American (Gut) Gothic: 5 things you can do for a healthier microbiome in 2013

In the summer of 2008, a 26-year-old man from Shanxi Province walked into a lab at Shanghai Jiao Tong University, and 23 weeks later walked out 113 pounds lighter. He had not participated in a clinical trial of some new secret weight loss pill, or signed up for a punishing Biggest Loser-style exercise program, nor had he been fussed over by behavioral scientists who made his plates and drinking cups smaller with each passing week. The researchers, who were microbiologists, had simply put the man’s gut microbes on a diet.

americangothicOne of the huge mysteries in studies of diet and exercise is the difference between people who get the same treatment but have remarkably different outcomes. Inevitably, some people in a study show little improvement despite weeks or even months of following what might seem like draconian changes in their normal diet and lifestyle. Other people apparently drop weight just by getting out of bed in the morning, and also improve their circulating triglycerides, total cholesterol, and biomarkers of inflammation with apparent ease. We all know someone like this in our daily life.

But why are there such extreme differences between people?

Is our DNA to blame? Our human genes may be involved in some cases but we generally share more than 99% genetic similarity with other people; more interestingly, the huge differences in peoples weight gain/loss may be driven more by the different bacteria in our intestines, which can be more than 90% different between one person and the next.

In addition to the familiar human genome that we inherit from our moms and dads, each of us also has hundreds of trillions of microbial symbionts, each with their own genomes. Research programs such as the Human Microbiome Project have revolutionized our understanding of our microbial bodies, which outnumber our human cells ten to one, and account for more than 2 pounds of our body weight. We know microbes can change profoundly in each of us throughout life, and that we can change them through diet, medications we take, hygiene, etc. We know that how we enter this world – C-section versus vaginal birth – can impact your initial “seeding” of microbes, which further change during breast- or formula-feeding, and what you eat later in life also affects your gut microbes and even how healthy you are as a senior citizen. We know that people in more traditional societies have different microbes than those in more Westernized populations, and that diet can play a role in these differences. You can also change the health prospects of a mouse overnight by changing its diet and thus its microbes.

Advances in bioinformatics (fancy word for data analysis) and refinements of DNA techniques – not too mention a significant increase in computing power – is changing everything. The evidence that life events and diet can shape our gut microbes is increasing, but which direction should we nudge them? What is a healthy or optimal mix of gut microbes? The honest answer is nobody knows (yet), but projects are underway – that you can participate in – to help us to better understand the role bacteria play in our health and lifestyle.

In the meantime, as you contemplate your New Years resolution to join the gym (again), lose weight, improve your diet, or to purchase the latest gizmo to track your every move, you might want to consider whether your microbes will support your decision. After all, they’re in control. Take that you anthrocentric ape!

Below are five suggestions on how you might improve the health of your gut microbes (and some other microbes in your life) in 2013.

No. 5. Antibiotics. It’s a familiar story by now: over zealous use of antibiotics are driving antibiotic resistance among microbes at an alarming rate. But it gets worse: the average child in the developed world will likely receive 10-20 courses of antibiotics before his or her 18th birthday. This, coupled with the low therapeutic doses in animal feed – and ipso fact our feed, may be shifting our gut microbes into an unhealthy state and possibly contributing to the metabolic disease of obesity. It’s also well documented that following a course of broad-spectrum antibiotics, it could take weeks, months or even years for your gut microbial community to bounce back – or at all. During this period of imbalance, opportunistic pathogens can set up shop. Or worse. While antibiotics are clearly needed in some (probably most) scenarios, ask more questions in 2013 before downing them without a care.

No. 4. Open a window. For 99.99% of human history the outside was always part of the inside, and at no moment during our day were we ever really separated from nature. Today, a National Activity Survey found that between enclosed buildings and vehicles, modern humans spend a whopping 90% of their lives indoors. Though keeping the outside out does have its advantages – protection from the elements and decreasing your chances of being eaten by a zombie – it has also changed the microbiome of our home. Studies show that maybe opening window and increasing natural airflow will improve the diversity and health of the microbes in your home, which in turn benefit the inhabitants.  In the not-so-distant future, building codes will likely reflect the biological benefits of rewilding our living and workspaces. Never hurts to get a head start.

Forthcoming book by the folks at Human Food Project. Click Here if you would like to receive a notice when this book becomes available.

No. 3. Adopt an ecological perspective. In 2013 familiarize yourself with the writings of Aldo Leopold, John Muir, and other important and interesting – past and present – naturalists and ecologists. The human-microbial superorganism is a vast ecological system, subject to the same rules of resistance, resilience, and balance as any ecosystem on the planet. The sooner you learn to tend your microbial garden, the sooner you will understand how human ecology and your health is nothing more than understanding our history and place in the larger biosphere.

No. 2. Eat more plants. This is not a hard one. I don’t mean to give up meat, but I mean to eat a greater diversity and quantity of whole plants. This is the single most important (in my opinion) dietary strategy for improving the diversity and health of your gut microbiome. In short, your gut microbes thrive on a diversity of fermentable substrates (aka dietary fiber). But not all fiber is the same (physically or chemically), so consuming a diversity of whole plants will assure a steady flow of substrates for your resident microbes. And make 2013 the year you eat more of the whole plant, not just the soft and tasty parts. Consume the entire asparagus, not just the tip; consume the trunk of the broccoli, not just the crown; consume all of the greens at the top of the leek, not just the bulb. By doing so, you will guarantee that the harder-to-digest portions of the plant will extend the metabolic activity of your microbiome deep into your bowels. Also track how many species of plants you eat in a week – shoot for 30-40, or more.

No. 1. Get your hands dirty. More to the point: start a garden. Getting your hands dirty and covering more of your body (and food) with mother nature’s blanket will help you not only connect with the natural world we have tried so hard to remove ourselves, but will reacquaint your immune system with the trillions of microorganisms on the plants and in the soil. The loss of this interface with the terra firma of our evolutionary past – body to soil, body to nature – is where the wheels came off the wagon. As people of the world move from poverty to middle class, they also move from the gritty reality of our ancestral life to the promise of modern development and its triple-washed produce and squeaky-clean surroundings. Reconnecting with ecosystems, through gardening or some other ‘outside’ means, will allow you to understand and manage your inner-ecosystem. There is no better way.


*Joining the American Gut project might not be a bad idea either. Education and understanding does a body (and microbiome) good.

79 Comments Add yours

  1. Cate says:

    Thanks. : )

  2. Peter Kent says:

    Thanks, very useful.
    What about fermented foods, though; surely those are very beneficial for a healthier microbiome, right?

    1. Jeff Leach says:

      Absolutely. Tried to spread the ‘opinion’ around a bit (windows, gardening, food etc). Fermented foods would definitely be on anyone’s top 10!

      1. Ed Ozols says:

        Great! I’m going to try some fermented grapes right now.

        1. nadine says:

          Hi hi hi

  3. Do we have a figure yet of how many varieties of microbes are in the core human microbiome? Although there can, of course, be 1000s of varieties of microbes found in the soil, I believe researchers are saying that there is a core of only about 150 varieties in the plan mircrobiome, 150 varieties that are absolutely essential for providing the ‘enivronmental services’ that keep a plant healthy. I’m assuming the actual number of varieties we NEED in our gut are just as limited. (ie hundreds, not millions of varieties) What say (at this point) ?

    1. Jeff Leach says:

      possibly tens of thousands of strains – in soil and the human gut. since nobody knows (yet), its hard to say which services they provide. but the lab coats on it!

      1. Thanks for your quick reply, Jeff. It was my understanding from the paper published in Nature by Dr Jeff Dangl and cited below that the actual number of ‘bacteria’ in a plant’s microbiome was rather limited. Sure, there are thousands of varieties in the soils but the plant itself is only feeding and working with around 150 varieties (but the varieties may vary according to the stage of plant development and to environmental stresses) Here’s the citation

        Defining the core Arabidopsis thaliana root microbiome

        Derek S. Lundberg, Sarah L. Lebeis, Sur Herrera Paredes, Scott Yourstone, Jase Gehring, Stephanie Malfatti, Julien Tremblay, Anna Engelbrektson, Victor Kunin, Tijana Glavina del Rio, Robert C. Edgar, Thilo Eickhorst, Ruth E. Ley, Philip Hugenholtz, Susannah Green Tringe & Jeffery L. Dangl
        AffiliationsContributionsCorresponding author
        Nature 488, 86–90 (02 August 2012) doi:10.1038/nature11237
        Received 29 September 2011 Accepted 15 May 2012 Published online 01 August 2012

        I’d like to know how you read this information.


        1. Jeff Leach says:

          Thanks for the note. The paper you mention is a great one – but only deals with the rhizosphere (area around root)…
          Note in another paper: “The richness of the bacterial and archaeal communities ranged from <4,000 to >12,000 phylotypes per sample” See

          1. I think we are talking about different things. I was attempting to point out that the actual number of microbes (bacteria) in symbiosis with a plant are rather limited (150, rather than thousands) the study you pointed me to appears to be talking about the diversity of microbial communities in soil itself. There’s a lot of ways for a microbe to make a living in soil without directly supporting the health and well being of a living plant, hence the possibility of high diversity in soil itself while symbiots are much more limited. This becomes important, I would think, if the diversity of symbiotic bacteria in the human gut biome is relatively limited as well. Not looking to argue, Jeff, just trying to be clear. (BTW – I’m selecting ‘notify’ below my comments, my email address is correct, but I don’t get notification when you make replies or when there are new posts.)

          2. Jeff Leach says:

            yeah, i think we are. my bad. but note the strain diversity in the human gut not limited. at the moment, it’s falls in the black matter category. but individually – or collectively – these low abundant strains may be key. only time will tell.

        2. Derek Lundberg says:

          I am Derek from the Nature paper cited above. A friend pointed this blog out to me. First, I agree with all the healthy living suggestions! Would just caution about eating all parts of a plant that things like apple seeds contain a bit of cyanide, .. do a little homework before just chomping down every part of a plant! Don’t learn the hard way (once I was in Mexico and saw a whole cashew fruit, with the nut in the case at the bottom.. I cracked it open carelessly and just kind of bit without paying attention, not knowing cashew is related to poison ivy and the oil in the nut casing just as rash causing.. horrible face rash!).
          Regarding the discussion of our paper – I would like to comment that it is very tricky to say exactly how many types of bacteria are in an environment. For example, how many types of people are there? 7 billion? Or do we want to split it by gender and say there are 2 types of people? It’s complicated with bacteria too. So the ~150 number.. for this reason we must take that with a grain of salt. But Allan your point is right – the number of bacteria that comfortably live inside plants is smaller and more specific than all the stuff in the soil. A tiny bit of anything from the soil might make its way into roots through tiny cracks, but to live there in the plant, a bacteria needs some special skills which seriously limits the diversity of bacteria that thrive there. Likewise, many bacteria may make their way through the human gut and be found there (who knows what someone’s gonna eat!), but the bacteria that actually thrive there and perform a service to us is more limited. Finding the important bacteria, both in humans and plants, is definitely an active area of research.

          1. Jeff Leach says:

            Thanks for chiming in Derek – great points. Much of the point on ‘eating the whole plants’ focuses on getting more cellulose / hemicellulose / pectin etc in things like broccoli, leek, skins (when safe) etc – not seeds. I’m currently in east Africa collecting poo among the Hadzabe hunter-gatherers – longitudinal study of the impact of seasonal changes in resources on the gut microbiota. Its interesting to see the amazing diversity and variability on plant parts eaten.

    2. Glenn Atkisson says:

      Alan, I realize this discourse has already developed a bit along the line of varieties of microbes actually in some kind of reciprocal relationships with plant roots, etc.

      However, your first question, and I’m assuming the one most important to a human biome project, is “Do we have a figure yet of how many varieties of microbes are in the core human microbiome?” and here the key word is “core”.

      From my readings, “core” is not the best word or concept to be using with respect to the gut biome, as it implies the type relationship you are talking about in plants. But, again, just from my readings, I think the words that are used when delving into the importance of our gut microbiome, are more likely “dominant” species or genera, and “variety” of species or genera. And this I surmise is because in many studies what is looked at is NOT the actual substances that bacteria produce that are beneficial to the host such as fats and vitamins, but just the effect of the presence of the variety of species. These have effect on the immune system, and apparently the immune system is strengthened by having a large variety of species present in the gut, and the more change in low-count species, the better for the immune system.

      How this all works can be found in documents such as:


      Some of the findings of these papers are that there is actually more diversity in our gut microbiome than is indicated by simple fecal assay, and that the whole-body human immune system seems to always be enhanced by greater diversity in the number of microbiome speces.

      From these conclusions, I infer that dominant species are not so important, except that as they are supportive of our life, they should REMAIN dominant, and that the trace species are very important in that they function as an exercise laboratory for the immune system which is provided both by our Immunoglobulin, and also by the ability of our dominant bacterial species to remain dominant by being able to recognize the large contingent of minor-count species which are always trying to divide and grow their numbers.

      So by this analysis I come the conclusion that every single microbial species that can be introduced to the gut has some small advantage for us, as long as it isn’t introduced in such a massive load that it would become dominant and threaten life.

  4. Bonnie Nordby says:

    I think having pets that spends time both outdoors and indoors is probably a good way to improve ones microbiome too. Some of the research on improved health of infants and small children when a pet in the house points to this. Pets spending times outdoors close to the ground must track in lots of interesting microbes into our homes including our beds. And petting or being licked or occassionally directly kissed by a pet who licks all parts of their own anatomy must transfer many mouth and gut microbes. I am always impressed by how healthy my dogs who eat each others poop and our chickens and cats poop are too. It would be interesting to look at the difference in the microbiome of those with pets and/or who spend time with farm animals.

    1. Jeff Leach says:

      yes indeed. good points.

      1. May you elaborate about the triada health-biome-parasites. If we are getting our microbes from soil-food then plenty of viable eggs will find their way too. Is it that a healthy biome will keep them in check?

    2. Just remember Dogs only live 10-15 years…and are prone to parasites. They share those too. 😉

    3. Yes but look up Toxoplasmosa Gondii for a sobering view of what else animals can share… A parasite that up to 2/3 of the human population may harbor and which causes schizophrenia. I’ll take my microbiome from plants and fermented foods, thank you.

  5. Sherie Edenborn says:

    Excellent article! That you for citing the science. Scientist worked VERY hard to provide this evidence, so acknowledgement of our participation is really appreciated!

    1. Jeff Leach says:

      Thanks Sherie. Your pasture/organic farm soils research looks interesting.

  6. Just as a farmers products are the reflection of the quality of the soil, so are we a reflection of our inner soil. This is what I tried to express here

    1. Jeff Leach says:

      Thanks. will check it out.

      1. Jeff – I get the ‘impression’ that you favor feeding the biome appropriately as the way of developing effective gut function rather than continually ‘supplementing’ the gut flora with new microbes through probiotic fermented foods (such as kefir, yogurt, kimchi, natto, kraut, etc) While most natural health programs advocate for eating as much fermented food as possible, a few writers I’ve run across recently contend that microbes that come in with foods do not necessarily find a home in our guts but instead are seen as unwanted invaders by our established gut fauna, so more energy is used up as the gut tries to maintain ‘homeostasis’ (Your view appears to be that we build a diverse but community primarily by feeding the gut community well, not by adding as many microbes as we can to it.) Am I off base?

        1. Jeff Leach says:

          I think all the strategies are a good idea. however, some sources are more transient than others. i for whatever gets people thinking about their gut health – and the ecosystem that it is… 🙂

        2. Mike says:

          I was under the impression that fermenting foods plays two roles. Introduce a variety of microbes into our gut and to predigest the food to make nutrients more bio-available… aka simulating the mulch-chambered stomach of a ruminant.

          1. Jeff Leach says:

            i think you are right on both accounts. but perhaps the latter is a ‘tad’ overstated by some. but i’m not an expert of fermented foods.

  7. Ross says:

    “….The researchers, who were microbiologists, had simply put the man’s gut microbes on a diet….”

    Which microbes, which diet, and based on what underlying science, please? Citation requested if one is available.

      1. Ross says:

        Excellent, thanks.

        Asians are usually Type B blood, fwiw.

        I have tried to join the project (get the mails, etc.) but there was a bug (not the enterobacter kind) in ordering gut flora testing at the time. Can you recommend a best/fastest link to order this, and support the project (and get me a report on my gut flora?)

        Thanks for this work.

  8. heather says:

    interested in reading more about fermented foods – what they are, what role they play in gut health and recipes or sources

    1. Heather – Check out Sandor Katz’ THE ART of FERMENTATION or the Weston A Price Foundation site (approx url 😉 OR listen to Sandor Katz’ interview on….for starters (no pun!!) (btw Jeff, the ‘notify me’ is now working)

      1. Ross says:

        Allan — will we still be able to do shotgun genome sequencing after they take our microbe’s guns away? Food for thought. Enquiring minds want to know…..

    2. “Healing with Whole Foods”. Paul Pitchford. Recipes and wisdom.

  9. Martin says:

    I feel awkward promoting dirty hands in a business environment where everyday handshake is a norm.

  10. Heather says:

    Thank you Allan for your summay of Katz’ work… much appreciated and understood.
    I can easily swallow his findings (no pun intended – just makes good sense) the problem is I dont know where to start in preparing the fermented foods I can eat (I am dairy – not just lactose – intolerant, also grains & beans intolerant)…
    I know I can buy sauerkraut in the market – I might even be able to find some that is not pasteurized but can i prepare fermented foods myself – is there a “cookbook” or source of recipes? I would really like to try this… at present I am taking a probiotic (VSL#3 – 450 billion cells – 5 different species) and I’m thinking prebiotic fermented foods would boost its effectiveness… am I thinking along the right lines? so appreciate the wisdom here!

    1. Ross says:

      The Sandor Katz books are an excellent start for recipes — plenty of them. … Allan mentions (oddly, I don’t see his comment here, only in the alerter-email I got..) soaking for disabling certain toxins…I wonder if you, he or anyone else is aware of research on treatments that might disable lectins and agglutinins in wheat?

      1. Sorry, Ross, I don’t see any mention of agglutinins or lectins in Sandor’s newest book. I think wheat is to be avoided, at best. (Just my opinion.)

        1. Ross says:

          I meant to be clear I asked about research done elsewhere — Sandor’s work is to leverage “good bugs”, my question was more about how to disable troublesome proteins (like treating phytates, etc.)

          BTW, for you Sandor Katz fans — look him up. He’s all over the US this year, promoting his new book and giving lectures, workshops, etc. Busy schedule.

    2. Heather, check with Dr Paul Jaminet at He has some kimchi/kraut like ferments that are just vegetables put in salted water in quart bottles and then eaten in a few days (weeks?) very easy and full of benefits. Paul will answer questions for you about the process there. YOu s.b. able to find the basic ferment recipe through the ‘search’ panel and should be able to ask questions in the general discussion area. Another excellent source is any WAPF-related blog or the WAPF site itself. Sandor’s book is FULL of recipes, of course. 😉

      1. heather says:

        perfect – thanks… both sound like a good place to start… much appreciated, heather

    3. Body has pictures and step by step guides for making fermented vegetables and kefir with coconut water or milk if you prefer. The book also explains it all. The web sites sells the starter cultures for both kefir and cultured vegetables.

  11. Brian says:

    Great list, but you left off fermented foods and/or probiotic supplements. We want to populate the gut with “good” bacteria as we try to starve out the “bad” ones.

    1. Jeff Leach says:

      thanks. didn’t leave off – fermented foods go without saying and they say! wanted to highlight some ‘not so obvious’ things folks can do.

      1. bug says:

        So, Jeff, how ’bout those probiotics? Worth the money? Citations?

        1. Jeff Leach says:

          i don’t really follow probiotics – couldn’t tell you. though there is a growing consensus probiotics might be a tad over sold.

  12. justice4all says:

    Jeff – Have any studies been done showing the impact of pesticides on the number and diversity of microorganisms in the soil? If so, do you have anything you can report? It would be interesting to see just how much of an impact industrialized farming is having on biodiversity.

    1. Jeff Leach says:

      Not aware of any. Great question.

  13. Michelle says:

    I really like this article – but I wonder about eating 40 or more species of plant per week. I think about ancient people’s microbiota… I’m sure eating what they could grow would not have been 40 or more plant species per week, would it? Especially considering things like Kale, Cabbage, brussel sprouts and Broccoli (staples in our house and growing climate) are the same species. I’m all for eating a variety, but I think eating local is extremely important to sustainability.

  14. bradh says:

    Would it be possible to re-publish this on my blog?

    1. Jeff Leach says:

      what is your blog?

  15. Claudia K. says:

    “Avoid as many toxic metals, chemicals and GMOs as possible” would be a sixth point probably worthwhile making.
    Other living beings who never took antibiotics (directly) or changed their diets seemingly see their microbal world altered to a point of illness or extinction because of sudden fungal imbalance, decreased ability to fight viral infection, etc.
    This project is great, long overdue and will hopefully help leading us back to more respect for nature.

    1. Jeff Leach says:

      Thanks. This list could easily be expanding – but selected 5 not so obvious things (however, antibiotic overuse is pretty obvious)

    2. Avoiding Roundup Ready GMO foods as much as possible would be my 6th recommendation.

      Glyphosate treated plants include glyphosate in the food that results for human and animal consumption.

      Glyphosate is already shown to adversely affect the microbiota of chickens.

      Glyphosate is also suspected of adversely affecting the microbiota of cattle.

      Why would we expect human microbiota to not be similarly harmed?

  16. Hey, I did a little research on the diets of slum kids in Ethiopia. I don’t know about the kids your study was about but typically they get lots of sourdough breads. there are several different types popular in Ethiopia, each one if probiotic (something I can’t get my head around. Sour dough bread is pro biotic, even though it’s been baked) They also have fermented grain drinks, not alcoholic, which are probiotic. None of their cultured things are done with cultures, they are all ‘wild fermentation,’ which could account for seasonal diversity of microbial intake.

    Whaddaya think?

    1. Jeff Leach says:

      I’m pretty sure the high temps associated with bread baking terminate all of the bacteria in the sour dough bread – but I could be wrong. Some bacillus can survive the heating environment, but those are typically not used in traditional sour dough breads. But I could be wrong.

      1. I’m on the run right now or I’d dig up the references I ran across. One of the major assertions, and this was from food scientists not traditional foodies, was that bacteria may die from baking but many of their genes are still functional and are utilized by a certain class of lactic acid bacteria to modify their own genetics with these ‘spare parts’ and become an effective probiotic population very rapidly. I know, this, to me, challenges the whole concept of sterilization, but it appears to be a fact. I’ll send more info when I get a chance.

  17. Bug says:

    I may have a sixth thing to do. I wonder if drinking filtered water is another way in which we are sterilizing ourselves / our environment to our own detriment? What if all the bacteria that gets filtered out of our reverse osmosis water isn’t bad for us?

  18. Dan says:

    Great summary, Jeff. I follow a so-called paleo diet that avoids legumes and grains, and it works well for me. Aside from leafy greens, what other foods would survive the small intestine and feed the hungry bacteria in the large?

    1. Jeff Leach says:

      just eat as many whole plants that you can – a diversity of dietary fiber (and resistant starch) would be ideal. leafy greens have very little fiber.

  19. Elise says:

    What are your thoughts about “natural” fruit and vegetable washes that purport to remove waxes, chemicals and soil from produce? Most contain grapefruit seed extract as a primary active ingredient. Could using these sprays significantly decrease and/or negatively impact the flow of substrates from the whole plants we eat to the microbiome? Thanks for your time!

  20. mike wallace says:

    Meat (more so bones) contains GAGs–polysaccharides, also known as fiber.

  21. The microbiome is fascinating but one simple reason why people experience different effects from the same regime is biochemical individuality. ie we are not all the same. The low meat, low fat, high carb diet that is promoted as the ideal for everyone caused me weight, energy and health problems for years because my body needs a different mixture. Yes I juice wheat grass and sometimes make fermented veg but learning about my metabolic type is what transformed me.

  22. Tobey Vee says:

    Some people suggest eating some actual soil once in a while. Do you think this would be a good or bad idea (or are you unsure at this point)?

  23. Hi Jeff, I am trying for 30-40 different plants a week, but struggle with writing a list and actually being able to purchase that many here in the UK. It seems that this country hates veggies. Shoot!
    Do you have a tip on how to get to 100g fibre a day?

    Thank you.

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