Meeting My Microbiome

American Gut Project Illustration

“I can tell you the exact date that I began to think of myself in the first-person plural — as a superorganism, that is, rather than a plain old individual human being. It happened on March 7. That’s when I opened my e-mail … from American Gut.” ~ Michael Pollan

Have You Heard of the American Gut Project?

It’s the largest scientific exploration into what lives inside the human gut ever, otherwise known as our microbiome. These are the trillions of microbes (and their genes) that live inside us and affect the function of every cell in our bodies. Did you know that 90% of your body is made up of microbes? We are only 10% human. And when it comes to genetic material, we are only 1% human, having 99 microbial genes for every one human gene. It’s mind blowing to realize, but it also explains how diet and lifestyle affect our health so dramatically. Back in 1999, when scientists sequenced the human genome (the 1%), they expected to make major scientific advances, essentially curing all disease. That didn’t happen. In fact, they discovered that the human genome was simpler than expected and didn’t really explain disease at all. More recently, they learned that healthy people have an average of 400 genetic defects, including ones for diseases they don’t have. How is this possible? In elementary school, we were taught that our genes determined our health. Clearly, that’s not true, at least not for human genes.

The microbiome has been called the second genome, and the American Gut Project seeks to sequence and understand it. Over 6,000 people have sent in personal samples, and the project is still open to participation, which means you can discover what’s in your gut, too. You’ll get a personal report like the ones I’ll share in this article, but more importantly, you’ll be contributing to a cutting edge research that is the first step to potentially understanding (and finding the cure) for countless diseases. This research is in its infancy, so it will be a while before that goal is achieved, but what an important goal!

Meeting Myself

Eileen's American Gut Report

  • A few facts about me: I have rheumatoid arthritis. When this sample was taken, I had been paleo for almost a year and on the autoimmune protocol for 4 months. I eat low-starch also (based on GAPS diet principles) but not low-carb.
  • The bar chart: The column on the left is my microbiome. The columns in the middle are the average microbiome balance for everyone in the study, as well as people of similar age, weight, gender and diet. (Although by diet, they mean omnivore, not paleo.) The column on the far right is the microbiome of writer and food activist, Michael Pollan, who eats a grain-based omnivore diet.
  • Drawing conclusions: This is very new science. They haven’t even identified all the microbiota yet, never mind discovered all the ways they function in our bodies. As I analyze my chart and point out certain facts, I can pose some theories about what it all means, but keep in mind, they’re only theories. Still, I find the whole field fascinating.
  • Major bacteria groups: There are 2 groups of bacteria that make up the majority of the human gut: Firmicutes and Bacteroidetes. On average, people have about 50% of each. You can see that I have far more Bacteroidetes. Some people say this is good, because the reverse ratio has been linked to obesity. I would have guessed this was a result of the paleo diet, but Jeff Leach, one of the leaders behind the American Gut Project, eats a paleo diet and has the reverse ratio (far more Firmicutes than Bacteroidetes). Jeff says that the Firmicutes-obesity connection is outdated. Their research is showing a wide variety of ratios between these two groups of bacteria, with no connection to weight. The first step toward knowledge is unlearning what you thought you knew.
  • Inflammatory bacteria: The next group of bacteria on the chart is Proteobacteria, which has been linked to inflammation. It’s the light orange bar, and I have less of this than average, which I take as a very good sign. Month by month, I have felt the inflammatory pain in my body reduce. If I had taken a gut sample when I was first diagnosed with RA, before dietary intervention, I’m guessing my Proteobacteria count would have been much higher than average. In fact, there’s another American Gut result available on Healing Hacker that shows a woman with RA who, to my knowledge, doesn’t eat paleo, and she does have a higher than average amount of this bacteria. The American Gut Project has found that people who eat a paleo diet generally have less Proteobacteria than others.
  • Missing diversity: The other notable difference of my microbiome compared to the others is that I don’t have enough Actinobacteria or Verrucomicrobia to show up on my bar chart. While these aren’t abundant in the comparison columns, most people have at least enough to register. I came to paleo through the GAPS diet first, which posits the theory that an overabundance of certain bacteria in the colon causes inflammation and susceptibility to autoimmune disease. A low-starch version of the paleo diet starves these bacteria, with the goal of restoring balance. Here’s the catch. Every group of bacteria contains both beneficial and pathogenic organisms. When I starved out the pathogens, did I also starve out some of the beneficial ones? Maybe so.
  • Abundant, enriched and rare: In addition to the bar chart, American Gut gives you the names of your most abundant, enriched and rare microbes.
    • 6% of my sample is Paraprevotella (which is 15x more than average). It’s in the same family as Prevotella, one of Michael Pollan‘s abundant microbes. Jeff (from American Gut) says that this family of bacteria is connected to grain consumption (Michael) but also autoimmune disease (me). Of course, this makes me think about Loren Cordain’s theory that grain consumption can trigger autoimmune disease. Michael is healthy, but I ate grains for my entire life before RA got triggered in my body at age 43. I stopped eating grains a year before this sample was taken. I wonder if this number would have been even higher before I changed my diet.
    • 5% of my sample is Ruminococcaceae. This is a common family of microbes, across a wide variety of diets and health issues. Its presence doesn’t really indicate anything special.
    • I have 20x more Oxalobacteraceae than average. Laura from Ancestralize Me is the only published report that shows a similar abundant microbe. This bacteria is connected to the successful digestion of oxalates, which is a good thing. Some people with autoimmune disease have trouble with oxalates; I never have, and this is probably why. Earlier in this article, I mentioned that every group of bacteria has both beneficial and harmful organisms within it. While Proteobacteria has been associated with inflammation, that doesn’t mean all Proteobacteria are inflammatory. In fact, Oxalobacteraceae are in the Proteobacteria family and help prevent kidney stones. Another beneficial Proteobacteria is Acetobactor (present in all vinegars and kombucha). Lesson? It’s more important to have the good guys in every category, than try to eliminate a category altogether.
    • I have 8x more Barnesiellaceae than average. One study found that this bacteria is effective in fighting off antibiotic-resistant infections. Sweet!
    • I have 9x more Rikenellaceae than average. I could find no information on this one, and it didn’t show up on anyone else’s published reports, so it remains a mystery.
    • I also have one rare kind: Stenotrophomonas, which is a Proteobacteria. Due to its rarity, very little is known about it.
    • Yeast remain a mystery. Bacteria compose the vast majority of the human microbiome, and that’s the focus of the American Gut Project. However, other microbes live in the gut as well, including both harmful and beneficial yeasts. Sadly, they don’t yet have the technology to successfully sequence yeast at this time. People on a SAD diet usually have an overabundance of candida (a harmful yeast). My hope is that I have an abundance of beneficial yeasts, since I eat fermented foods daily (which contain them). I would have loved a snapshot of the yeast balance in my gut as well. Someday.

Meeting My Husband

Husband's American Gut Report

  • A few facts about my husband: He was given penicillin daily for approximately 10 years as a child. He was born with a heart murmur, and they feared the potential for a life-threatening infection. It turns out this was an unnecessary fear, but it was standard treatment back then. Not surprisingly, he’s had digestive problems ever since. He eats about 80% paleo now, but snacks on SAD foods at the office.
  • Pathogen alert? Looking at his bar chart, he has a large amount of a group of bacteria that is minimally present in most people’s microbiome: Verrucumicrobia. Looking at his abundant microbe list, Akkermansia comprises 20% of his microbiome (7x more than average). It’s a member of the Verrucumicrobia phylum and apparently accounts for entire green stripe in his column. In small quantities it likely plays a beneficial role in the balance of the microbiome, but in large quantities, it can pose problems. It’s a “mucin degrader“, which means it eats the mucus lining of the colon. in high numbers this could irritate the intestinal wall and leave it susceptible to permeability and/or infection. My theory is that years of penicillin use allowed this opportunistic bacteria to take root. In addition, he has one rare bacteria that is also usually a pathogen: Peptococcus.
  • Learning about inflammation. If you look at his chart, you’ll also see that he has no measurable Proteobacteria at all, the bacteria group most closely linked to inflammation. Does that mean he doesn’t have inflammation? No. He has rosacea, osteoarthritis and borderline high blood pressure, to name just a few. This shows that more than one bacteria group is connected to inflammation. For him, it might be the overabundance of Akkermansia.
  • An abundance of Clostridiales. This is typical for someone his age (63), and contains many beneficial species, as well as a famously harmful one: C. difficile. That said, they have found that if you have a diverse population of this group of bacteria as a whole, you are less likely to develop a C. difficile infection. So the good guys in the group keep the bad guys under control. Hopefully that’s happening for him. He has 13x more Christensenellaceae than average, which is in the Clostridiales group. However, little is known about it.

Other People’s American Gut Results

Collage of American Gut Reports

  • Here is Michael Pollan’s report in more detail, and here’s his article in the New York Times about the project overall, and his experience. One interesting experiment they did was take a sample before and after he did a “preventative” course of antibiotics prior to oral surgery. The result was a dramatic decrease in the diversity of his microbiome, with less bacteria considered to be healthy and more bacteria connected to inflammation.
  • Here is Jeff Leach’s report in more detail, and here’s an interview he did with Chris Kresser about the American Gut Project. As a scientist, Jeff is much less likely to draw conclusions from his report. He sees all this data as just the start of understanding the microbiome. However, he personally makes an effort to eat 20-30 different species of plants every week. Why? Because the fiber in plants feeds the microbiome, and he figures the more diverse the type of fiber, the more diverse the bacteria he is feeding. He also doesn’t eat fermented foods, saying that his microbiome is higher in Lactobacillus and Bifidobacterium than people who eat fermented foods and don’t get enough fiber. In his opinion, prebiotics (foods that feed bacteria) work better than probiotics in shaping the microbiome.
  • Free the Animal shared the results of “Tatertot Tim”, a man who had been on a primal diet for 2 years and supplementing with resistant starch for 6 months. He started RS supplementation after reading research which linked resistant starch with colon health, improved cholesterol, better glucose control, and weight loss, and indeed he saw improvements in all of these areas. Then, he started wondering if it was changing his microbiome, so he sent a sample to American Gut. His report shows an abundance of Bifidobacteria (11x more than average). That is far more than any other published report I’ve seen. I would say Tim has proven that his RS supplementation is having a strong effect. The question is whether it’s a good one longterm. Bifidobacteria is one of the most studied bacteria, and it’s definitely beneficial. But is it better than the bacteria we don’t know as much about? Where Jeff is feeding diverse bacteria from diverse whole foods sources, Tim is targeting specific bacteria with a supplement. I’m not saying he’s wrong to do so; I’m saying the science is too new to know which method is better.
  • Laura from Ancestralize Me shared her results, and she has almost no Bacteroidetes at all, which is very unusual. She has a history of chronic Lyme disease and spent 6 months last year taking 5 different antibiotics daily. She’s guessing that caused her unusual profile. Although she follows a paleo diet, she also has an average amount of Proteobacteria (paleo people usually have less than average). She decided to do an experiment for the next month. She’ll supplement probiotics and resistant starch daily, and then send in a new sample to American Gut. Her hope is that her new results will show an increase in Bacteroidetes, a decrease in Proteobacteria, and an increase in Actinobacteria to a measurable level. (Like me, she shows no Actinobacteria on her bar graph.)
  • Healing Hacker shared 3 generations of results: her mother, herself, and her son. Her mother has rheumatoid arthritis. She has Raynaud’s syndrome. Her son has asthma and eczema. I don’t know anything about their diet. It has been theorized that a lot of our microbiome is established in infancy, and biological families have similar microbiomes. Healing Hacker shows that isn’t true, at least not for them. Their microbiomes are very different from each other.

Feeding Our Microbiome For Change

  • Eileen Reintroduces Starchy Vegetables: Now that my husband and I have our reports, we have the option of trying to address some of the imbalances it revealed. When I began paleo 18 months ago, I adopted a low-starch version of the diet, based on GAPS diet principles. Since I improved, I stuck with it, never testing whether avoiding starches was a necessary part of the protocol. Chris Kresser, Sarah Ballantyne and Paul Jaminet have all expressed concern about avoiding starches long-term. The risk is that by starving the harmful bacteria, I have also starved some beneficial bacteria (which may be why I have no Actinobacteria on my bar chart). Some of the most well studied beneficial probiotics are part of this group, and even though I eat fermented foods daily, they’re not a measurable part of my microbiome. While I can geek out on all this science, I’m a practical girl at heart. I’m paleo because I have rheumatoid arthritis, and it’s reduced my pain by 95%. Some people (like Charles Comey) have found a direct connection between starch consumption and pain flares. It’s time for me to test this for myself. I prefer whole foods over supplements, so I’ll be reintroducing starchy vegetables like sweet potatoes and green plantains and see how my body responds. If I continue to feel great, I’ll reincorporate these starches as food for my microbiome. If my pain increases, I’ll return to a low-starch paleo diet.
  • My Husband Tries Resistant Starch. My husband has a very unusual microbiome with a large amount of one kind of opportunistic bacteria, likely caused by years of penicillin use. For this reason, it makes sense to address this imbalance supplementally, and resistant starch is showing promising results in this area. If he can increase his Bifidobacteria (as Tim has demonstrated above), it might displace his overabundance of Akkermansia and resolve the digestive issues that have plagued him his entire life. It’s certainly worth a shot.

How To Meet Your Microbiome

You can participate at many levels, from the basic report I received ($99) to an “ultra-deep” and detailed genetic mapping ($25K). They welcome participation from anyone, anywhere, with any dietary background, and any health status. The more diverse their volunteers, the more they’ll learn.

Credits: Illustration at the top of the page is from American Gut, and the embedded video is from NPR.
This post is linked to the following blog carnivals:
Natural Living Monday, Fat Tuesday, Healthy Tuesday, Allergy Free Wednesday, Wellness Wednesday, Waste Not Want Not Wednesday, Simple Lives Thursday, Healing With Food Friday, Paleo Rodeo,

30 thoughts on “Meeting My Microbiome

  1. Pingback: Meeting My Microbiome | Paleo Digest

  2. Glad to see you put your results up for everyone to see. It’s important to get these out so everyone can benefit. One day we’ll hopefully know what a perfect gut looks like and how to get it.

    You were right, not much out there on Rikennellaceae. I found this on wikipedia, so you can see it’s a bacteriodete at least.

    Scientific classification
    Kingdom: Bacteria
    Phylum: Bacteroidetes
    Class: Bacteroidetes
    Order: Bacteroidales
    Family: Rikenellaceae


    Here’s a little thing i put together about the phyla, some from the AmGut handout and some from other places:

    Firmicutes (Latin: firmus, strong, and cutis, skin, referring to the cell wall) are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative. They have round cells, called cocci or rod-like forms. Many Firmicutes produce endospores, which can survive extreme conditions. Firmicutes make up the ‘compost pile’ in your guts–they love to eat plant matter, both inside and outside your body. It’s Firmicutes that give that pile of old leaves it’s wonderful smell and also the group that makes your expensive wine go sour. Some strains of Lactobacillus and other lactic acid bacteria ate Firmicutes and may possess potential therapeutic properties including anti-inflammatory and anti-cancer activities,They are found in various environments, and the group includes some notable pathogens–such as Antrax and Tetanus. This phylum generally makes up 20-75% of most people’s gut microbiome…it is a large phylum with hundreds of different genera. It’s also very diet, age, and geography related. Don’t worry too much about the size of your Firmicutes.

    Bacteroidetes is composed of three large classes of Gram-negative, nonsporeforming, anaerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments and seawater as well as in the guts and on the skin of animals. Members of the genus Bacteroides are opportunistic pathogens. Rarely are members of the other two classes pathogenic to humans. Bacteriodetes are the second major phylum in your gut. Don’t be surprised if they account for nearly half of all your microbes. These microbes are voracious eaters and will happily eat anything you give them, producing in return, gasses and smells galore. A well-nourished gut will be full of less noxious Bacteriodetes than a gut starved of it’s more preferred foods, such as plant fiber and resistant starches.

    Proteobacteria include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera. Carl Woese established this grouping in 1987, calling it informally the “purple bacteria and their relatives”. Because of the great diversity of forms found in this group, the Proteobacteria are named after Proteus, a Greek god of the sea capable of assuming many different shapes. If your report shows a relatively high percentage of Proteobacteria, it could be an indication that you need a diet overhaul or lifestyle changes (quit smoking, start exercising), these microbes are associated with inflammation, but they are not a death-sentence, in fact many of these type of gut bugs are necessary for producing certain chemicals used in digestion.

    Actinobacteria are a group of Gram-positive bacteria. They can be terrestrial or aquatic. Although understood primarily as soil bacteria, they might be more abundant in freshwaters. Actinobacteria is one of the dominant bacterial phyla. Actinobacteria are mainly all ‘good guys.’ These bacteria produce antibiotics and are excellent decomposers of plant matter. Bifidobacteria belong to this phylum and are some of the most sought-out microbes as they have been identified as “super-bugs” for human health.

    Verrucomicrobia is a recently described phylum of bacteria. This phylum contains only a few described species. The species identified have been isolated from freshwater and soil environments and human feces. Evidence suggests that verrucomicrobia are abundant within the environment, and important (especially to soil cultures). Though not very abundant, their presence indicates a well-balanced microflora. These may be more important to other microbes than to you. Excessive cleanliness and sterilizing every morsel you eat is a reason for a lack of Verrucomicrobia—playing in the mud and eating veggies that are a bit dirty is the best way to attract these gut bugs.

    Tenericutes lack a cell wall and therefore are Gram negative. Notable genera includes the Mycoplasma, Ureaplasma and Phytoplasma. These are found in very low number in gut microbiomes, but important nonetheless. They are found in the guts of most mammals and can be either completely harmless or extremely pathogenic–they have been implicated in pneumonia, bronchitis, and other respiratory illnesses.

    Cyanobacteria is a phylum of bacteria that obtain their energy through photosynthesis. The name “cyanobacteria” comes from the blue color of the bacteria. Not much is known about these and what they may or may not do for us. These bacteria are the most hardy in the world, being found in the world’s most extreme environments such as deep-sea sulfur vents and on the bare rocks of Antarctica.

    Fusobacteria is a rod-shaped Gram-negative bacteria. Found commonly in the intestines of all animals, some are good, some are bad. These will barely register on most people’s reports if at all.

    • Hi Tim! Thanks for commenting and sharing your bacteria summaries. It will be interesting to see how much of this information will still be “true” and how much will appear completely different as the research evolves. From one self-experimenter to another, it’s fun to share in the experiment. I wish you a healthy, blissful life.

  3. Thank you so much Eileen for this nice summary. So much to learn and so little is known at this time. It would be interesting to get the same test done twice a year for several years to see how it changes following diet modifications.

    • That would be interesting! A lot of the scientists on the project are doing multiple tests on themselves and their families, for exactly this reason. I look forward to seeing what they discover.

  4. I too eat Paleo to control my Rheumatoid Arthritis, and am symptom-free when I stick to it. About a year ago I started reintroducing starches (sweet potatoes mostly), and I’ve been supplementing with potato starch in kefir 2-3x a week for a few months. I haven’t had any RA flares associated with it… Hopefully you won’t either!

      • I am 33 and was diagnosed with RA a year ago. Iv declined any traditional treatment and am already experiencing deformities and very limited mobility. Almost ready to give in with meds. How severe is your ra? Have you ever used traditional treatment? How long did it take to experience releif on paleo? Sorry so many questions im hopeful to find an alternative to methotrexate. Thanks in advance! :)

        • Hi Anita. My onset of RA was severe, but I turned to diet immediately and was able to avoid the meds. However, if I were in your situation, I would start the meds and the diet simultaneously, seeing the meds as a temporary measure and trying to reduce them after 6 months to a year, after my body started to heal. That’s the path the leaders in the field suggest (like Dr. Terry Wahls.) Here are links to my story: part 1 and part 2, to give you a sense of my symptoms and the pace at which I improved after going on a healing diet. Everyone’s different, but this diet does help a lot of people. Gentle hugs to you.

  5. Eileen – great article! I found it very interesting. I’m particularly envious of your abundant Oxalobacteraceae. I have major issues with oxalates – I’ve had kidney stones 3 times, and I excrete over 3 times the normal amounts of oxalates in my urine. I’ve stopped eating spinach, beets, and Swiss chard as a result, and I really miss them! I don’t have the money to participate in the America Gut project right now, but maybe someday I can. I lean towards eating a wide variety of plants, and I do eat a lot of sweet potatoes for the carbs. I’m so glad they are doing this research. In some ways, it’s pretty similar to the fairly early-stage research being done on soil life and how critical all those various species are, especially to the health of the plants growing in it and the animals eating the plants. We seem to know more about moon rocks that we do about the life under our feet (or in our guts)! And I suspect there may be a closer relationship between healthy soil biome and health gut biome than we currently realize. Thanks again for this article.

    • I wish I could tell you why my oxalobacteraceae are so high, but it’s a mystery. They say our microbiomes are like fingerprints. I think we each have natural strengths and weaknesses in terms of beneficial bacteria, and then diet and lifestyle affect so much. Your comment is so insightful about the relationship between a healthy soil biome and healthy gut biome. They have certainly both deteriorated with modern agricultural practices. I know the scientists behind American Gut highly recommend getting outside and playing in the dirt, so your passion for gardening is beneficial to all 100% of you.

  6. Thanks for posting all of this and adding the other people’s results for comparison. Obviously all you have very different diets and not surprising that your gut flora are different, and none of you have major gut/digestive problems that you know of? I am interested to see results for people with clearly dysfunctional guts. It would be interesting to see the plots that show how you and your husband cluster with the other Western/Venezuela/Malawi samples.

    • When you say “clearly dysfunctional guts”, are you thinking of people with Crohns or Ulcerative Colitis? Hopefully someone with those diagnoses will post their results soon. Since over 6,000 people have participated in American Gut, and the numbers keep growing, I think we’ll see more and more reports. I would love it if American Gut does a subset study related to autoimmune disease in general – how our guts compare to the general population.

  7. Thank you for sharing this interesting article. I have my microbiome results back and am like your husband. In fact I have even more Akkermansia (33.7%). I also have long-standing digestive issues for 28 years that might be related to antibiotic use. I also suspected that too much of this is not good but have been thinking more about what it displaced or keeps it in check. I eat paleo now and that is helpful but still far from great. Perhaps we can help each other. Has your husband ever had his T cell subsets checked (CD4, CD8, NK)?

    • Wow, that’s fascinating. No, he’s never had his T cells tested. I’ll be writing a post in the future based on our starch experiments. It will take a few months probably for us to fully test how our bodies respond. At this point, we aren’t planning to do another American Gut sample, but just listen to our bodies. I’m hoping to stay painfree and be able to diversify my diet. My husband is hoping for improvement in digestion. Time will tell!

      • I asked about the T cells because low counts have been associated with translocation of microbial products across the gut wall. If he had that then our similarity would be even more significant. Can you say something about his digestive troubles? In a nutshell mine are of the IBS-C variety with a history of food intolerances.

          • Examination has shown that sometimes my mucus membranes dry up. Normally Akkermansia helps to regulate and thicken the mucus but perhaps as you suggested an overabundance may have the opposite effect. Dry membranes will certainly cause constipation. I am trying to get a more complete survey of my microbiome that might shed light on what might be missing. American Gut said they would post more detailed results soon but it still may not be sufficient. I do not have acid reflux and that seems to be a separate or indirect issue.

  8. This was surprising “healthy people have an average of 400 genetic defects, including ones for diseases they don’t have.” Wow! It will be interesting if they find more research and see if there is a common theme among those genetic defects… Thanks for sharing this at the hop! :)

  9. Eileen,

    This post is absolutely incredible. A while back I heard about The American Gut Project on NPR. I found it fascinating. Thank you for breaking everything down in such simple terms. You’re amazing.

    Sharing this week on AFW!


    P.S. That is so crazy about your husband and the 10 years of antibiotics. I’m not surprised though. On a personal note, they gave it out like candy in the 80s. I was constantly on a around of antibiotics. If my brother was sick (or sister) they would prescribe for us all. So sad and necessary!!!

    • Thanks, Amber! That’s wild that they used to give antibiotics to your whole family. I think antibiotics are still overprescribed, but clearly it’s much better than 30-50 years ago.

  10. This is fascinating. You are the first person who I have seen writing anything about this. I would love to get some of my family analyzed but it might have to wait for now. Thanks for sharing this at Healing With Food Friday. Sharing on my various social media.

  11. Jeff Leach is doing some fascinating self-experiments in 2014. Here’s a quote from a recent blog post:

    “Throughout 2014 I will undertake a series of dramatic shifts in my diet and lifestyle in attempt to whack my microbiome around. For example, 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 various 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 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.”

    He’ll share his results with scientists who study the microbiome, and also with the public. If you’re as fascinated by microbiome science as I am, I recommend subscribing to the Human Food Project’s email list:

  12. Completely fascinating!! Thanks so much for sharing at Wellness Wednesday! I hope that yeast mapping is their next project! It’s so hard to know if it’s a chronic issue for me or if there are other things going on. I eat low grain and sweeteners and definitely feel best this way, but is it yeast? Or just my make up, ya know?m This testing is tempting just to see how everything else in there is doing!

  13. Very interesting. Did this help you in any practical way? You say that this science is really in infancy as of now.

    I am actually considering participating. Do they recommend that we stop taking probiotics before taking the samples? I just started taking some probiotics.

    • There’s still much to learn about what constitutes a “healthy” microbiome, but I learned that my no-starch diet seemed to starve beneficial bacteria along with the harmful and so I’m testing reintrucing starches into my diet again. My husband learned that he has a high amount of a harmful bacteria, which motivates him to try to alter that as well. So, I would say we both gleaned some interesting information from it. If you choose to participate, I recommend taking a sample without changing anything in your current protocol, so you can get a snapshot of how your current diet (including probiotics) affects your microbiome. I learned for myself that very few of the probiotics I take in the form of fermented foods seem to be getting to my colon anyway. It’s interesting that eating foods that feed the bacteria that are already there seems to have a stronger effect than eating the bacteria themselves.

      • I am not eating any probiotic food like pickled/fermented vegetables now that I learned that vinegar is extreme salicylate, instead I was taking probiotic capsules with 5 strains and 10 billion CFU per capsule. But I just read here that “these ‘probiotics’ can temporarily provide some of the functions of gut flora, because they are bacteria, but they don’t grow in the gut.”

        So I am not sure if taking these capsules is part of my “current protocol” as you say, or I should stop them to get a better snapshot of what is in my gut now. Very interesting topic.

        • In an act of excellent timing, I received an advance copy of the Paleo Approach to review, and the author talks about the benefits of probiotics beyond changing the final composition of the gut. As they move through the digestive tract, they have anti-inflammatory and anti-microbial effects and also tighten the junctions of the intestinal wall, helping to heal leaky gut. So, it’s not an either/or situation. The best course for health would seem to be both consuming probiotics/fermented foods (as I have been), but also consuming foods like resistant starch that feed beneficial bacteria in the gut (which up until now I haven’t been doing). I learn new things all the time!

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