Going Feral: my one-year journey to acquire the healthiest gut microbiome in the world (you heard me!)

Unless you’ve been holed up in a cabin in the Siberian outback, it’s been hard to miss the avalanche of research and associated press coverage ballyhooing the connection between microbes and human health and disease in 2013 – and 2014 will be no different, as fecal transplants become the new black!

DSC_2189Name just about any ailment plaguing humanity and you will find some researcher, somewhere, working the microbial angle for a causal or correlative connection. More federal funding please!

But reading between the lines of the near breathless and optimistic reporting on the human microbiome, sits a sobering fact: scientists know very little about the connection between disease and the potential microbial culprits (these are early days). Science is hard and the human gut is a vast and diverse ecosystem. As with any ecosystem, it’s the community as a whole that’s likely more important, not single members per se. Connecting the dots when there are lots of them – and they are shape shifting all the time – is proving to be tough (a similar reality has slowed our understanding of the role of human genes in disease). This will take some time – but the writing is on the wall.

That said, projects like American Gut (think about joining the project!) are trying to map the diversity of the human gut. By sequencing the gut microbes of tens of thousands of regular folks – of all shapes, sizes, and of diverse diet and lifestyles – we hope to see coarse-grained patterns shaped by disease state, age, diet, lifestyle habits, and so on. These broad strokes will then allow researchers from all over the world (yes, de-identified American Gut data is open source and made available to the research community – thanks good folks over at Earth Microbiome Project) to dig a little deeper to see what might matter the most when it comes to maintaining a healthy microbiome at different stages of life (yup, a 2 year old harbors different microbial compositions than grandpa).

In addition to a large sample of westerners, we will also able to compare these tens of thousands of samples to other data sets – including groups from Africa, India, South America, and so on. Excitingly, our work with the Hadzabe hunter-gatherers in Tanzania will allow us to compare our western selves to people who still hunt and gather the majority of their food, have limited access to western medications, are all born naturally and breastfed for 2+ years, live outside more or less 24/7, are covered in microbial-laden soil (natures blanket), and that have an intimate connection to a vast (natural) microbial world that we in the so-called developed world have moved away from. We don’t know what we will learn over the coming years, but it’s a given we will be a little smarter when it comes to modulating and nudging our gut microbes in a healthier direction with diet and lifestyle choices (I sure hate to see Big Pharma drug our microbiome into compliance – lets not let it happen folks!).

As researchers continue to build the scientific case for the microbe-health connection in 2014, I’m embarking on a little self-exploration. On January, 1, 2014, I began the first of many diets that I hope will lead to a better understanding – at least for me – of not only what a healthier gut microbiome might look like in a modern world, but also more importantly, what it shouldn’t look like. I will be collecting daily stool samples along the way for subsequent 16S rRNA analysis throughout the next 365 days.

On Jan 1 I started a high fat-protein diet with very, very little carbohydrates and near zero quantities of dietary fiber. In short, I’m attempting to starve my microbes of much-needed substrates for growth – such as dietary fiber, resistant starch, etc. I’m not arguing that anyone should do this on a regular basis, nor am I suggesting this is a good or bad dietary strategy, but I am trying to whack my microbiome around a bit to demonstrate that significant shifts in your gut microbiota can be achieved in very short periods of time with significant shifts in macronutrients.

I experienced this past summer how dramatically you can shift your gut bugs with diet when I traveled from New Orleans to West Texas where I was held up for a few months trying to finish a book (BLOOM will be out this year!). As I drove out of New Orleans, I left behind a diet heavy on meat, but with a quantity and diversity of dietary fiber that would make Michelle Obama smile. But once I landed in the parched landscape of West Texas near Big Bend National Park, the little writers shack I rented lacked some modern niceties – like a kitchen. So I ate most of my meals at the local watering hole(s). Below is a graph of what happened to my gut microbes.

As the pie charts below reveal, I look like an entirely different person – microbially-speaking. On the left my New Orleans microbiome were dominated by the phyla Firmicutes (74.80%). But after only 2-3 weeks of greatly reduced consumption of dietary fiber – remember, I still ate lots of meat – my Firmicutes dropped to 28.63%, while my Bacteroidetes shot up. In other words, my Firmicutes and Bacteroidetes traded places in my new desert belly.


Digging a little deeper in the data reveals that much of this dramatic shift can be attributed to a handful of genera. The bar graph below shows that my Bacteroides (in the phyla Bacteroidetes) seem to really like my no, to super low plant intake – going from a mere 15.91% relative abundance in New Orleans to a whopping 56.59% in my near plant less desert diet. Consequently, the relative abundance of the Family Ruminococcaceae took a hit along with the Family Lachnospiraceae and the Genus Ruminococcus. These three are known plant fermenters – that is, they metabolize dietary plant polysaccharides – that didn’t seem to compete very well as the fermentable substrates (fiber, resistant starch) dried up.


Also of interest are my Bifidobacterium levels which went from 5.46% in New Orleans, to 0.10% and my levels of Paraprevotella (kissing cousin of Prevotella) went from a paltry 0.40% to a monstrous 7.20% in the desert (red bar spiking on right-hand side of graph). In the case of Bifidobacterium levels taking a hit – note I like Bifidobacterium as they are often cited as being part of a healthy and balanced gut flora – I would go out on a limb and suggest they were suppressed due to my lack onions, garlic, leek etc. Though I suspect I could be wrong – but that’s my hunch at the moment. As for the increase Paraprevotella, I would again go out on a limb and suggest this spike is attributed to my modest intake of whole grains via Muesli-like cereal – essentially eaten dry every morning in my desert home. Something I didn’t do in New Orleans. Anyone that follows this blog knows I have something of a (Para)Prevotella fetish and attribute the increased relative abundance in many/some folks as a sign of “whole” grain consumption, not fiber intake per se as often argued. Strikingly, elevated levels of Prevotella have been noted among HIV-infected individuals who exhibit chronic gut inflammation. In this study, the researchers suggest that Prevotella may thrive under conditions of inflammation. In another study, researchers found that Prevotella strongly correlated with new-onset untreated rheumatoid arthritis. On the flipside, reduced rather than increased levels of Prevotella correlated with kids diagnosed with autism compared to symptom-free neurotypical children in a recent study. However, it’s interesting to note that many families will place ASD kids on a gluten and casein free diet following diagnosis. Therefore, if my “out on a limb” theory that Prevotella levels are associated with whole grain consumption is near the mark, then lower levels of Prevotella in these diagnosed youngsters is not completely unexpected. In other words, in diagnosed ASD kids the lower to no levels of Prevotella may have more to do with diet than the disease state. But we will wait and see how this shakes out over the coming years.

A new coffee-table-like book about our work in Africa will be available soon. Click here (http://eepurl.com/7X8YX) is you want to receive an e-mail when the book is available. 100% of the proceeds go to the research.
A new coffee-table-like book about our work in Africa will be available soon. Click here if you want to receive an e-mail when the book is available. 100% of the proceeds go to the research.

If you spend anytime reading the literature on Bacteroides – the genus that dominated my desert belly – you will quickly surmise that most researchers attribute it to a high fat western diet. It’s close to dogma. However, in my little New Orleans to desert diet experiment, my levels of meat and thus by extension, fat and protein, stayed more or less the same. The only thing that changed that much was my reduction in plants and the fermentable fibers they contain. So in my Sample Size of One, changes in my intake of meat can’t really explain the striking shifts seen in the graphs above. So rather then Bacteroides thriving in a fat-soaked environment of my desert gut, they likely gained a toehold in my increasing alkaline gut. Like many microbes, many strains of Bacteroides seem to be pH sensitive. And the main driver of the acidity of your colon is fermentation. Reduce the amount of dietary fiber and resistant starch reaching your colon (ie, no plants), the pH rises and becomes more alkaline due to a reduction of short chain fatty acids and other organic acids that are byproducts produced during fermentation. As pH rises, those microbes that are otherwise pH sensitive bloom. So, my “out on a limb” interpretation of the dramatic shift in my microbial community in the example/experiment above is not driven by increased meat consumption, but rather my shift in pH due to the lack of fermentation which ultimately provided fertile ground for Bacteroides to dominate. My increase in the phyla Proteobacteria from 0.03% in New Orleans to 2.63% in the desert, suggests this new, less acidic ecosystem may have favored some opportunistic pathogens. And in one final gut check – and most concerning of all to me, is the overall diversity of my gut microbiota was halved in the desert (as measured by species equivalent OTU’s). And as Ecosystems 101 teaches us, a less diverse microbiota is less resilient to perturbations and may tip one a tad closer to an unhealthy state.  One recent study suggests that my reduction in gut microbial diversity – while not dramatically altering my sanitation and hygiene practices in the process – may have had a lot to do with my reduction in dietary fiber. This is also been seen in mice fed high versus low fiber diets (personal communication, Justin Sonnenburg, Stanford University)

My little experiment coupled with a steady flow of papers suggesting diet and lifestyle can dramatically impact your gut microbial composition in short period of time, has led me to my 2014 goal of acquiring and catching the healthiest gut microbiome in the world. By catching, I mean it’s not all about what you eat, but how and where you live – and whom you live with – and your interaction with the microbial world around us.

Throughout 2014 I will undertake a series of dramatic shifts in my diet and lifestyle in attempt to whack my microbiome around. For example, aside from the high fat/protein diet I just finished at the first of the this year (taking poo samples along the way), I will go on a raw food diet for a few weeks, followed by a juicing diet, possibly followed by a vegan diet, followed by an Atkins-like diet, followed by a Mediterranean diet, followed by a period of fasting, possibly a weeks of lots of fermented foods, followed by a Paleo diet, followed by Jenny Craig and Weight Watchers diets, followed by a Master Cleanse Diet, and so forth – repeating some diets several times. I will also go on the occasional drinking binge, exploring the impact of beer, wine and Jose Cuervo on my microbiota. Don’t tell John Boehner, but I will also explore the impact of copious amounts of weed as I wake and bake for a week while holding IMG_9678various diets constant. But perhaps the most interesting will be my hunter gatherer plunge I will take 2-3 times as I live and work among the Hadza hunter gatherers of Tanzania – where I started working in 2013 (Science did a nice 3-pager on our project recently if you want to learn more – see also tiny blurb in Nature). As a newly minted hunter-gatherer I will live in a grass hut, forage for plants and consume wild game (zebra, impala, kudu, baboons, wart hog, birds, etc.) and drink their water, all the while collecting my stool samples. It will be interesting to see if I can shift my western gut – which ever one I have at the time – to look more like the Hadza. I suspect my exposure to the microbes in the Hadza environment will dramatically alter my microbial composition and increase the overall diversity. But will it last when I return home?

I’m not sure what I will learn at this point, but will share my results with colleagues and ask them to weigh in on the microbial compositions generated by the various diets. I will ask them to do so without knowledge of the diet that produced the results in an effort to remove bias against any particular diet/strategy/lifestyle – such as the bias we see over at US News & World Report as they continue to deliver an ass whopping to the Paleo diet every year as they rank the healthiest diets on an annual basis. Will I nail down the diet and lifestyle that results in an optimal microbiome – whatever that is? Don’t know for sure but I’m pretty confident I will learn which diet and lifestyle choices yield less than optimal outcomes for my gut bugs. If anyone out there has any diets – crazy or mainstream – they would like me to consider, ping me. Let the games begin.

323 Comments Add yours

  1. Deb says:

    Best of luck – what an amazing experiment!

    1. sandra says:

      Have you watched documentary –
      Fat -Sick and Nearly Dead?

      1. Jeff Leach says:

        not yet, but will now

        1. sandra says:

          You can watch for free on Hulu or Netfix streaming- also from Website – Fat sick nearly dead- hulu link- books you might find interesting – The Story of the Human Body- Evolution, Health, and Disease-Daniel E. Lieberman-Grain Brain- author -PerlMutter. Eating on the Wild Side.
          All on Amazon. Would like to know more about Pre-biotics and Epigenetic effects re Flora.

        2. Jerry says:

          Please do view the film and also check out the ‘nutritarian’ eating style as described by Joel Fuhrman, MD (Eat to Live, Eat for Health, etc.) who was Joe Cross’s physician and appears in the film. Perhaps it is a diet that is high in diverse phytonutrients that supports a healthy gut microbiome.

          1. Jerry says:

            You also might want to check out nutritionalresearch.org/ We are interested in researching how beneficial and harmful bacteria are affected by diet.

        3. Peder Madsen says:

          Hey Jeff, just finished reading rewild and loved it. I am very interested in getting a FMT for my wife. she had a full stool analysis’s done via genova and it its very clear she needs to repopulate. There are a
          number of other reasons why we want to consider FMT but we are still unsure. Can you advise

          1. Jeff Leach says:

            need to check with your doctor 🙂

          2. joe says:

            Go to; PowerofPoop & The Fecal Transplant Foundaiton

        4. Jane says:

          Hi Jeff, I recently interviewed the daughter of a 99.4 yr old man who recently passed who had a daily regimen which included dipping the equivalent to a cue tip in sesame seed oil (In India) and putting it in his ears, up his nostrils, in his belly button and up his posterior daily for his whole adult life. Wanna try this? I’m interested in longevity and am starting to interview humans around the age of 95+. I’m not sure if this made a difference to his life of not but found it an anomaly compared to the other information I gathered. Interested to know what researches analysed as a result of your 365 days bias-free and what you discovered. Thanks. Jane

      2. Avishek says:

        This is an amazing experiment. Just discovered this site btw, very well thought out posts.

        But…as interesting as your experiments sound, you’re missing a balanced long term sustainable diet in your experiments. How to maintain a healthy gut microbiome on that diet is what I think would be most relevant for everyone. This diet includes sweets, beer, “processed” foods, as well as healthy foods. Good luck excited to see the results.

        1. Jeff Leach says:

          Yup. good points.

        2. I’m sorry, WHY are processed foods and sweets, and beer supposedly necessary for long-term sustainable diet? Just because you have to eat crap once in awhile to be happy?

          1. joe says:

            You are right Rob, eating processed foods, and all types of sugars along with animal protein are feeding the bad microbes. We should be starving them, and concentrate on feeding our good microbes.

    2. Cheryl Coder says:

      How about the Body Ecology Diet by Donna Gates?

  2. Cate says:

    Paltry? Maybe not poultry..?
    Cool, watching with interest.

  3. Ali says:

    Can you do the Jose Cuervo experiment first? In particular, as a chaser after two tablespoons of potato starch. All kidding aside, THANK YOU for being our guinea pig. I wish I could test at home like I do for blood ketones and glucose. Maybe someday.

  4. Onur says:

    Firstly, I just wanted to say I’m following your hard work on your gut microbiota and thank you very much for sharing the information. You are not alone in the points you make against some other researcher, etc, because I think many of your readers trust in the results you share and the points you make are exactly what any knowledgable person in your situation should consider, so, if you have more out on a limb thoughts, please don’t hesitate to share them.
    I think something you might like to do may be, instead of following only certain diets, also determining what kinds of other diets you might like to try and trying them.
    When it comes to fiber, the best easy source of information I’ve found yet is the 5 part fiber manifesto of Sarah Ballantyne at http://www.thepaleomom.com/?s=fiber
    In part 2 the types of fiber are classified as insoluble/soluble and fermentable/nonfermentable and explained further. You may want to create diets of different concentrations of different fibers and try them. Another thing I’d add is not to forget that too much of a good thing may be bad, and it applies to fiber and bacterial overgrowths, I’ve experimented it myself after eating plates of steamed jerusalem artichokes, so keep a limit of fodmaps such as inulin, which is a fructan, other fructans, polyols and foods with a high ratio of fructose/glucose. Something I’ve found out helpful is that pulverizing some fodmap foods greatly lessened the disturbing effects, possibly due to breaking fibers into pieces significantly and therefore giving less of a chance for the overgrown bacterias to feed on them. You may find a good list of fodmaps at http://www.eat-real-food-paleodietitian.com/paleo-diet-and-fodmap.html which I first found at http://www.thepaleomom.com/2012/08/modifying-paleo-for-fodmap-intolerance.html
    You may also want to try some supplements that change or may change gut microbiota, such as berberine and Prescript Assist.

    Good luck !

    1. BarleySinger says:

      I think it is also important to realize that the use of wild yeast in bread products (with very long fermentation/rising times) has a very different effect on both the grain and the gut… than 10 to 15 minutes “rising time” in a factory using one strain of yeast does.

      Then we also have the amount of damage done to the gut biome (as well as the villi and microvillli) by constant exposure to Gylphosate, Triclosan, “2-4,d” (all of which are indiscriminate killers of microbes) and emulsifiers like Polysorbate-80. This is all quite real. Gylphosate & Triclosan are now present in all surface & most ground water in North America, as well as in the rain and in breast milk.

  5. Inge says:

    Jeff – what role would bacterial genes in the food one eats play for the fecal microbiota analysis? Do you think these genes could add significant noise to the American gut analyses, so as to not be sure of how much of the genes that come from external sources as compared to bacteria actually residing in the gut?

  6. Hunter Purdy says:

    Fascinating! How about Gut and Psychology Diet? I’m at 2 years on this diet with drastic changes in my quality of life.

  7. Frederica Huxley says:

    I would also be interested on the gut effect, if any, on the various forms of IF.

  8. Curious says:

    Amazing study, but would the same results apply to women?

  9. Shawn says:

    Drink nothing but full fat grass fed raw milk for a week and see what happens. 🙂 I’d love to see if it does to you what it did to me ( hives upon eating again, high meat and fat diet ) and then if it goes away from your rapid diet change. Then again, it sucked, so I’d hate for it to do that to you as well… The good news is vegan diet fixed it after long term struggling.

  10. Brooke says:

    Wow! Cannot wait to hear the results!!

  11. Dave Mayo says:

    Awesome N=1, can’t wait to follow it. I was wondering, and you would be the guy to ask, if you thought that the diversity in the gut is responsible for our metabolic flexibility as well as our ability to adapt to changing seasons. It seems to me that these shifts we see in in meat-based diets could be a way to switch on thriftiness traits that may either slow metabolism or affect nutrient storage. For example, could the inflammation related to a meat-based diet be a mechanism by which you could induce insulin resistance and become more adept at storing bodyfat or better preserve glucose? It seems to make sense that as you shift seasons and plant materials become more scarce, there would be an advantage to being able to shift some of the last remaining carbohydrate intake in to fat deposition for the upcoming “lean” season.

    1. Jeff Leach says:

      i written about this in a few places. i think the low grade inflammation (endotoxemia) associated with high fat diet (LPS leaking into gut) is an evolutionary strategy to trigger insulin resistance which conserves glucose. you see this among the hadza – when there is lots of meat, carbs drop off a bit.

      1. Dave Mayo says:

        Interesting. Found this study you might enjoy the other day via Science Daily that discusses fiber, butyrate, and how they reduce inflammation in the gut.


        1. Jeff Leach says:

          Yup, saw that when it came out – amazing study, important. Thx for chiming in.

  12. Glenn says:

    I will be following your progress.. Good luck.

  13. DA says:

    How about a gluten free diet?

    1. Jeff Leach says:

      will cover this when I do Paleo

  14. YourMom says:

    Would be fascinated to see you do a GMO diet and also a processed Foods Diet.

    1. Jeff Leach says:

      pretty sure there this wouldn’t yield anything. if it did, not sure how as GMO vs conventional isn’t going to change substrates to the colon and provide anything out the ordinary to the gut bugs. but u nvr know. would need a very well controlled study with a considerable amount of participants.

      1. Not that I would wish a GMO diet on anyone, but it would appear that there is research showing that the accumulated pesticides in GMO soy could affect gut bugs: http://www.sciencedirect.com/science/article/pii/S0308814613019201

        1. Jeff Leach says:

          might. but the study u linked isn’t about gut bugs.

          1. Dan says:

            Will be following this closely. Even if there was little microbial change with GMO and processed foods it would be interesting to see the results anyway. I think this would also appeal to a broad audience.

          2. I agree with Dan, “This would appeal to a large audience.”

      2. laura livingston says:

        The process of creating any and all GMOs requires first a vector (pathogenic bacteria or a virus) to enter the target cells with the new DNA, second some DNA for antibiotic resistance attached to the new DNA to be inserted, so the cells with the new DNA can resist the antibiotic selective agent to sort out the ones that didn’t take. So, all GMOs contain pathogenic bacteria (mycoplasma) or viruses, viral or bacterial susceptibility in order to contain the new DNA, and antibiotic resistance to survive the sorting process. Combine that with microbial ability to exchange genetic material in the gut. You would probably end up with a gut full of super bugs resistant to antibiotics but susceptible to viruses which cause evolutionary mutation. (It’s not antibiotics in animal feed causing antibiotic resistance, but antibiotic resistance in human feed.)

        1. Jeff Leach says:

          Horizontal gene transfer in the gut happens non stop already.

          1. laura livingston says:

            Yes, it does. It always has. What I’m saying is that genes transferred from GMOs to our guts have some scary qualities. They have antibiotic resistance built in, so if you do acquire a pathogen in your gut, it can grab the antibiotic resistance gene from your GMO food. Also, commensal viruses and bacteria in our guts can grab pathogenic abilities from the vector DNA in GMOs. When biowarfare scientists were searching nature for antibiotic resistance to include in their bio-potions, they found it in bacillus thurengensis. So, all Bt GMOs can share antibiotic resistance with any microbe they come in contact with. When we eat GMOs, we are brewing antibiotic resistance inside our guts.

          2. Brian says:

            Amen Jeff; solid point. Also, ‘Laura’, do any work in genetics? Because I make mutations in bacteria and eukaryotic cells all the time and it does NOT require “pathogenic bacteria or viruses”. Many species are able to transiently take up eDNA, which could have simply been a PCR product of any random gene. In addition, one could easily do ‘Mendelian’-style breeding and come up with almost all of the GMOs that you speak of, it would just take much longer and cost way more. In fact, some companies are attempting to do this right now because people freak out about the title GMO for no reason. Look what ‘conventional’ breeding has done to canines…many breeds die because of traits that owners have purposely selected for. But that must be okay right? Because it was done the old fashion way….

      3. YourMom says:

        Jeff, this is a TED talk published June of 2013, Ex-Biotech Scientist Gives TED Talk on the Dangers of GMOs. Interestingly, he specifically speaks of the impact on Gut Bacteria right after the 00:08:00 minute mark.

        Thierry Vrain is a former research scientist for Agriculture Canada. He now promotes awareness of the dangers of genetically modified foods.

        For most of Thierry Vrain’s career, he supported the cultivation and consumption of GM crops, but in the last 10 years he has changed his position because of the flow of published studies coming from Europe, some from prestigious labs and published in prestigious scientific journals, that questioned the impact and safety of engineered food.

        He refutes the claims of the biotechnology companies that their engineered crops yield more, that they require less pesticide applications, that they have no impact on the environment and of course that they are safe to eat.

        When the first GMO crops were introduced in the mid-1990′s, they were marketed (and received) as ‘magic’ — a perfectly safe, practically water-like substance that erased pest problems without changing the quality of the food.

        In this TED talk given recently to an audience in America, Thierry explains the rising phenomenon of superweeds, genetic pollution, antibiotic resistance and food allergies, all attributable to GMO agriculture.

        The Gene Revolution, The Future of Agriculture: Dr. Thierry Vrain http://youtu.be/RQkQXyiynYs

      4. Karlie Cole says:

        GMO or not, it is likely higher consumption of pesticides, herbicides, fungicides, etc would have a measurable effect on the gut microbiota as these substances are meant to kill the little critters. Genetic modification itself probably unlikely to measurably impact but higher levels of little critter killing substances in food likely would impact the gut microbiome. It’d be real interesting to study gut bacteria of GMO farmers where the fields are soaked in glyphosate.

      5. Jeff,
        Curious what your opinion is on this, concerning GMOs, glyphosate, gut microbes, and disease:

        Correlation isn’t causation, but is it not a hypothesis worthy of further investigation?

        (Agreed that your sample size of 1 wouldn’t cut it here, though…)

  15. Thanks, Jeff, for the incredibly important work you are doing. We’re having a lot of fun with the data you are providing over at Heisenbug HQ. I’m glad to see some confirmation of the Bacteroides/alkaline connection — the idea that they somehow thrive with meat/fat intake, apart from fiber/plant intake, never made much sense to me.

    So I take it you think the Proteobacteria bloom is a response to the overall rise in ph, and not a direct response to the drop in Actinobacteria/Bifidobacteria?

    Oh, and please feel free to go “out on a limb” more often — it’s the only way to ever figure out anything useful!

    1. Jeff Leach says:

      good points and yes, i think my drop on actino (didn’t feed them) along with other fermenters greatly reduced SCFAs and thus pH. i “think” this opened the door for some proteo. but not 100% sure. we will see. thx for comments!

    2. Bernie Cullen says:

      I see the Proteobacteria going to 2.63% after the desert diet, but I don’t see any Proteobacteria listed in the bar graph. What kind of Proteobacteria was it?

      1. Jeff Leach says:

        i only plotted the top 30 in the bar chart – was getting too hard to read including more. the proteo seem to be (will sort out which strains are likely in a few weeks):

  16. Melissa Reading says:

    Unless you’ve been “holed up” not “hold up”. This isn’t a robbery. It’s a reference to someone being out of touch, as a badger in its burrow, or hole.

    1. Jeff Leach says:

      oops. auto correct on iPad

  17. adinaverson says:

    can’t wait to hear what you find!

  18. Denise says:

    I agree with you and inflammation/grains/Provotella. What you are talking about is the conclusion I have reach through my own experience. I had been ill 25+ years and found that a paleo diet was a big factor in managing my condition/symptoms so only ate veg and protein, if I had any sugars or carbs then the brain fog, disbyosis, cognitive and fatigue symptoms would sky rocket. I stumbled on this connection when I first tried the Atkins diet. I thought this might have been because I lacked a diversity of gut flora having been on a lot of antibiotics during my life both as a child for a heart murmur and then as an adult for various infections. Then to years ago I under went two weeks of donor stool infusion at the Centre for Digestive Diseases in Sydney – Prof Thomas Borody. He put me on the antibiotic Rifampacin to sterilize the gut, with his permission I incorporated Dr Anju Usmans (Autism Research) biofilm protocl for two months with the antibiotic. At about the 6 week stage of the preparation the weight fell off me, I could never get my weight down before this, if I ate carbs overnight a couple of kilos would go on and this would continue whilst I ate carbs. I then underwent daily donor stool infusion for two weeks. I was glowing with health and vitality, I looked 20 yrs younger and felt incredibly well, like a teenager again. No more leaky gut, no more food intolerances, all my symptoms gone and hence I went back to work . My general Dr congratulated me on these results. However this effect slowly subsided and after about 8 weeks my symptoms crept back in. and my cognitive ability declined so I had to stop work again. So about a year later I did my own donor stool infusions from an approved donor for about 3 weeks. But nil, nothing, zilch, no benefit at all. Then about 12 mths later I found out I had lyme disease. Now on IV abx and again the abx Rifampacin, so I expected the weight to drop of again and the inflammation to go. But no this didn’t happen and it has been 3 months on the abx. So my conclusion is that the diet is the missing peace, I haven’t been eating grains or high fructose fruit but did have berries in my diet. so I decided to eat just meat and veg again, now two weeks into this and I am now again starting to see the fluid/weight come off me well I am pretty sure it is inflammation, just as you mentioned in your post above. My hunch is that 2 months on from now on just meat and veg with the abx all the inflammation will have gone again. I am very interested in your experiences as it directly affects me. Once I have finished with abx I will again undergo donor stool infusion, but realize this is only part of the puzzle, I have to feed the desirable flora so they will establish in my gut and flourish. So I am following you with great interest. Good luck and thank you for your GUTS to be the guinea pig in your research!!!

    1. joe says:

      Denise, please watch “Food Matters” on Netflix. Re-establish your flora with an FMT, and then stay on a healthy, fresh vegetable and fresh fruit diet. Unsalted and unroasted nuts and seeds, and raw honey. Stay away from all processed foods, all types of sugars, and meats (almost all meats have antibiotics in them). It’s called feeding your good microbes, and starving the bad ones.

  19. Hello Jeff. Thanks for your post. I agree with Deb – what a great project!
    I hope that you and your trillions of microbe friends all enjoy your journey together.

  20. JMD says:

    I was very excited to read about your experiment, and will be following your progress closely. I have been following a diet for the past ~ 16 years that you may be familiar with; the Specific Carbohydrate Diet (SCD). This diet was developed by Dr. Sidney Valentine Haas, a New York City pediatrician and professor of pediatrics, in the 1920’s to treat Celiac’s disease.

    The SCD was brought to the public’s attention by Elaine Gottschall when she wrote “Food and the Gut Reaction”, and later, “Breaking the Vicious Cycle; Intestinal Health Through Diet”. In her book she recounts her experience taking her young daughter to a then ~90 year old and still practicin, Dr. Haas in a last ditch attempt to avoid surgical removal of her daughter’s colon due to refractory ulcerative colitis. Her daughter followed the SCD strictly and after 2 years was completely symptom free and has remained so throughout adulthood. Since publication of these books many people around the world have used the SCD to treat both Crohn’s disease and UC, with a lot of anecdotal success. The only officially recognized SCD resources, should you be interested in discovering what the SCD entails, are the book “Breaking the Vicious Cycle; Intestinal Health Through Diet”, by Elaine Gottschall, and the website http://www.breakingtheviciouscycle.info .

    We SCDers have organized ourselves into networks that help each other with the implementation of the diet and support each other throughout the healing process. Many of us have been told that “diet has nothing to do with IBD” by our doctors, and have been actively discouraged from following the SCD. This is very galling, since the diet has not been studied, for one thing, is a well-balanced, nutritious diet (IBD patients are often severely undernourished), for another, and lastly, the medical community does not have many good options for treating these diseases and do not know what causes them!

    The hypothetical explanation for the efficacy of the diet is that it selectively starves pathogenic bacteria while feeding beneficial bacteria in the gut as well as maximally nourishing the patient. Research needs to be done in this area to either support or disprove this theory. An intriguing fact: this diet has been noticed by the ASD community and is being used very effectively by parents to treat their children on the autism spectrum, (anecdotally of course). These parents report very positive results: why is it helping these children?

    Lastly, although US physicians are now prohibited by the FDA from using FMT to treat IBD patients, there is nothing stopping them from advising patients to try FMT or from supporting patients’ own DIY FMT sessions at home with how-to instructions and donor screening. I’m told that some of these patients are being advised to follow the SCD during and after FMT treatments. Many success stories are being shared in FMT networks.

    Something is going on here, and it is not a newly discovered phenomenon. THIS DIET NEEDS TO BE STUDIED!!! Please consider adding a trial of strict SCD into your experiment. Thank you for your consideration.

    1. Pat says:

      I’m also following the SCD diet, please include in your study if you can – thanks.

  21. Tom says:

    Another informative and enjoyable article Jeff.

    I have been asking my gastroenterologist for a fecal transplant for years. I suspect a fecal pill will be available soon and his services will probably no longer be necessary.

    A suggestion for another diet would be the Perfect Health Diet which is basically Paleo with safe starches (potatoes, white rice, etc) and milk. I currently follow this diet although I don’t consume milk products (homemade yogurt and kefir) any longer. I moved to Wisconsin, “America’s Dairy Land”, recently and the backwards state doesn’t allow the sale of raw milk.

    Another suggestion would be to follow the Weston A. Price Foundation dietary guidelines.

  22. Hannah says:

    I am so excited to follow this. Will you/have you done any experiments to see if consuming lots of fermented foods actually alters gut flora?

      1. Onur says:

        +1 to a diet rich in a variety of fermented foods

      2. Once and Future Runner says:

        I added daily amounts of sauerkraut after reading the following blog entry: http://blogs.scientificamerican.com/guest-blog/2013/01/29/the-sieve-hypothesis-clever-study-suggests-an-alternate-explanation-for-the-function-of-the-human-stomach/
        It was of particular interest to me as i’m over 70. Unexpectedly after a month of this i swear my night vision got much better. Also no colds since then.

        1. Kris Kramer says:

          Thanks for leaving the link! Fascinating read.

  23. Hannah says:

    “and my levels of Paraprevotella (kissing cousin of Prevotella) went from a poultry 0.40% to a monstrous 7.20%”
    This cracks me up, but I think you want to edit it!

  24. Terry says:

    Wow. Wish I could join you on the hunting & gathering. Thank you.

  25. Saul says:

    You might want to try CRON –calorie restriction with optimal nutrition. Such diets are usually very strong on vegetables. Also of interest (perhaps together with CRON) is reduction in protein — this tens to lower IGF1). It would be interesting if the lower calorie food — which has many positive effects in global health — might also have distinctive effects in the gut microbiome.

    — Saul

  26. Carrie Elsass says:

    Very curious to see your results, as the AGP profile showed me to have a huge amount of proteobacteria, which is not associated with normalcy or good health. I had a hospital infection a little over a decade ago, and I imagine my normal flora was wiped out at that time by strong antibiotics. I hope I can repair the system…

    1. Jeff Leach says:

      whats your diet like?

      1. Brian says:

        Maybe it might be time to explain that high Proteo may not necessarily be a bad thing. We’re looking at best Genus, and sometimes Family designations here (not the fault of research, just current abilities based on cash, time, molecular genetics and sequencing platforms). I’ve worked with and there are many well known instances of species being ‘mis-classified’, subspecies that really don’t exist and MAJOR strain-based differences WITHIN a given species (I’ve got a bug that differs up to 12% within the genomes of just 5 sequenced strains). I haven’t been (very) sick/taken antibiotics in over 5 years and I had/have 30% Proteo as of last month with my AGP output. To note why I don’t think it’s always a bad thing… I am doing my PhD in Microbiology (so it hasn’t caused ‘brain fog’ otherwise I wouldn’t have made the cut) and have managed to row and/or run to medal podiums in on-water races, 6 marathons, 6 half-marathons, and various shorter distances. Also, BMI of 22, BF of 8%, RHR of 38. Try thinking about Escherichia coli Nissle 1917 versus EHEC or EPEC!

        1. Jeff Leach says:

          Great comments. Would be great to have you weigh in more. Please do..

        2. Brian,

          I think you make a good point — phyla classification can only tell us so much when even strains can differ greatly (like your example of E. coli Nissle 1917).

          But to provide a counterpoint: we can still tell a lot from correlations. Every study I’ve ever seen that attempts to tease out the connection between microbiota and disease by looking at phyla-level fluctuations has Proteobacteria ALWAYS positively correlated to worse disease profiles. In other words, if you see Proteobacteria rise, it never seems to mean good things. And vice versa. I would love to see a study that showed something different, but I have yet to see it.

          1. Brian says:

            Point taken Sir. Just saying, I work with multiple gastro-instestinal tract species every day, help to set up clinical trials and do genetics/genomics work, so I see 1) how ‘pathogen’ is frequently niche-specific, whether that niche is physical in the host or potentially the host’s specific immunological state 2) that clinical study enrollment/design can have many flaws (not enough people to do power analyses or simply taking white females…ect.). Frequently when people see high Proteo in studies I believe it’s a almost complete replacement of everything else, very transient also; yet as for myself, I still have 40% Bacteroides and 20% Firmi. The great part about this work at AGP is that it will give a large swath of data to look through. But when people quote books or blogs by people who are non-scientists or do not do their own research it does scare me a bit. A potential purpose of this study seems to ‘debunk’ (neither good nor bad way) what the ‘normal’ flora has been found to be so far by adding in many more samples (as well as potentially confounding variables). I think the study is a great project, but the idea that ‘1 diet does this’ or ‘1 species does that’ is going to vary so greatly across a population. General correlations will probably hold true and be good, but look at any one given person and there will probably be high variance. Just think of why we need to have so many replicates in animal experiments; it’s not because we love working with massive colonies of mice!

          2. Jeff Leach says:

            couldn’t agree more. the AGP is yielding some interesting correlations. but we will see how this looks at 20,000 participants. we will be out putting some additional study-wide results in the nxt month or so. as for my DIY, almost everyone working with the gut microbiome has sequenced their own poo – i’m just taking a bit further. as for debunk, not my goal. just curious for my own reasons…and yes, sample size of 1 is limiting, as i indicate. preaching to the choir on that one…

        3. Jeff Leach says:

          would be interesting to know what strains u have in your proteo. hard to know if its a good or bad thing unless u know who’s in there. big diff between a cat (kitty) on your kitchen counter or a CAT (as in big cat).

          1. Brian says:

            Jeff, good points and need to reiterate that I love the study! ‘Debunk’ was a bad usage of the word, and I didn’t quite mean that. You’re building on very solid previous work done by labs such as Relman, Gordon, Turnbaugh, Fishbach, Goodman, and Gilbert (mainly gut but obviously others have done oral, nasopharengeal and skin). But previous sample sizes, restrictions to studying specific diseases/populations and such have probably hampered microbiome research in general.

          2. Jeff, I think we all probably agree more than we disagree. But I wanted to make one more point: the value of looking at correlations is in phlyum-level fluctuation, not species composition. In other words, if you have done something to make your microbiome more hospitable to Proteobacteria, I do believe that’s relevant — isn’t alkaliphilia a phylum-wide characteristic of Proteobacteria, regardless of species? In other words, ok, we can hope that it’s all E. coli Nissle 1917 in there, but even if it is, have we not swung the door wide open to any and all Proteo? Has that kind of fluctuation ever shown to be a good thing? And that’s why correlations are so uniformly negative in this regard and probably shouldn’t be so easily ignored.

          3. Jeff Leach says:

            note sure, we will see. note also im measuring biomarkers of inflammation in my stool as well – and blood samples. for serum, i’m mainly interested in LPS levels.

          4. Oh, that’s fantastic. Would love to see. SCFAs too, by any chance?

          5. Jeff Leach says:

            Yes indeed. Also measuring a number of other things as well

        4. joe says:

          It has been observed that athletes tend to have more diverse microbiomes. Is this a role ?

    1. Isabel says:

      I second that!

    2. Maureen, this experiment WAS a low FODMAP diet. Very low carb, no plant fiber. These are the results of a low FODMAP diet. No surprise: it’s a diet designed to stimulate little to no fermentation in the gut.

      The only exception might be lactose — I don’t know if Jeff consumed milk or not. But lactose is optional on a low FODMAP diet anyway.

  27. roger says:

    Atkin’s is SCD lite.Take a shot at Specific Carbohydrate Diet.

    1. Amy says:

      Yes, and / or GAPS…you might really need to go on GAPS for a while after all of this experimenting!

  28. Mary says:

    I hope you take samples of the water you are drinking and bathing in as well – and record anything you put in your mouth, even toothpaste, herbs, NSAIDS, etc. or on your skin.
    I am curious if all the flora in the gut microbiome have been identified and what your global experiment will find.
    Since in the past scientists have reached for conclusions too hurriedly it would be good to avoid that tendency. Haste makes waste.
    I wonder if Ayurveda or TCM or even diets like the Blood Type diet (which I have felt doubtful about but which people report success with) might be meaningful to consider as dimensions for your analysis – if you are consuming foods that are basically not agreeable to your constitutional type it probably can’t be that good for your gut.
    Best wishes! – this will be very interesting to follow.

  29. Try GAPS and Weston A Price diets, if you can add them, please!

  30. Sarah says:

    Weston price please. 🙂 Lots of people think he was a quack.

    1. rick says:

      I can’t imagine how any intelligent person could read his work and think he was a quack.

  31. Lissa says:

    Curious – did you note any changes in body composition to accompany the microbiome changes you experienced in Texas?

    1. Jeff Leach says:

      Not really, but did drop a few pounds. But was also a tad more active, so can attribute to one thing over another…

  32. Christina says:

    I can’t wait to hear which diet leaves you with the best, most diverse mix of gut microbes. Be sure to keep us all informed along the way so we can improve our guts, too. Thanks for being the guinea pig Jeff. You rock.

  33. Mel says:

    How about the Specific Carbohydrate Diet, I use it to control my Crohns medication free. (Basically gluten (all grains really) lactose, starch, sugar free) I have experimented with my gut for the past 6 years trying to find the right food balance to stay med free. I would say I am working in the blind since I don’t get to sample, rather I pay close attention to what my body tells me about the food I eat. Processed food is the devil for me. I have also travelled a lot and noted the differences in food quality are huge. (Example 10 weeks in Romania on all local cuisine had me feeling great and eating most anything, meat heavy but a lot of veggies I do not normally eat, but I have added to my diet now) Back in a tropical climate (HI) now is a bit more difficult, of course each climate has also seen marked lifestyle changes … activity and exercise matter a lot.
    Just some of my own observations in the fight to make my gut bugs happy.
    Can’t wait to see the results of your journey.

  34. msapiens says:

    I want to know how you feel after the desert diet, compared to how you felt on the New Orleans diet; please include how the various diets make you feel.

  35. Alan says:

    Could you try a low-carb-high-fat (LCHF) diet? LCHF includes an adequate protein (say ~20% of total calories) intake. This could include many vegetables with fiber slathered in butter, olive oil, or ghee.

    see: dietdoctor.com

  36. kathy says:

    Second vote for WAPF diet — basically paleo with a priority on grass-fed saturated fats, some raw, with soaked/sprouted seeds/nuts/grains and fermented vegetables.

    I’d also love to see the results of an exclusively full fat, cultured, raw, grass-fed dairy diet. Thanks for sharing this info!

  37. Walter says:

    Awesome experiment. Any chance you be taking blood samples for glucose levels, cholesterol inflammation indicators, etc. Also will you be testing insulin sensitivity and possible changes to sleep habits?

  38. Brian Kerley says:

    I don’t get the Boehner reference. Have you seen his son-in-law?

  39. RuthAnn Buchweitz says:

    I recommend SCD (the Specific Carbohydrate Diet); it took me from being really sick to good health.

  40. gothamette says:

    There’s something I’m not quite clear on.

    You kept fat/protein calories stable, but lowered carb calories – so, overall, you were eating less calories, right?

  41. Alyssa Lawton says:

    I’m gonna second JMD’s suggestion and say you should try SCD! I’ve been on it for 5 months to treat Crohn’s disease and I have seen better progress in the last 5 months than the last 3 years on prescription drugs.

  42. Joanna says:

    Fascinating stuff. I’d love to see you try the GAPS Intro diet. It’s specifically designed to heal “leaky gut” and rebalance the gut flora. Would be interesting to see its impact. It’s based on this book by Dr. Natasha Campbell-McBride: http://amzn.com/0954852028

  43. Karlie Cole says:

    Well, you could do the Super Size Me diet….but seriously – love to see this a Super Size Me style documentary…which means filming starts now!

  44. Bridget says:

    Have you heard of Plexus? I have been told by more than a few people that taking it while not changing any other aspect of one’s diet can alter your gut chemistry enough to resolve insulin resistance, chronic yeast problems, resolves all sorts of GI issues, etc. It is also supposed to improve weight loss. I haven’t started taking it but am contemplating. I have PCOS (Poly-cystic Ovarian Syndrome) and am trying to get it under control, along with all the issues that come up because of it.

  45. Karlie Cole says:

    My son is on the autism spectrum and has the homozygous MTHFR genetic mutation for A1298C affecting methylfolate/folate metabolism. It would be quite intriguing to look at interactions between folate metabolism and gut bacteria especially since the study mentioned comparing autistic symptoms with Prevotella levels and diet found diet to be largely unrelated. In other words, what about folate metabolism interacts with the gut microbiome?

  46. Rina says:

    if you don’t study water don’ t get exact result.

  47. Gus says:

    I read your higher grain consumption as higher gluten and MYCOTOXIN consumption(grains are usually contaminated with toxic mycotoxins from molds) that would’ve caused you gut inflammation resulting in higher undesirable provatella and lower desirable bifidobacteria bugs. Please don’t forget to think about toxic mold mycotoxins that are usually present in all grains and particularly corn. Also, over 90% of coffee is contaminated with mycotoxins as typically are blackened or fermented fruits and veggies. I think that much of the Hadza food is likely contaminated with mycotoxins. Yikes!

  48. Angela says:

    Jeff, really looking forward to your research. I would put in another vote for the WAPF dietary guidelines. I would especially be interested in seeing the different between refined grains vs. whole grains vs. fermented/sprouted whole grains. Traditional societies almost always fermented or sprouted grains so it would be helpful to see the different that makes in the gut microbiome. Many people might not be able to tolerate grains now because of the way that they are processed instead of grains being inherently problematic (as argued by Paleo/Primal folks). http://www.westonaprice.org/basics/dietary-guidelines

    1. Anne says:

      My daughter follows WAPF diet and all her children have become sensitive to grains, even though she is using ancient grains, Spelt, Kamut etc. and soaking them or sprouting them. The youngest (2yrs.) was covered in hives for 3 weeks. He slowly got better after she quit feeding him grains. Also he can’t drink even raw cow’s milk. It may have something to do with poor microbiome development which is seen in the young current generation. Sally Fallon says that people can eat properly prepared grains if a person has healthy gut flora, but something is happening too the gut flora of Western children born today.

      1. joe says:

        Anne, if you read Dr. Martin Blaser’s book, “Missing Microbes”, you’ll find the explanation you are looking for.

  49. steve says:

    is there a way to calculate our “species equivalent OTU’s” from our American gut sample to track diversity? thanks!

    1. Jeff Leach says:

      we will likely be providing that at a project wide in the near future.

  50. This is such a great contribution to society. If I had enough money, I would live to come with you!

  51. Rosa Jo says:

    I’ll suggest Kitavan diet if it hasn’t been already.

    1. Jeff Leach says:

      Nice one! That would be interesting.

    2. La Frite says:

      This diet should include the daily smoking of cigarettes, I guess …

  52. Onur says:

    Also please try a generalised paleo autoimmune protocol which excludes grains, legumes, dairy maybe except ghee, nightshades and egg whites and puts limits on omega6/omega3[or maybe better, linoleic acid/(Total Omega 3 – alpha-linolenic acid)] ratio and total fructose consumption(better including the half of sucrose, which is also fructose).
    This may be out on a limb but maybe gamma-linolenic acid may also change microbiota as omega 3 intake is suggested to effect the microbiota, so you may try capsulated(because it goes rancid quickly) evening primrose oil, or freshly ground hemp seeds for GLA.

    1. Onur says:

      A generalised paleo autoimmune protocol also emphasizes consuming lots of bone broth, vegetables, seafood(especially high EPA and DHA ones) and organ meats. Actually Sarah Ballantyne suggests consuming over 9 cups of vegetables a day but I don’t think it’s much practicable, except maybe with juicing most.

  53. Lydia Hunter says:

    If you could do a progression from the gluten/casein free. then to SCD, then to GAPS. We are usually told to try these diets with our autistic children; very curious when you do them back to back how things change. You are super awesome for doing this–very much appreciated!

    1. Jeff Leach says:

      can’t do the cigs – yuck. but will be smokin me some weed.

  54. La Frite says:

    Hello Jeff,

    Very interesting!
    Your invitation to recommend or suggest some crazy diet made me think about this dude who calls himself Durianrider, and his girlfriend Freelee. They adovcate one should eat at least 30 bananas a day … You may have heard of them. I don’t recommend you do it as well but anyway, I thought it should be mentioned 🙂

  55. Caitlin says:

    It will be interesting to see your bowel habits change to help those with IBS-C.

  56. Kris Kramer says:

    I’m wondering what does this all mean? Is it healthier to have more Firmicutes than Bacteroidetes or visa-versa? I’m guessing it’s just diversity we’re looking for. Any clues what all these different microbes “do” for the body? Would love to see an article discussing the health aspect of these findings. Apologies if there is one and I missed it. Or more likely, no one knows for certain.

    1. Jeff Leach says:

      the firm:bacter ratio in healthy people swings both directions, so who knows.

  57. Brooke says:

    It’ll be interesting to see how you define paleo when you get to that phase of the testing. Will it be higher carb full of starchy veggies and tubers or more similar to your low carb, high fat and protein diet? Will it have bone broths and ferments?

    Also, have you consider experimenting with resistant starch supplementation?

    Can’t wait to hear more!!

  58. Natalia says:

    Good luck on your undertaking; looking forward to the results!!! Just a thought re: “Strikingly, elevated levels of Prevotella have been noted among HIV-infected individuals who exhibit chronic gut inflammation. In this study, the researchers suggest that Prevotella may thrive under conditions of inflammation. In another study, researchers found that Prevotella strongly correlated with new-onset untreated rheumatoid arthritis. On the flipside, reduced rather increased levels of Prevotella correlated with kids diagnosed with autism compared to symptom-free neurotypical children in a recent study. However, it’s interesting to note that many families will place ASD kids on a gluten and casein free diet following diagnosis. Therefore, if my “out on a limb” theory that Prevotella levels are associated with whole grain consumption is near the mark, then lower levels of Prevotella in these diagnosed youngsters is not completely unexpected. In other words, in diagnosed ASD kids the lower to no levels of Prevotella may have more to do with diet than the disease state.” Here is my “out on a limb” theory: what if higher levels of Prevotella are similar to a fever – i.e. they are a body’s effort to bring the pathogen/inflammation down? If this is the case, then lower levels of Prevotella in kids with autism maybe a sign that their body/immune system fails to react in an appropriate way to all the inflammation. I think this is a more plausible explanation, as gluten-free diet does not equal no grain diet, and the majority of kids with autism are never placed on any type of diet at all (just drawing on what I see in our schools; usually my son is the only one or one of two kids in a class on a gfcf diet), most people know nothing about diets unfortunately. In addition, disrupted immune response such as lack of fevers is a very frequent occurrence in kids on the spectrum. I’m curious what you think.
    Good luck on your journey(s) and please post frequent updates!!!

  59. julialoha says:

    This is a wonderful thing you are doing. Have you considered checking and reporting on lab results such as A1C and lipid profile? Might have to stay on each diet longer to be fair. The other thing I would be interested in is what you actually ate – like a menu diary. You said you ate dry cereal every day – do you think that eating sprouted bread or sour dough bread instead would have made any difference? As in, is it the gluten or the wheat protein that is bothering so many of us? Or the unaltered phytic acid? What amount of plant intake, what kind of plants and how were they prepared. Was your animal protein often beef or more often fish? What if you just ate raw fish ( so the protein and enzymes wouldn’t be altered) such as pickled herring? And what is your blood type? I will be watching for your next episode. Thank you so much. All the best. Can’t wait for your book.

  60. Shodo Spring says:

    You really should try the Weston Price diet. Book is Nourishing Traditions, has facts and recipes, and I’d love to hear the results. (Also – wondering how you FEEL with those various statistics.)

  61. JT says:

    Jeff, thank you so much for your research, this could be the single most important medical discovery of the century. Some thoughts and questions:
    1. Try a raw meat, or all meat diet ala the Inuits.
    2. Try the diets or live in the regions with the most centenarians: Okinawa, Sardinia, and in America: the 7th day Adventists.
    3. Try adding large amounts of capsuled probiotics like bifido or acidophilous, and see if they actually change the gut bacteria vs. what fermented foods do.

    I have a question regarding gut bacteria and kidney stones. There is some research showing certain bacteria ( Oxalobacter formigenes and Lactobacillus and Bifidobacterium) produce enzymes that help digest oxalates and prevent them from entering the blood and then the kidneys. It begs the question if some people are missing the right bacteria, and this is a main contributor to re-occuring kidney stones. Any info or work on that would be helpful to many of us with that very painful disease. Thanks again, and bon voyage!

    1. Jeff Leach says:

      yikes. not sure i can do the raw meat.

      1. elissa says:

        Jeff, I’m with JT on this one…try the Primal Diet a la Aajonus Vonderplanitz – raw everything, including meat, eggs & dairy. I’ve been doing it myself for nearly a year with awesome results – even my eyesight has improved. If you consult his books you’ll discover his premise that ALL micro-organisms are “good” for us, which is what would make the Primal Diet such a fascinating addition to your poo studies. He taught that bacteria are our bodies ‘janitors’ & went so far as to eat rotted, or “high” meat in order to replenish his bacterial load (this is also described in Weston Price’s observation of the Inuit culture). Aajonus was a controversial dude, but brilliant in his own way. Let me know if you have questions. Have so much fun on your adventure!!

        1. Jeff Leach says:

          will do friendos. thanks for chiming in 🙂

          1. elissa says:

            Absolutely Jeff!

            Kris, no sushi on the primal diet because…
            – aajonus advises against dehydrated “raw” (Nori seaweed)
            – very limited complex carbs (no rice)
            – no soy
            – no salt
            – “sushi grade” fish has been frozen

            Sashimi is good as long as the fish is fresh/wild, never frozen.

            This would such a great addition to your experiment. Aajonus taught that the germ theory of disease is incorrect. He believed that ALL bacteria, fungi, viruses, & parasites serve a purpose in the body: to consume diseased/damaged body tissue. Vomiting/diarrhea are the result of the microorganisms performing their job/detoxification. There is a system to it, you may need guidance – I’m going to suggest my friend Noah Hittner join the conversation – he just wrote an article on Primal Dieting for pt on the net.

            Aajonus was unconventional, but his ideas can be liberating – lose the fear of your natural environment, live symbiotically with ALL microorganisms, not just “good bacteria”, because that is truly what our ancestors did. They did not sterilize, pasteurize & overuse antibiotics & then selectively reintroduce a handful of happy ones. IMO that is the newest form of dietary ‘fortification’.

            Jeff, I think you’ll be fascinated by his ideas, even if you don’t agree. Again, best of luck to ya 😉

      2. Eve says:

        Raw meat, fish, seafood, and raw everything else paleo has been the basis of my raw paleo diet for three years. It deserves its place as the authentic hunter-gatherer diet of the early paleolithic – before mastery of fire, before milk from domesticated animals, and before the use of cooking vessels. Humankind did most of its evolving on this type of diet.

      3. T says:

        I think number 3 would be interesting. Fermented foods vs capsuled probiotics/yogurt.

  62. Christina Memoli says:

    I would like to see the diet principles of Ray Peat PhD followed. It is a low fiber/low polyunsaturated fat diet meant to lower endotoxins and estrogens, and increase thyroid and metabolism. Milk, cheese, beef and lamb, orange juice, cherries, grapes, melons, refined sugar, shellfish, liver.

  63. You need to include the WAPF traditional eating diet as well!!!

  64. kvsnyder says:

    A very grateful thank you for your pursuit of these projects – both your one-year challenge and the AGP. Getting my initial results from AGP led to interesting conversation with my Dr, who mainly works with ASD kids.
    Although not very ‘scientific’, please feel free to expound on your ‘out on a limb’ thoughts. They provide great food for thought. Also, you should talk a bit about what you experience physically, mentally, emotionally with the changes in diet. Sure it is only anecdotal, but that is the underpinning for where most of good research starts.
    Keep up the great work !

    1. msapiens says:

      “talk a bit about what you experience physically, mentally, emotionally with the changes in diet.”
      Here’s an idea for making that easy & quick:
      before switching to a new diet, answer the question: How old do I feel when I wake up in the morning?

  65. AG says:

    Will you be obtaining fecal samples from someof the Hadzabe at the same time as yours? I think this might be very educational.

    1. Jeff Leach says:

      yes, we started sampling various camps back in the summer and will continue doing so for 2 years – seasonal changes in resources are particularly interesting to us.

      1. AG says:

        Can we get an advance sneak peak at the Hadzabe’s gut biome so we can compare it to Tatertot’s?

        1. Jeff Leach says:

          that data will be out mid/to late this year. sorry.

  66. Allan Folz says:

    Sounds exciting, Jeff. By chance have you seen my little N=4 experiment? I was inspired by Richard Nikoley & Tim Steele.

    We haven’t started yet — still waiting on the kits to arrive (hint, hint 😉 ) — but are really looking forward to it. Cheers.

    1. Jeff Leach says:

      Ah very cool. let me know how this progresses!

  67. Beatrice Latherings says:

    Fascinating. I sure hope there is a book *with*data* coming out after this.

  68. Matt says:

    Hi Jeff,
    Your chart has made me very curious. I’m a lifelong consumer of vegetables and fruits, and, in the past 3-4 years, my diet has evolved from Paleo to PHD/ancestral.
    In addition, I’m healthy and consume some fermented foods, but my gut bacteriome test result shows no traces of Bifidobacterium!
    So, can you speculate how one consume plant fibres and resistant starch, but have no Actinobacteria?

  69. The comment thread contains some interesting suggestions for diets, but most are not connected to “how and where you live.” Here’s one that is: Try living on and eating from a diversified farm, one that relies on compost from pastured animals to provide farm fertility & grow produce. Take part in collecting eggs, milking pasture-fed dairy animals, building/turning compost piles, working with veggies, fermenting foods (veggies, dairy, grains, etc.), and/or butchering meat, among other things.

    It so happens that my husband & I could offer such an experience in the name of exploratory science. (Though we can’t promise milk in 2014; not yet sure about the pregnancy status of the goats.) The small professional farm that we run is dedicated to producing delicious food in an ecologically diverse setting. Seasonality is a big deal here, thus adding interest and complexity. Let us know if remotely interested. This could be a good quiet place to do some writing, too, as we can offer a private room & bath.

    1. CM says:

      Please contact me regarding experiencing your lifestyle. I am a student and private researcher into synbiotics/microbiome diversity through dietary intervention. I would love to visit and include my experience in my research.
      email me here: cmhenneyml@gmail.com

  70. Brandy says:

    I find your quest so interesting! I have been on a lot of diets in the past couple of years trying to see if I could cure my ailing gut. I tried gluten-casein free, sugar free, Candida diet, GAPS diet, 80-10-10 raw vegan, low oxalate and maybe one or two others. None of them helped long term. Then I read Donna Pessins, Unique Healing. I found her theory of gut bacterial health fascinating and decided to try it out. 2 1/2 months into her program and I am eating things I thought I would never eat again (wheat in the form or sourdough, oats, beans, tons of fruit, honey – it’s been a bit of heaven). Anyhow, hopefully the results last and I continue to heal in the coming months. Her program is supposed to take a year or so but I would highly recommend her book before you being your diet journey. It was quite the “food for thought” about gut health.

    So I guess I would recommend her book and adding bentonite clay into your regimen for experiment. Clay has a rich history in the diet of indigenous people and is said to help balance the gut bacteria as well as rid the body of toxins.

    Can’t wait to follow your discoveries!

  71. Heather says:

    Fascinating study and look forward to the results. I’m curious about how you arrived at the order in which these experiments are to be done and the timeframe which each is to be given. There’s one variable that I was wondering if you were considering: nutrient lockout. I know from my former days as a hyrdophonic gardener that unless you start things at the proper ph, a deficiency of just one nutrient can grow into a systemic catastrophe with lockout. I’m wondering if you’ve considered how your data might be skewed by this?

    1. Jeff Leach says:

      No particular order other than I will return to my typical diet before starting a new one. So what is proper pH? It changes dramatically from one end of the GI tract to the other. Of interest is the colon – which changes proximal to distal, which is all impacted by substrates entering the colon. Not the pH of a food or drink has no impact on colonic pH –

    2. Kris Kramer says:

      Interesting comment regarding pH. I’ve been messing with my pH a bit lately–trying HCL supplements in hopes of getting off Digestive Enzymes by getting my body to start producing enough acid to then produce enzymes to finally digest properly. Also, alkaline diets are all over the place. Lots of debate there.

  72. georgia bronte says:

    Hi Jeff, I work for Vice magazine and I’d really like to get in touch with you for a short interview for a piece I hope to write about your work. If you’re in Tanzania with the Hadza this will obviously be impossible, but if you’re still in Western society I’d love it if you could get back to me on georgia.bronte@vice.com

  73. MJ says:

    Very interesting article, thanks. Have you ever heard of the Primal Diet (Aajonus Vonderplanitz)? It’s a raw diet that really opened my eyes to the importance of using friendly microbes for gut health. Mainly, the diet stresses the importance of raw foods (including raw dairy), but it’s different than most other diets in the aspect that it also promotes the healthful aspects of raw meats. The author spent a considerable amount of time with Native American Communities, and even dared eating a fermented meat dish prepared by the Inuit Community (something I wouldn’t do, but he survived, and is convinced his gut flora is stronger because of it, among many other things he’s done). I would be interested in seeing if this diet could be compared to the other diets you are considering. Personally, although I was hesitant in trying this diet, it’s been the best choice of my life so far. Food for thought…if you have time to reply, I’d appreciate your input on this. Best wishes for your research!

  74. tyler says:

    Jeff this is so exciting! You are the Neil Armstrong of Gut Exploration! This is one small poop for man, one giant plop for mankind!

    I don’t know if this one has been mentioned already but I would like to see effects of the Japanese Village Diet. Something that mimics the Okinawan diet. There is a high percentage of centenarians in Okinawa, They are one of the longest living people in the world. Their diet consists of lots of seafood, sea vegetables, sweet potato, white rice, bitter melon, some unpasteurized traditionally fermented soy products like natto, miso, and soy sauce, etc. and the odd pig from snout to tail and everything in between.

    I like the Hadza trip because you are matching the diet with environment and lifestyle. The other diets you will attempt sound interesting but it sounds like you would get much more useful information by travelling to various regions, living and interacting with the people and matching diet with their traditional dishes. You could do this in various regions around the world like India, China, Peru, etc.

    For comparison, it would be interesting to live with the Hadza for a period but eat a standard American diet. This way you might be able to distinguish between lifestyle/environmental and dietary factors.

    What about testing the effect of behaviors on gut flora? The effects of “hyper-hygiene” like constantly hand sanitizing, bleaching and wearing face masks vs “low-hygiene” not using soap, rarely showering, touching lots of icky things, etc.

    Enjoy the amazing adventure!

    1. Jeff Leach says:

      would be great to travel to various areas and try their diets in context, but crazy expensive. but to your point, i think the environment is a key piece – something we hope to show with the Hadza… as for the current 2014 strategy of whacking my gut microbiome around, we stick mostly to shofts associated with diets i can follow at home so to speak…. thx for the kind words… and the “plop for mankind” quote…

  75. clairehirsch@mac.com says:

    I’d be very interested to know what the effect of dramatically reducing oxalates is, especially on a Paleo diet.

    1. Onur says:

      Why ? Oxalate-degrading bacterias may decline without an easy reversal. Who may want to try that ?

      1. Jeff Leach says:

        there are hundreds of variables and things to test – can’t do it all – and i’m “mostly’ focused on significant macronutrient shifts 🙂

        1. Agatha says:

          This is ery exciting – can’t wait to see your results.

  76. Eric Tran says:

    Hi Jeff,

    I just read the transcript for your interview with Chris Kresser. You mentioned that you would eat leeks, onions, and garlic if you were stranded on an island. You talked about the benefits of garlic on the gut. What is it about leeks and onions that is helpful to the gut? Are there any other foods you would recommend as helpful prebiotics? I know that you said lentils were good too which is great because I enjoy eating them!

    The reason I am asking is because I am looking to repair my gut because I was on a 1-month stint of Accutane in high school and get a yeast infection after 2 weeks. It went away after I stopped but I suspect that the constant malaise and low-energy that I have been experiencing in the past few years can be attributed to that anti-biotic stint. So any suggestions would be appreciated!

  77. Dan says:

    What an amazing premise!

  78. AGH says:

    Hi Jeff! Just wanted to put in a comment and say thank you for all the great work you do. Having a great time following your self experimentation and really enjoy the links you put up on facebook to recent articles on the microbiome. Did you see this recent post: http://bretcontreras.com/genetics-of-the-21st-century-microbes-affect-disease-susceptibility-body-weight-and-ability-to-build-muscle/

    Interesting article that seems to focus more on the genetic material than the microbes itself.

    Keep up the great work!

    1. Jeff Leach says:

      There is a god after all – however, the distilled booze is something entirely different.

  79. Heather B. says:

    I find myself more and more wondering about the impact of required sanitizers in commercial kitchens and the residue that’s left on the pots, pans, dishes, etc. I own a natural foods store and so many of my customer have had or have developed gut problems over the past five years it seems it must be more than just diet and lifestyle. Really looking forward to following your results this year…

  80. This is such an amazing project! I’ve been doing all sorts of biohacks recently to alter my microbiome, resistant starch, soil based organism probitoics, inulin, and importantly fermented foods like Sauerkraut, Kimchi, etc. I only wish I had had the chance to do this test already so I had a before and after!

  81. Wendy says:

    How about an Ayurvedic cleanse? It involves eating nothing but a cooked mixture of rice and dahl and Indian spices. Lots of those spices (like turmeric) are purported to aid beneficial microbes.

  82. Ian S says:

    Hi Jeff:

    +1 on the high meat suggestion. There are many references to it in older literature. And stories of superhuman endurance feats performed after consuming high meat. Lots of online links about making your own. I’d love to know what’s behind it.

  83. James Livengood says:


    You’re the man!

    I’m about to do a fecal transplant this weekend. I have Reactive Arthritis (similar to Ankylosing Spondylitis).

    I don’t consume any prebiotics (no starch or FODMAPs) because I can’t tolerate them and they make my symptoms work

    but I eat a lot of fiber – collard greens, kale, radishes, melons

    Do you think I should starve my gut biome before the fecal transplant?
    Or would that be bad because it would make my gut more alkaline and then less receptive of the good bacteria from the transplant?

    Thank you I love you,

    1. BSL says:

      James, how did the fecal transplant go? Very curious as I have a similar condition that I treat in a similar manner (SCD).

      1. cavemanzen says:

        I’m not sure to be honest. I’m able to consume Resistant Starch now (in the form of raw green plantains) but I’m not sure if I would have been able to before the FMT, I never tried it. I definitely still have problems – can’t eat digestible starch or FODMAPs without joint / skin / anxiety issues. It may have helped somewhat. Sorry for the unclear answer 🙁

    2. joe says:

      I hope you didn’t use the blender method.

  84. Brad says:

    Jeff. Hope your heroic 2014 is coming along nicely. Remind me how we can all follow along with the results as they come in. Eager to keep pointing our readers in the right direction. For now, you’re “Best of” in our book:


    Eagerly following along…

    1. Jeff Leach says:

      Thx for the kind words. In Africa now – churning along.

      1. Cindy C says:

        Hi Jeff,

        Any thoughts on this study? It seems to say the more variety in diet, the less diversity in microbes, at least in fish. Thanks.


        1. Jeff Leach says:

          hadn’t read yet – will check it out..

  85. Patrick says:

    Jeff, wonderful work. I recently read an article on the theme of “eat to boost good bacterial, and avoid foods that promote bad bacteria” where Dr. Oz cites research from Australia’s Monash University regarding rapidly fermentable sugars (RFS). Oz draws the conclusion from the research that you should avoid: Garlic, onion, leeks, cabbage, cauliflower, mushrooms, asparagus, broccoli, and more. I found what appears to be the source he is referencing and link to it here. I find it contrary to positive things I have seen on your site re: garlic, onion, unless I misread or didn’t get the whole picture. Any thoughts? For quicker viewing you can scroll to bottom it lists the FODMAPs check list http://www.todaysdietitian.com/newarchives/072710p30.shtml

    Note it is focused on IBS, but I do not have that and am focused on your general insight into it, would you think, if out on a limb, that the same “cautions” be warranted for health guts (non IBS?)

    If nothing else, perhaps its a good food list style diet to experiment with in your year of experimentation to see what happens.

    1. joe says:

      Patrick, for some people with IBS avoiding certain foods, as you mention seems to help. See FODMAP diet. For others with IBS it doesn’t seem to help. IBS is complicated, as some people have certain microbes that are missing and others have different microbes that are missing.

      However, if you don’t have GI issues and are in good health, then eating the vegetables you mention are excellent choices.

  86. Jennifer says:

    I would be very interested to know how Splenda impacts the gut microbe.

  87. tim says:

    i am curious if you observed the hadza using any form of dental hygiene. frayed ends of sticks rubbing teeth. charcoal, ashes, rubbing on teeth? i know it does directly connect to gut micro biota but if they don’t at all i wonder if there is a connection to dental carries and what percentage was there.

    1. Jeff Leach says:

      picking teeth with sticks – that’s about it — so far.

      1. Alexandre Vlassov says:

        Love your experiment Jeff! Please let me know if you’d like some help with the reagents/kits- I can send you eg some next gen kits that we developed for isolation of DNA from stool. Good luck! Sasha. email: sasha.vlassov@thermofisher.com

      2. Fisheries PhD says:

        Do they use something like a miswak? Many cultures use things from the neem tree for instance. The actual item used to “floss” may have beneficial properties.

  88. April says:

    Do you have any idea the impact of the microbiome on a person with celiac disease?

    1. Jeff Leach says:

      we appear to have an increasing number of celiacs in our american gut project – so we should have something to say – or not – in the coming months or years.

  89. Jean says:

    This is fantastic! I can’t wait to see the results. Could you consider the McDougall Program it is a modified Vegan – low fat. https://www.drmcdougall.com People with MS and other autoimmune diseases have had some great results on this diet. My guess is that changes to the gut are helping. It’d be great to understand what the diet does to the gut bacteria.

  90. Plant Based Ryan says:

    I’d like to see how food sanitation affects your results. I use a combination of hydrogen peroxide and vinegar to wash my vegetables before consuming them (https://www.sciencenews.org/blog/science-public/wash-your-veggies).

    1. joe says:

      There are actually good, helpful microbes on fresh fruits and vegetables, the ones we want…………

  91. Brooke says:

    Any chance we will get a mid-year update?

      1. cavemanzen says:

        Could you also shed some light on their plant consumption, specifically where they get their carbohydrate from?

      2. cavemanzen says:

        Could you also shed some light on their plant consumption, specifically where they get their carbohydrate from?

  92. Onur says:

    Hi Jeff, it’s me that recommended trying Prescript Assist and I’m very selective but this page concerned me a little, so I thought I should share this with you too:
    I’m not sure if those hso’s don’t have existent interaction as I also saw a paper about the bacterias in prescipt assist being present on common foods but opportunistic HSO’s part and especially pseudomonas fluorescens seemed somewhat annoying.
    I also wonder what you or others visiting here may think about this as I’m not much knowledgable about it.

    Best wishes

  93. Diets to try: Ketogenic Diet. Just completed reading the Wahls Protocol. She describes three diets, the first two would be similar to Low Glycemic/high vegetable, and Paleo/high vegetable. The last one is a ketogenic high vegetable, mostly coconut oil for fat diet.

  94. Karin Pine says:

    I love your project!! Thank you! My boyfriend and I have recently dropped as much of ALL starch out of our diet as possible, based on recent research by Dr. Ebringer that suggests a strong relationship between Ankylosing Spondylitis and Klebsiella pneumoniae. Apparently quite a few AS sufferers are halting the progression of their condition by eating this way. It has been fascinating to observe the changes weve been going through. Good luck! We will be following your blog with tremendous interest.

    1. cavemanzen says:

      Karin, do you have AS? I have Reactive Arthritis, the “first cousin” of AS and I’ve been troubleshooting with different diets for about 18 months now (completely in remission after 5 months of being in a wheelchair) and would be interested to talk to you.

      1. Karin Pine says:

        Cavemanzen, my boyfriend is the one with AS. I am a bodyworker/alternative healing practitioner. I’ve been keeping him mobile for 10 years…. barely. The AS diagnosis and the Ebringer research shed a LOT of light on what has gone on with his body… and I’m feeling like we finally have a chance of reversing this thing! Please feel free to message me privately at FB or planetshpr@aol.com. I would be very interested to hear how you got your arthritis to go into remission and to share info with you that we’ve learned.

  95. cavemanzen says:

    Could you shed some light on their vegetable consumption, specifically where they get their carbohydrate from?

  96. tracey says:

    impressed by all your research…keep us all posted…;)

  97. Nan Achziger says:

    You mention that your Prevotella was up in the desert and that it could do with grain intake. I also saw that someone mentioned trying a gluten free diet. You had stated that would be covered in the Paleo diet. Have you tried a diet that is strictly gluten free however pseudo grains such as quinoa, amaranth and teff are consumed and if so did that have the same effect as gluten grains?

    1. Jeff Leach says:

      not yet – good thoughts.

  98. jjoensuu says:

    Something that I think would probably be useful is to check the gut bacteria of centenarians (and especially maybe the supercentenarians).

    Perhaps they have some bacteria that allows their system to form some components (e.g. more energy rich, or otherwise different from what happens with the general population) from the food they eat?

  99. Mischelle says:

    My 20 year old daughter and I started on The Microbiome Diet because my daughter has always had bloating, a finicky stomach, etc. This is a gut bug diet. While I know research is still out on what you need to have in your system for optimal health, after reading the book, I could not see how it could hurt. The first three weeks of the diet focus on removing possible problem foods, such as cow’s milk products, grains, starches, and chemicals. Smoothies make up my morning meal, although you could make fruit salads, fruit and nuts (no peanuts), my lunches often include salads rich in garlic, onion, radishes, jicama, spinach, kale and tomatoes, and with a homemade vinagrette. Dinners include a lot of soups and stews with beef, chicken and fish (preferably hormone, mercury, and antibiotic free). Turnips, parsnips and carrots are popular items in the stews and soups. Fermented foods like sauerkraut and kimchi are encouraged, as is coconut oil and olive oil. The idea is to rebalance the gut microbiome so that you are getting maximum nutritional extraction from the foods you eat. Tumeric, tarragon, cinnamon, and ginger are used frequently.

    Since we started this two weeks ago, I have lost 7 pounds and my daughter has lost 4, both of us no longer have an extended stomach, and I no longer hear my knees pop when I walk up the stairs. I am sleeping better, I wake up without a lot of grogginess, and I have more energy. I don’t get those energy crashes around 3pm that I used to. I have always loved veggies and fruits, but I also love fried chicken, pastries and bread. It was an adjustment to skip “go-to” foods like bread and cheese. I am 51 and perimenopausal, so I have lots of issues I deal with, and this has helped so far. Interestingly, there is no counting calories in the diet, and I eat until I am satisfied. However, I recorded a day’s worth of foods on Fitness Pal to see what my actual intake was, and it was lower than I expected it to be.

    Next week, we will start on the 2nd phase, which introduces cheeses and dairy back in (sheep or goat, preferably), yogurt and kefir, grains like rice and quinoa, and some starchy foods. At this point, the idea is that you have made significant changes in your microbiome and it can handle the newly introduced items better. If you see that you are responding poorly, you know that one of these foods is probably the culprit.

    The final phase will be maintenance, and the assumption is that if you follow the diet most of the time (70% or more), you can occasionally splurge and have a little of the things you enjoy most and miss.

    My attempt is not scientific in the least, but I am observing how my body is reacting to the changes. My stools have changed a lot, I urinate more, my dreams are more vivid (not sure why that is), and I have less gas (after the first couple of days). My nails are growing faster, and my skin looks brighter. It has not helped or hurt my seasonal allergies so far, which are minor and are more itchy eyes and a bit of stuffy nose, mostly. My biggest change is the level of energy and the lack of aches and pains from being older and over weight.

  100. I love the work you do and love that you’re going to try all these diets. I just love that you’ve even going live off the land in Tanzania!

    I’d love to also see an organic vs non-organic produce diet compared as well as one with grass-fed meat vs conventional meat.

    I would love to think that we could find one ideal way of eating for everyone but there are so many other factors that come into play and I think we’ll have to figure out the ideal diet for our biochemistry at a particular point in time in our lives. For example: do you have heavy metal toxicity? do you have an candida overgrowth? do you have small intestinal bacterial overgrowth? do you have an autoimmune disease? do you chew your food well? do you eat on the run or sit down and eat slowly? are you stressed with high cortisol? are you going through menopause? what was your mother’s diet like?

    I work with anxious women and the gut flora plays such a big role in good mood! Your work is so valuable and I can’t wait to see your results and look forward to your new book!

    1. Fisheries PhD says:

      Those are good questions. Mother’s diet, medical history, and any indication of her microbes would be great data to collect in an ideal world. Mental health factors as well.

  101. Jan Goldberg says:

    What a very exciting and timely experiment! Can you share how you are investigating your feces samples? It is funny that I just found this site as I have been reading about commensal bacteria and links to autoimmunity as I embark on a quest to improve my own and my son’s autoimmunity. As a functional nutritionist, I have a firm belief that the foods we eat and assimilate (according to our own unique physiology) play a key role in gut health and the development of disease. I wonder about the probiotic craze and its impact on disease states. It seems to make a huge difference in a lot of disorders, but wonder about possible negative affects in certain individuals predisposed to autoimmunity. Do you have any comments about this? I haven’t fully explored this site yet, perhaps it is discussed somewhere in one of your blogs.

  102. julialoha says:

    I’m wondering if you are going to try Dr. D’Adamo’s Eat for Your Blood type diet. If you don’t, would you consider telling us what your blood type is when you write up your final reports? Some people have found it relevant and I am curious.

  103. Holly says:

    I am sooooo excited to hear the results!!!!

  104. I have many questions about soap and dairy and breastmilk:
    Firstly: What microbes exist in breast milk. It is from the lymphatic system, which should be teeming with good bugs. Which ones?
    Second: Early Celtic societies used soap bce500. I was raised with lots of dirt and it didn’t save my gut flora from devastation of antibiotics. Detergent started to be used in the 1960’s, as did pesticides. Before that everybody used soap flakes to wash hair, dishes and clothes…Is this where the recent rise in autoimmune disease comes from?
    Third: Fermented milk products. The Celtic societies were using milk and fermenting milk. The first use of domesticated animals was milk production in neolithic times. The original shift in gut flora came about a long time ago. Was the co-evolution of bugs and their humans successful in the sense that they remained healthy and thrived on the extra protein?

    1. x0ender0x says:

      I was thinking of trying a upper GI biome reboot using breastmilk probiotics but I can’t find enough info about what constitutes healthy bacteria in breast milk, or even what the bacterial makeup was of a healthy woman who had healthy children. I do know recent studies indicate that the bacteria actually travel from the bowels to the breast and speculation that the body may facilitate the transfer. If I find any information, I will be sure to let the world know. In the meantime, if you find any info about where I can find the same info you’re looking for, please let me know.

      1. La Leche League may have some information on the flor in breastmilk. All my kids were tested as (breastfeeding) toddlers and did not have healthy flora so something was wrong.

        1. Something may very well not have been wrong with your breastmilk or its flora, but with your own gut flora to begin with 😉 You pass this on to your children and it’s of the utmost importance for even the second wave of (breast) bacteria to stay alive in their immature guts…

          As a gut flora therapist, I see a lot of breastfed children who don’t have optimal intestinal florae, because their mothers and grandmothers didn’t either. They just got set up for failure because of the changed food, medicine and stress environments they were in.

          However, breastfeeding of course still is the best choice, for in an already impaired gut, bottle milk will bring further imbalances.

          1. I guess that is what I meant to say. But of course the flora is transmitted through the breastmilk. We were told long ago that it was the vaginal canal that transmitted flora. Now they know the breastmilk itself contains flora.

  105. x0ender0x says:

    Thank you for exploring this, would do it myself if I could afford the testing. Have you had any negative or positive long term effects that you can report on yet? When will you do a part 2 post to update us?

  106. Drew says:

    This is fucking cool! Can’t wait to see how this all goes down. Thanks for doing this for everyone

  107. thermaikos1977 says:

    I had my own experience with gut bacteria: Fusobacterium varium. Actually it was my significant other, but it affected me too, and it seems to have been the reason for her Ulcerative Colitis which held us in its grip for 10 long and difficult years. Until we, totally accidentally, found a solution to UC which has kept her symptom free for last 11 months so far.

    I spent US$ 350 to translate our story (which I authored in German language) into English, so that I can hopefully spare as many people as possible the hard times we had to go through. Whoever is interested in reading because they are directly or indirectly affected, this might be your way out of misery:



  108. Ray says:

    I’m a freshwater ecologist and many of my colleagues and I spend a lot of time snorkeling in rivers and creeks that aren’t exactly the most pristine. At conferences there is often mention of someone coming down with a weird illness, high rates of autoimmune diseases and GI aliments. Though this is all anecdotal evidence, I think there is something to be said about the nature of our work and our bodies’ microbiomes possibly being out of whack. It would be interesting to see if some of my colleagues symptoms would improve with a diet/gut microbe make over.

    I’m also an avid home brewer. It is well known in the home brewing and home fermentation communities that you can ferment wine, ciders etc. with the natural bacteria and yeast that occurs on the fruit. Depending on the location and season that the fruit was grown you can get a vastly different flavors due to the differences in microbial communities. In reference to traditional diets and changes from region to region culture to culture people are not only getting different microbes, but maybe they are getting the microbial communities appropriate for their diet and microbes that have co-evolved to breakdown the foods that they eat. Eat dirty I guess just like hunter gathers did, pick it off a tree or pick it up off the ground a little water rinse and eat away. Also is there a better diet for different races or ethic backgrounds one that evolved with that culture.

    I’m switching career fields and going into medicine. I find this project truly fascinating and can’t wait to learn more about the intersection of ecology and healthcare found in the foods we eat and the microbes we harbor. Thank you for all your hard work and sharing your research with us Jeff!

    1. Joe says:

      I would suspect that the “high rates of autoimmune diseases, and GI ailments are actually due to damaged/disturbed microbiomes. When we take antibiotics and other medications we unwittingly affect the good helpful microbes of our microbiome. We’re killing off our good guys. Already, the average American has lost 40% of the diversity of their microbiomes, as compared to remote tribes that have never had antibiotics.
      I think you are spot-on on your observation of eating fresh and raw. The fresher the better.
      There are already 12 to 15 companies racing to be best in market with a method/product to repair the microbiome. The two top researchers inworld doing FMTs are working hard to find the best protocol to reverse disease.
      It’s an exciting time.

  109. Paul Stackhouse says:

    I like your writing style and your sense of adventure (gutventures). Interesting to see how gut flora dramatically change based on diet in the graphed results of your Self-Survey method. My gut gets out of whack once in awhile and I whack it back into line with some capsuled probiotics for a few days. This is not backed up by any back-end science (i.e. stool sampling), but I think it works. However recently I read that the stated strength of probiotics is all over the map, i.e. sometimes BS, but as you pointed out a few billion sounds good but doesn’t make much of a dent compared to the population numbers where it’s headed. To get to the meat of my missive though is a recent Self experiment which is related to the idea that modern highly cross-bred wheat is a problem for the older hunter-gatherer digestive system – no, not the cult of anti-gluten but just the complex modern wheat protein. I have found that I get mild but persistent skin rashes from eating too much wheat being mostly the whole grain version, which is an intolerance symptom. Recently though I was wacking my system again but this time using Bio-K, a made in Canada liquid fermented probiotic (requiring refrigeration) containing “L Acidophilus + L Casei” bacteria. To my surprise, my mild itchy skin rash disappeared for about a month with no change in my diet after just a few days of consuming said product. My assumption is that this temporary change in symptoms was due to the bacteria processing the wheat protein differently – i.e. I could now digest it, as a skin rash is often the body trying to get rid of food that could not be fully processed. Not an intentional experiment, but a real change in my “health” due clearly only to different bacteria in my system. No other probiotic I’ve used has had this effect. I’m signed up for your book, and look forward to reading it. I think this area of investigation is one of the top key health research fields of the 21st Century – just a gut instinct. :o)

    1. Her says:

      I didn’t see any mention of the Weston A Price diet which is basedon traditional cooking styles, including fermented foods. I hope you have heard of it, because it is right up your alley. Another interesting book I have been reading recently that addresses these issues is Bill Mollison’s fermentation and human nutrition. Fabulous focus on gut biomes, even though it was written decades ago.
      Seth P

    2. Joe says:

      I’ve tried several different probiotics (back when I had my IBS), and at best I only got some temporary relief. Then one day during my research, I stumbled across a statement by a medical researcher, “probioitics do not attach to the intestinal wall”. It has something to do with the way they are manufactured. Anyway, I pretty much gave up on probiotics giving me a lasting change after that. Eventually, I did a home FMT, and reversed my IBS-D. It worked.
      As I continue to study the microbiome, I asked myself one day; what are the sources for good microbes, the ones that help our microbiome diversity. On a hunch, I looked into fresh fruits and fresh, raw vegetables. It turns out that they have good fresh microbes on them. So, I’ve been eating a wide variety of fresh fruits, and fresh, raw vegetables, and unsalted un-roasted nuts and seeds, along with raw honey. All good sources for good microbes. I’ve also been mixing in some Kimchi, sauerkraut, Kefer and summer sausage, Things have been great down there. I’ve noticed a positive affect. I think it’s even helping on my sleep requirements.

  110. Anne says:

    I have stopped smoking and am bloated with large weight gain on the tummy area only. Apparently when you stop smoking proteobacteria and bacteroidetes increase at the expense of firmicutes and actinobacteria. I do not understand mich of this despite extensive reading. How would I redress this imbalance and change it back to higher firmicutes and so. K

  111. Angelique Gertig says:

    Jeff, it has now been just over a year into your project. What are your results, findings? How is it going? Is there a summary anywhere….this string of comments sure is long!!!!

    1. Jeff Leach says:

      Still working on – year 2 underway now… one year not enough!

      1. msapiens says:

        Aw c,mon. You have your poop tested every week or so, you must have some observations.

  112. julialoha says:

    But we probably have to wait yet another year after that for you to publish your book. I promise to buy it even if you give us some heads up info in the meantime. Some of us are struggling to maintain our health in the midst of all kinds of conflicting diet information. One big issue with this whole study is that we don’t know what kind of body you have. We don’t all metabolize the same. Are you going to do 23andme? And again – I am very grateful for your work on this and can’t wait to get more information. I’ve actually been worried about you since the poop transplant – there was only one post since and that was quite a while ago.

  113. Max says:

    have you started looking at results?

  114. Tina says:

    Hi Jeff,
    I am very fascinated by your bio hacking experiments. The only thing that I have found surprising is that I expected here back to IDT’ The only thing that I have found surprising is that I expected here bacteroidetes to be the dominant bacteria in your high fiber diet and the firmicutes to be in the minority. This is based on the work of Brenda Watson’s research and book The Skinny Gut Diet.
    My understanding, according to Miss Watson and others in the field is that high bactrousered to firmicutes is the typical ratio found in high fiber diet and in those of lien mice and human beings. I would appreciate your thoughts on this. also, I was wondering where you posted the rest of your experiment of one results.

  115. Jacinta says:

    How do we follow your journey and find out the results? I’m soo very interested!

  116. Sam says:

    This stuff is really interesting. I noticed you talking about resistant starch. Here’s a link on resistant starch and a couple more by guy who believes it controls his diabetes.




    What I find amazing is a lot of people do well on very meat based diets and a lot do well on plant based diets. It seems high carb high fat is the problem. You can have only one or the other. Diet is very confusing.

  117. Greg Nolan says:

    How do you suppose anaerbic microbes transfer from one person or one environment to another person gut.

  118. Greg Nolan says:

    It would be very interesting to see if breast milk changes the biome of an adult. I might have to find a wet nurse.

  119. Greg Nolan says:

    It would be interesting to take a persons biome, then human breast milk biome, then feed the person the breast milk for a few days or weeks and recheck the human biome to see what transferred.

    1. Fidel says:

      Are you a sulfide-gas producer? According to gg.gg/D-Piger , about half of us are. If you agree with those who consider hydrogen sulfide harmful to the colon, the way to reduce it is by eating less high sulfur foods and keeping the colon acidic with fermentable carbohydrates.

      You could test what a low sulfur diet does to your microbiome, but if you don’t have sulfide-producing bacteria to begin with, it might not be particularly beneficial for you.

  120. Stuart says:

    You are great and wonderful. 🙂 Amazing wirk!

  121. Hazel says:

    Jeff how do you view papers like is, which show weight loss from a higher bacteriodetes level? http://www.ncbi.nlm.nih.gov/pubmed/26061054

    1. Jeff Leach says:

      you will need access – most papers are behind firewalls.

  122. Steven says:

    Raw juice diet will produce the best test results.

  123. Mexigal says:

    GREAT article. I am quite confused by the Firmicutes & Bacteroidetes, & I’m hoping you can help me understand. I have read about both before & I had thought that it was the Bacteroidetes that enjoyed fermenting fiber. So I looked up many references & this is just one example of what I found: “. . . Moreover, when the diet is high in fat, the obesity-friendly firmicutes increase (the exception being a ketogenic diet), yet a high-fiber diet helps bacteroidetes increase. In addition, researchers observed that overgrowth of firmicutes led to chronic systemic inflammation . . . .”

    Yet, in your case, you seem to be saying that you believe the Firmicutes were the bacteria happily fermenting your high fiber NewOrleans diet, right? And the Bacteroidetes took over when there was much less fiber to ferment (your desert diet). I know that I now must read ALL that you have written, but I’m hoping you can “unconfuse” me soon, so I can better grasp the rest of your journey!

    1. Jeff Leach says:

      note the firmicutes argument for obesity doesn’t hold up at the population level – in the american gut data – and other studies – people fall along a spectrum… note the hadza – who are thin – are dominated by firmicutes….. note also when you see higher levels of bacteroidetes in some rural populations, it’s due to an increased abundance in the genus prevotella – which is driven by whole grain consumption. remove the whole grains, and the prevotella drops and thus the bacteroidetes…

  124. Christina Schwalbauch says:

    Hi, Jeff

    I was wondering what kind of plant fiber you were eating on your high fiber + meat diet? Were these typical veggies? Lots of onions? Starchy veggies or root veggies? Any grains?

    I’m just wondering if any fiber works to get the effect you had and when people talk about soluble fiber are they talking regular veggies like carrots and broccoli or including root veggies or grains?

    Thanks, it would help a lot 🙂

    I have eczema/food allergies since I was young and since clostrida was shown to eliminate peanut allergies (in mice) and clostridia is part of the firmicutes I figure trying to boost firmicutes is a good start.

    1. Jeff Leach says:

      all kinds of veggies. i really don’t focus on any particular green though i do like onions and leeks – a lot. should try and get a diversity.

      1. Christina says:

        Oh, and is there a way to edit my name on my first comment, I didn’t mean to add my last name? When I click on “contact us” it sends me to facebook.

  125. Christina says:

    Thanks for the reply!

    On your high plant fiber + meat diet, how much would you say consisted of plant fiber, 20%, 50%? And is that what your diet normally looks like?

    I’m not trying to be a stickler I was just wondering for comparison purposes and to maybe get an idea of how much of the diet should be from plant fiber.

    And, sorry, I just wanted to make sure I understood – when you say, “I don’t focus on any particular green,” do you mean you don’t eat a lot of green colored veggies or were you just saying you don’t focus on any veggie in general – sorry if that was obvious

    Thanks for all that you do, this emerging info is really helpful

    1. Joe says:

      Eating a diet high in fresh fruits and fresh vegetables feeds our good microbes. Cooked vegetables are OK, but remember to eat a large variety of fresh fruits and fresh vegetables every day. Feed your good microbes, starve your bad microbes. This means; stay away from all sugars, and processed foods. We are mostly microbe, it’s time we started eating the foods that feed our good microbes.

  126. Elle Shesie says:

    Ok let us cut the c… literally. I want to loose this fat that accumulates around my liver in my tummy. How do I change my microbiome, with what. I have started the real yogurt and probiotic thing and despite not eating way less or any change, i am loosing a bit. What helps, what does not help ? Short of getting a microbiome transplant of someone who has been thin for ever and does it matter if it is a man or a woman) ?

    1. BarleySinger says:

      Milk based probiotics (acidoph, biff) do not last in the gut. They are very temporary. The gut microbes that colonize (stick around) tend to be soil microbes. You know, all ove rthings around us…the ones kids wind up with in their system due to shoving everything into their mouths.

      You might want to look into PrescriptAssist. It is a fully vetted SOIL based probiotic. Incidentally (and not directly related to supplementing any flora) when I went 100% organic on my diet (the same things, just far lower in sprays) I lost 50 pounds while still eating pizza & ice cream (and now I am thinking of ice-cream pizza…shudder)

      1. I have had amazing results on Prescript-Assist. Yeah, I really wish I had gone 100% organic before getting all my food allergies so that I could enjoy ice cream pizza as well. Sadly, the gluten and dairy in them make me too sick. I do cauliflower pizza now instead, which is alright I guess :-/

        Great comment!

      2. Joe says:

        Barley Singer,
        I read that most probiotics on the shelf do not have the proper enzymes or ‘passwords’ to survive or attach in the intestine, thus they don’t offer lasting relief, it is temporary at best.
        Also, we have from 2,000 to 4,000 bacterial species in the gut, maybe more . Taking a pill with 10 strains and expecting these ten strain to supply you with your missing strains is rather unrealistic. This is why a microbiome transplant, which implants the whole ecosystem works. It re-balances the system.

      3. Joe says:

        Barley Singer,
        Some of my new research has revealed : avoiding processed foods is a smart move to improve the health of your microbiome. It turns out that many processed foods have emulsifiers, which it turns out are harmful to the microbiome. Avoiding all sugars is also a wise move, as sugars feed our bad microbes. Throwing away your antibacterial hand soaps is also smart because it is just one more unneeded exposure to antibiotics and antibiotics wreck havoc on the microbiome, disrupting the balance and killing species. Chlorine and chloramine in our drinking water “may” be another cause of problems. After all, they kill bacteria in our water, so what do they do to our good helpful bacteria in our microbiome ? We need more research on chlorine and chloramine and the affects on the microbiome. Mouthwashes are most likely another damaging habit. Restoring the natural balance and health of the mouth microbiome would be a wiser move, instead of constantly bombarding it with the ingredients in mouthwash. We do so many things wrong……… Avoiding meat that has been raised with added antibiotics to increase weight gain is also another wise move to help our microbiomes. We should be eating a diet high in fresh fruits and fresh vegetalbes, and cooked vegetables, with just a little meat. The resistant starches in fresh vegetables are great for our good helpful bacteria, they thrive on these. Kimchi and sauerkraut once per week are also good. Kefer may also be beneficial.
        That miniscule, tiny spec of dirt on your fresh celery MIGHT just not be so bad for us.
        I expect more of us will take mud baths in the future, just to help our skin microbiome. A little good, clean, uncontaminated, dirt for a nice soak might be just what we need. No pesticides, fertilizers, etc, for this of course.

    2. Joe says:

      I would suggest you start a new diet of fresh fruits, fresh vegetables, unsalted and unroasted nuts and seeds, and raw honey. Cut down on the carbohydrates to almost nothing. Include some natural probiotic foods such as sauerkraut and summer sausage, with some Kimchi, and also some Kefer once in a while.

      These are all good for your microbiome.

    3. Joe says:

      Barley Singer,
      Where did you read about “the gut microbes that colonize tend to be soil microbes” ?

  127. Andreas says:

    The 801010 diet! (Doug Grahams book/diet)

  128. Ron says:

    Jeff: have you written a blog/paper about this 2014 experiment? Thanks Ron

  129. meme Grant says:

    I have my husband on a Ketogenic diet for cancer, it has stopped his melanoma (stage 4 in 2010, tumor free for over 2 years now), but would love to know what it has done to his Microbes. He is very healthy, does not get sick, exercises regularly and has plenty of energy. He has 80% fat, 15 % protien, (1gm/kg body weight) and 5% carbs. between 15 and 20 net carbs a day all low carb veg with a few berries and a bit of coconut.

  130. PCT Hiker says:

    What do you feel is more important to overall health, a diverse but inherently fluctuating microbiome, or a more specific but stable microbiome? Supposedly pre-European native Americans ate near-exclusively bison pemmican during winter and had very few health problems relative to modern native Americans on a varied western diet, despite pemmican consisting of 40%+ pure fat. I’ve been theorizing that when you have a diverse but fluctuating diet, your microflora is never stable and balanced for any particular meal, whereas on a highly restricted diet, your microflora is already in the proper balance to effectively utilize that meal, regardless of what that meal is so long as its consistent. I’m asking because I’ve been planning to hike the PCT and am considering eating exclusively pemmican due to both the low pack weight (6.6cal/gram), high density, and presumably a more effective use of those calories through a “trained” microbiome. If anyone can prove that this isn’t a good idea, without speculation (remember that those native Americans had no reported obesity or cardiological conditions), it would be greatly appreciated. I’m trying to be more healthy, not less.

    1. Cindy C says:

      Not sure where I read this, as I have read a lot about the microbiome, some studies say a animal(not sure if it was a study on man), that the less diversity in diet the more diversity in the microbes, Perhaps they did not compete with each other, to wipe out or reduce a species. A different diet will always cause fluctuations, I have read on the site Smashes head in some on currents and other not so sweet berries used to preserve the pemmican as well as eating the berries seasonally .


      Some of these wild plants may have been eaten as well, So try this site.


  131. Jennifer says:

    How do i follow your progress?

  132. Hi Jeff … have you published your results yet? I just came across this Jan 2014 blog of yours, and since it’s now Dec 2015 I’m eagerly hoping you have the rest of your journey online somewhere … yes?? 🙂

    1. Evalynne Engle says:

      Really looking forward to seeing your results, too!

  133. Joe says:

    A very interesting read. Good luck on your journey. I’m just one of the people in the world that has reversed their IBS, with an FMT. They work, if done properly.
    Recently, it dawned on me that in the distant past our ancestors could have gotten the good, helpful microbes that we need from the foods we eat. Sure enough, when I looked into it : fresh fruits and fresh vegetables have good helpful microbes on them. Another source is unsalted, unroasted nuts and seeds, and also raw honey.
    So, I’ve been incorporating a wide variety of fresh fruits, fresh vegetables, and fresh, raw nuts, seeds and honey into my diet. I’ve noticed a nice difference down there.
    I bring this up as a suggestion for your research project. Perhaps, Dr. Rob Knight might be interested in your findings, when you are done.

  134. James says:

    I’m sure you’ve thought of this but isn’t it important to collect stools from those hunter gatherers ? , Australian aboriginals , fish eating Eskimos etc ?
    Incredibly useful project you are running.
    Great work to all involved

  135. Pingback: Gut Health
  136. Elena says:

    Hi Jeff, great idea your experiment! Have you come up with a conclusion? I would love to read it! Have you post/published it somewhere? Thanks!

  137. Doug says:

    Jeff (or anyone), do you think it would be effective for a mother (who had in the past required antibiotics) to take a lot of beneficial probiotics in the weeks leading up to birth? Would these have a good chance of having a unique opportunity to influence the baby’s microbiome at birth? It is my understanding that birth is the one time this can be set up for success.

    1. Joe says:

      Certainly a diet high in fresh fruits and fresh vegetables would be beneficial. Avoiding processed foods and all sugars too. (processed foods have emulsifies which are bad for the microibome, and sugars feed the bad bacteria) It’s a diet to live with, good for our microbiomes, and good for us. Until we have independent verification of the efficacy of probiotics (by the government) we don’t have positive verification of their claims. Each of us need to be asking the FDA for this.
      A healthy diet, avoiding antibiotics, natural childbirth, and breastfeeding for as long as possible are smart moves. Let your children play in the the good, clean, uncontaminated dirt. A variety of adults visiting your home during the first three years will also increase the diversity as we shed our microbiomes as we travel, and babies establish their microbiomes over the first three years of life.

      Each day consider the fact that you are mostly microbe, you are covered with good, helpful bacteria, in and out, and re-evaluate your lifestyle to be helpful to these good guys, instead of harmful. Removing chlorine from your water ‘may’ be helpful. Avoiding antibiotic hand soaps is certainly helpful. Soap and water is all we need.

  138. Hi Jeff, I remember you mentioned that grains has a negative effect on microbiomes, could you please briefly explain what that is? I haven’t touched any grains now since 6 June, and follow your advice on consuming a wider array of plant species and I hardly eat meat either.Thank you.

  139. Colleen Robb says:

    Having experienced Chrohns like symptoms following a round of antibiotics, I am very curious to learn how recover a healthy gut, and the relevance to IBS and IBD. Your experiment sounds fascinating. I’d be curious to learn if FODMAP, SCD or the Gut and Psychology diets are truly beneficial to such conditions or are more harmful by restricting many prebiotics.

  140. sarah says:

    So fascinating . I have Ulcerative colitis failing all mainstream meds as of the past few weeks. I’m about to start the SCD diet(specific carbohydrate diet). Though I would be so curious what kind of diet you would hypothesize to help alter the inflamed gut. Thanks

    1. Joe says:

      Hi Sarah,
      According to recent medical research ; processed foods have emulsifiers, which are harmful to our microbiome (our good, helpful bacteria). So these should be avoided at all possible. All sugars should be avoided too, as they are feeding our bad bacteria (which cause problems.
      Chlorinated water (chlorine and chloramine) protects us from water borne pathogens by disinfecting our water supply. Trouble is, these have an affect on our good, helpful bacteria too. Bathing is even more of an exposure than drinking, so a whole house water filter to remove these products at the tap is a wise consideration.
      Throw away your antibacterial hand soaps. This is an unneeded exposure to antibiotics, which harm our microbiomes.
      Gluten may be causing inflammation. Red meat consumption may also cause inflammation.

      There are many things we are doing wrong with our modern diet and lifestyle. We can’t expect to fix our problems if we continue to make mistakes in how we treat our microbiomes, the ecosystem of bacteria that keeps us healthy. We are consuming things and doing things that cause inflammation, disrupt the healthy balance of bacteria, and kill off beneficial species.

      Eating any meat that has been raised with antibiotics to promote faster growth should also be avoided. This is one more exposure to antibiotics that we don’t want. (antibiotics wreck havoc on this ecosystem of bacteria we carry, and cause problems for us). Sure, they save lives, but we overuse and misuse them.

      We can’t expect positive changes to the health of our gastrointestinal tract if we continue to make mistakes.

      Once one reduces inflammation, good products are Kimchi, Kefer, Kombachu, Sauerkraut, and Yogurt, along with plenty of fresh fruits and fresh vegetables, if you can tolerate these.

  141. SarahSarah says:

    My son has autism, severe constipation, a leaky gut and a myriad of other issues. I am reading everything I can find that you’ve written to try to understand the biome and therefore heal him. I’m overwhelmed by all the information I’m trying to understand and absorb, but will persevere! I look forward to the results of your amazing experiment. Thank you for the knowledge and the inspiration (and the humour too), you’re brilliant!

    1. Joe says:

      Hi Sarah,
      You’re on the right track. A couple of suggestions ; get the book, “Eat Dirt” by Dr. Josh Axe. I’ve been reading everything I can find on the human microbiome for the last three years. This guy is on to something.
      Autism has been reversed, by an FMT. I am convinced that if we can restore the health of the microibome, we can reverse Autism to some degree, and possibly all the way.
      We have to stop waging war against this ecosystem of bacteria that keeps us healthy though. Processed foods are bad, their emulsifiers cause inflammation. Sugars feed our bad bacteria. Antibiotics are like a Carpet Bomb to the microbiome. Avoid them, as much as possible at least. Get the chlorine and chloramine out of your water. Avoid using meats raised with antibiotics. Throw out your antibacterial soaps. Re-evaluate everything you do, with the understanding that these bacteria, our microbiome, play a huge role in our health.

      1. SarahSarah says:

        Thank you so much for your reply Joe, i really appreciate it. I will read the book you suggest. I do all of the above, but my son is allergic to almost everything and then refuses to eat most else so has a shockingly restricted diet and doesn’t eat a single vegetable. I can’t even hide them because he’s allergic to phenols and oxalates, etc etc. I know these allergies will stop when I heal his gut (and therefore his autism) but I don’t know how to begin. Not one of the things I’ve tried has helped his constipation for example. I thought you couldn’t do a FMT unless your gut was healthy already, I thought that if you didn’t have a pretty good environment to begin with that the new microbes couldn’t survive. Is that incorrect? I hope I misunderstood.

        1. Joe says:

          They are doing FMTs for UC. Of course many treatments are needed to heal the colon. I wonder though if they are following the best diet when they do these for UC, as a harmful diet may reduce their success. You’re going to understand more when you read the book.

          Reducing inflammation is bound to help the process, and eating the right diet to reduce inflammation is very important. It may have played a role in my successful FMT for IBS.

          You are going to enjoy this book.

  142. Chris says:

    Jeff, Where is the results of your study?

  143. Sarah says:

    Not sure how far you are in or if you are still going but I’d love to know what effects regular coffee consumption makes

  144. Justin says:

    Yeah, hope you can share latest update status. Very curious too. Great work!

  145. k says:

    Thankyou for this . Is their any chance of contacting via email. I am needing some clarification on some advice to fix my gut microbiome currently very thin cognitive issues irrableness etc. I have my results which show only 0.65 ecol which should be 90% distribution specialists are still not understadning the importance at im at a loss with trying to educate them so i can recieve help. Thankyou

  146. yonason says:

    Ever heard of Dr. Alessio Fasano? He has some videos on the net on leaky gut, and he touches on the microbiome and it’s importance in one’s health. He might even be interested in what you are doing.

  147. Megan Adams says:

    “For example, aside from the high fat/protein diet I just finished at the first of the this year (taking poo samples along the way), I will go on a raw food diet for a few weeks, followed by a juicing diet, possibly followed by a vegan diet, followed by an Atkins-like diet, followed by a Mediterranean diet, followed by a period of fasting, possibly a weeks of lots of fermented foods, followed by a Paleo diet, followed by Jenny Craig and Weight Watchers diets, followed by a Master Cleanse Diet, and so forth – repeating some diets several times.” About how long did you stay with each cycle of eating habits. Was this what you did or was it something different

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