshold? Should I be asking 5% or 15%?

    I’m aware you have spent time in Australia and so have a flavour for the culture. As a reference point Australians spend more on alternative medicine than any other developed nation and in the last economic downturn (approximately GFC 6 years ago) the average spend on health and fitness increased. From a marketing perspective I need to KISS this and could really use your advice as to what experience has shown works best.

    My 6 year old son is about to start Primary school and is very excited. Having had a mostly free tertiary education to Masters level I am aware of its advantages in a global workplace and I would like to offer that opportunity to others born in less fortunate circumstances.

    Many thanks in advance to everyone out there.

    Joseph price

  28. Hi Tim. Great content. Could you maybe discuss the resistant starch & probiotics combination. I was kind of hoping to hear that question for the expert guests, but oh well … . What is your take on that?

  29. From the 23&me DNA evaluation (I got it done before they ran afoul of FDA and had to discontinue the health-related/inherited conditions part of the genetic report), I learned I have the alpha-1 anti trypsin variant. This is associated both with fibromyalgia and the condition known as “ICE” (“Intense Creative Energy”). Yes, for real. Journal citation to follow if you want it.

    It makes it much easier to deal with all the achy muscles when I can now tell myself that it is the “price of ICE.”

  30. this is my first time read about microbiome. I’m attracted at 90% bacteria 10% human topic.

    human contains 70% water 30% non-water..

  31. I would have liked to know the opinions of GMO’s and the effects to the micro biome. Really surprised this wasn’t brought up in the conversation.

  32. Fascinating stuff! Can’t wait to hear more as for research comes out. Definitely going to try the honey and vinegar drink before bed as I’ve had a hard time getting a good night sleep for several years now.

  33. I listened to this podcast when it came out. Extremely interesting! I just stumbled upon an article today ( about the very interesting and inspiring not-for-profit organization, OpenBiome ( The story behind this organization provides a GREAT perspective on the importance of the microbiome. This article is a great complimentary read upon listening to the podcast, and in fact makes me want to listen to the podcast again! (sidenote: also shed light on the importance of the content of our diet, especially as it relates to our food industry, and the poor government regulation of the food industry. More particularly, as it relates to the microbiome and C. difficile, the fact that industrialized animal treatment is reliant on antibiotics, and these antibiotics are passed on to us upon our consumption.)

    To learn more about the issue regarding our industrialized food industry, farmer Joel Salatin has a wealth of information on the issue, which is well extracted on episode #479 of The Joe Rogan Experience podcast


  34. Great podcast and, in particular, great podcast topic. Sometimes I sit back and wonder what ideas today will seem foolish in 20 years or 50 years or 100 years. I think the fact that we were so wrong to judge bacterial as clearly negative for so many years will be one of those silly ideas in the future. It already is, to a certain extent, in certain quarters. But I believe that we are just scratching the surface.

    Tim: If you see this comment, I am interested in what ideas from today you think we will laugh about decades from now.

  35. Happy to hear you recovered from Lymes disease!

    I’d love to hear more about how you personally recovered from antibiotic side effects.

    I personally was just on a strong cycle of antibiotics and my gut hasn’t been the same.


  36. Hello, a very interesting podcast to follow. I have had IBS-D for about 12 years and have had many tests done from different GIs, but have not come up with a diagnosis. I am interested in exploring the microbiome and am curious as to what suggestions anyone has for improving the gut flora, specifically fot this condition.

  37. Could someone comment on how the gut biome might be positively effected by what we do to control & enhance the mesenteric “second brain” through the autonomic system. We look strongly at how bacteria effects health and mood. Can we not look at how working on mood and health “macro” may, through autonomic flow/release, impact the bacterial “savanna” Great Pod Cast!

  38. Tim,

    I’ve been reading a few things about the microbiome on the one hand and ketogenic diets on the other that have raised an apparent inconsistency to which I haven’t yet been able find a satisfying answer. Hi fat diets are, thus far, said to promote firmicute growth in the gut. And a higher ratio of firmicute to bacteriodete in the gut is linked to obesity (while a lower ratio is linked to leanness). Nevertheless, ketogenic diet promotes leanness. What gives? There appears to be an article in Nature from January 2014 that goes into this, but rather than spend the 10 bucks to order it (and I don’t know how long to read it) I’m being lazy and asking you instead. Do you know how this is reconciled?

    Many thanks, and keep up the good work.

    1. I’ve been in nutritional ketosis since August 2013, and I look with interest at studies that purport to find problems with high fat diets. The answer often is in the types of fats. Many of the animal studies, including at least one that found an increase in firmicutes with a “high fat” diet, involve a standard lab “rat chow” that is mostly high omega-6 processed oils. Some of the human studies involved diets that were both high fat and high carb. Typically, when you review the study methods, you’ll find the supposedly problematic “high fat” diets were not akin to a well formulated ketogenic diet.

  39. After years of digestive issues I discovered that one of the fastest ways to detox the gastrointestinal tract of “Bad” bacteria is Calcium Bentonite Clay followed by probiotics and low to no sugar diet. Good luck on your journey.