An eaters guide to a healthy microbiome

“I have 15 cows, how many do you have?” Chief Jambiru asked me.

“How many cows do I have?” I thought. What an odd question. But I shouldn’t have that so, as I had just asked the Chief how many cows he owned.

Turning my bovine query back on me caught me a little off guard and it took me a moment to realize he was not poking fun at me, but seriously wanted know how many cows I owned.

“None at the moment,” I said.

So there we sat, in a dry, sandy creek bed high in the rugged mountains of northern Namibia near the Angola border, me cross-legged on one side of the crackling fire and the Chief in a deep squat perched effortlessly on a fist-sized stone on the other side, both thinking to ourselves how curious the other was. How could I not have any cows!

I was only the second white man the Chief had ever seen, according to our translator Ziggie. A few years back, the Chief had crossed paths with another white guy hiking in the mountains in search of what I gathered was exotic Aloe Vera plants. Though the translation was a little sketchy. I guess I shouldn’t have been surprised when Ziggie verified that a female colleague in our group was the first white woman the Chief had ever laid eyes on.

To be fair, the Chief and his three friends who also squatted effortlessly onto frighteningly small stones in the sand around the fire, along with the twenty or so other men, women and children in his dry-season camp located only a stones throw from our camp fire, were the first mountain Otjhimba I had ever met. It was a number of firsts all around.

Otjhimba kids.

As the evening went on and the Southern Cross appeared in the night sky, and the smell and sound of fresh meat – a gift from the Chief – sizzling atop hot rocks on the edge of the fire filled the cool night air, I began to wonder if we had found the people I had traveled 8,000 miles to the bottom of the world to find. Were these the Honey People of the mountains of northern Namibia – one of the last true remaining hunter-gatherer groups in all of southern Africa? The presence of cows, no matter how scrawny – and the distinctive “maaa” of goats in the distance – suggested no. True hunter-gatherers do not keep livestock.

Had globalization finally caught up with the Honey People, was I a few years too late, or were we in the wrong dry creek bed, on the wrong mountain, sharing meat with the wrong, though stunningly gracious, people?

I started to do the math. If I was only the second white man and the first was the Aloe Vera hunter, then these could not be the Honey People as I had learned of their whereabouts from a white South African who had spent several days with them back in 2006. That meant I should have been the third white man. Surely the Chief would have remembered white man number one.

My trek to the hills of northern Namibia and the meeting with the Chief took place this past summer. I was there because despite piles of peer-reviewed research and major research efforts such as the NIH’s massive Human Microbiome Project and similarly large efforts in Europe, we still do not have a good handle on what a ‘normal’ or ‘healthy’ gut microbiome looks like. And we may never know. It may be that our modern world of processed foods, antibiotics, fancy indoor plumbing and a wet wipe at every turn, may have forever altered our ancient gut inhabitants. (Remember your gut microbiome is all the microbes in your gut and their genes).

I thought about the Chief and why I had gone to Africa the other day while leaning against my shopping cart at our local grocery store – trying to decide what I should eat that night. More specifically, what should I feed my gut bugs. I spent a lot of time over the last few years pouring over every microbiome-related study showing how diet (and lifestyle) shift the composition of our gut microbiome. We know that most of us have more or less hundreds (if not a lot more) species of bacteria in our gut – some are permanent members who numbers go up and down and others are more transient (just passing through as they say).

Otjhimba women. The red body paint is ground up ocher with some animal fat.

There are countless studies showing that if you feed humans or mice either a low fat, high fiber, or All-American westernized diet, the composition of the bacteria shifts (some species/genus/phyla go up in number, some go down). These experiments reveal that you can start with one diet, check the composition of the bacteria using DNA techniques, then change the diet for a period of time, measure again, and then shift the diet back to the original (baseline), then analyze the bacteria at the end. Throughout this roller coaster of diet shifts (sound familiar?), the bacterial communities shift as well – depending on the study, the shifts occur at higher phylogenic levels (like shifts in the phyla Firmicutes and Bacteroidetes), but in some studies shifts at lower genus and species levels are apparent.

In either case, we can say with some level of certainty that dietary inputs shape the composition of our gut microbial community. But should we be worried that our gut microbial communities shift around as a function of what we eat and if so, which composition (or ‘state’ as the ecologists like to say), should we be aiming for? That is the million-dollar question.

We know that someone who takes antibiotics can dramatically shift their gut microbes. When this happens, the diversity of the gut microbial ‘ecosystem’ also declines. When diversity declines – among other things – the individual is susceptible to secondary infection. The most talked about secondary infection is by Clostridium difficile, or C. Diff for short. The scorched earth outcome of many broad-spectrum antibiotics is analogous to spraying poison all over your backyard plants and grass and waiting to see what grows back. In the case of your gut ecosystem – just like in your yard – invasive and maybe some not-so-good species (microbes in the case of your gut and some funky weeds in your yard) carve out a niche in the available gut/yard landscape.

From this perspective – gut microbial communities as ecosystems – the ecological principles of diversity and resilience start to help you think about how to fortify your gut against not only invaders that seek to do you harm (also think about E. Coli and others), but also about nurturing a diverse community within your gut that provides what ecologists call ‘ecosystem services.’ In the case of your gut bugs, the services they provide include harvesting energy from otherwise useless nutrients like dietary fiber, pathogen resistance through a number of mechanisms, synthesizing vitamins, assisting in the maintenance of the mucosal barrier that lines in the inside of your intestinal tract – which helps regulate immune response and reduce leaky gut – and the list goes on. In short, when your gut ecosystem shifts as a result of a perturbation – like an insult from an antibiotic, drug, or a shift in your diet maybe – then your equilibrium is out of balance and you tip towards an unstable state which may open you up to disease.

Cut and paste these coordinates ( -17 12 18.20, 12 59 16.62) into Google Earth, and you can zoom into the ‘general’ mountain area in northern Namibia where this group – and the Chief – live.

Some interesting studies in mice and humans have shown that a high fat diet can shift your gut microbes which in turn has the knock on effect of low-grade inflammation as measured by circulating levels (in your blood) of a plasma endotoxin known as lipopolysaccharide (LPS). LPS is the primary structural component of the outer membrane of Gram-negative bacteria found in the gut. So how can shifting your gut microbes cause an increase of LPS in your blood? Turns out, the high fat diet reduces (shifts) the levels of Bifidobacterium. These particular bacteria are known to produce short-chain fatty acids (butyrate, propionate and lactate) as a byproduct of fermenting things like dietary fiber. When their numbers go down – as with a high fat diet – the amount of short-chain fatty acids (SCFA) go down as well. These SCFAs are known to improve gut barrier function (think leaky gut) through a number of mechanisms.

So, in this ‘one example,’ if you change your diet (higher fat in this case) you reduce your SCFA production – which is an ecosystem service provided by your microbes – then your gut starts to leak and things that do not belong in your blood start showing up (LPS) and cause low-grade inflammation (the lab coats call it endotoxemia) which has been linked to insulin resistance, type 2 diabetes and obesity (click here for longer discussion on this). It’s interesting to note, that its not the fat per se that causes the Bifidobacterium to shift downward in abundance and thus cause a leaky gut, but the reduction of fermentable substrates. That’s is, you cut off the Bifido’s food supply and thus they slow down the SCFA production – which is prtective. As the famous Rajin Cajun James Carville might say, “It’s the Fiber stupid.”

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

So what should you eat to improve the diversity and possible resilience of your gut microbiome to reduce the risk to invading pathogens, unnecessary inflammation, leaky gut and so forth? Nobody really knows for sure and the answer is likely different for different age groups and populations. But at a minimum, you want that ecosystem service of SCFAs to keep churning along at high levels – so eat as many plants a week as you can (30-50 is a good number to shoot for – keep track and see how you do) – that is, keep the fiber (non-starch polysacchrides, resistant starch etc) flowing to your colon. And maybe cut back a bit on the easy to digest and hyper-cooked and processed foods – letting your stomach do a little extra-somatic work every now and then. Maybe even open a window every now and then, and for god’s sake, get your hands and food a little dirty. But if we ever hope to get a better handle on what a ‘normal’ or ‘healthy’ gut (or skin, oral etc for that matter) microbiome looks like, we will need to look at less westernized populations who are still undergoing the epidemiological transitions most of us have already undergone.

Getting a larger sample of westernized gut microbiomes is necessary as well and the reason we launched the American Gut project – to crowd source 10,000 gut microbiomes across the diversity that is the American Gut. And also the reason I was trekking in the mountains of northern Namibia. With detailed dietary and lifestyle data and the resulting microbiomes from the American Gut project, we will be able to see patterns not otherwise possible in smaller groups of people. By comparing this data set to more traditional societies – the microbial Noah’s Arks I like to think of them as – we might get a glimpse of how the process of village to urban life shifted and altered our ancient gut microbiome to its current – and very possibly –persistently perturbed state.

I will be headed back to that mountaintop in the next few months to see the Chief again, and explore a few new valleys and ridge tops in the hopes of locating these ghosts of our ancestral past. And hopefully they will agree to help.

51 Comments Add yours

  1. John Davies says:

    If the chief was surprised that you didn’t own any cows, what was his reaction when you explained what you were there to study?

    1. Jeff Leach says:

      Hah…. didn’t get that far!

  2. Suzanne says:

    I love this project. Just a question, though–has type of fat been studied for its effect on bifidobacterium? Are so-called “healthy fats” also implicated? I know, for example, that pasture-fed butter and ghee actually contains butyrate. Looking forward to the future when we might take free-dried capsules of fecal material from healthy people to replenish the guts of those affected by antibiotics, etc.

    1. Jeff Leach says:

      Good question – not completely sure and the moment. Will check on. But, as mentioned, and I don’t think the issue is the fat per se – but the reduction of fiber in the diet – ie, the food for the bacteria (ie substrates for fermentation). As for the fecal transplant. In the future, folks who go in for serious gut issues and invasive surgeries may be asked to ‘bank’ a stool (and freeze), so that after the procedure and possibly a coupe rounds of antibiotics they can ‘re seed’ their gut. This is in addition to ‘healthy donors’ – fascinating stuff.

    2. Suzanne-

      We certainly do not have to wait for capsules of freeze-dried poop in order to replenish our microbiota. There are countless variations of probiotic dietary supplements available right here, right now.

      Fecal transplants and the like are very interesting concepts, but we already have substantial evidence that prophylactic treatment of hospital patients with probiotic supplements is effective at prevention of C. diff infection.

      For example, a 2011 meta-analysis of prophylatic treatment of hospital patients with probiotics showed that administration of probiotics led to a risk reduction of 71% for Clostridium difficile-associated disease.

      Avadhani A, Miley H. (2011). Probiotics for prevention of antibiotic-associated diarrhea and Clostridium difficile-associated disease in hospitalized adults–a meta-analysis. J Am Acad Nurse Pract. 2011 Jun;23(6):269-74. DOI: 10.1111/j.1745-7599.2011.00617.x.

      1. Suzanne says:

        Thank you for taking the time to reply, Dr. Matthew. Good to know that probiotics have been found to be useful. The concerns that I’ve had with them has to do with the limited number of bacteria species available in probiotics when compared with the tremendous variety in the normal human gut. If replacing just a small amount of the variety is useful in preventing many C-Diff infections, then how much more effective might it be to have the full range of normal gut microbiome in the reestablishment of health for many disease states? We have much research to do to answer such questions and I am eager for such information. –Suzanne

  3. Excellent article: a very needed study!

  4. Jenny W says:

    Mice were fed a control (A04, Villemoisson sur Orge, France) or a high-fat,
    carbohydrate-free diet for 2 or 4 weeks following protocols. The diet contained
    72% fat (corn oil and lard), 28% protein, and 1% carbohydrate as
    energy content (17). They don’t split the lard and corn oil. This was an extremely high fat diet for mice, enough to render them obese and or diabetic in 4 weeks.

    1. Jeff Leach says:

      Yes, great comments… But the interesting finding is the presence of the LPS in serum. Not that fat makes you fat – but endotoxins cause inflammation and that gut permeability – at least in these ‘specifically-designed” studies – is linked to gut microbial composition. Also interesting to see:

      Cani, P. D., J. Amar, et al. (2007). “Metabolic Endotoxemia Initiates Obesity and Insulin Resistance.” Diabetes 56(7): 1761-1772.

      Cani, P. D., R. Bibiloni, et al. (2008). “Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet–Induced Obesity and Diabetes in Mice.” Diabetes 57(6): 1470-1481.

      Cani, P. D. (2012). “Crosstalk between the gut microbiota and the endocannabinoid system: impact on the gut barrier function and the adipose tissue.” Clinical Microbiology and Infection 18: 50-53.

      Deopurkar, R., H. Ghanim, et al. (2010). “Differential Effects of Cream, Glucose, and Orange Juice on Inflammation, Endotoxin, and the Expression of Toll-Like Receptor-4 and Suppressor of Cytokine Signaling-3.” Diabetes Care 33(5): 991-997.

      Laugerette, F., C. Vors, et al. (2011). “Complex links between dietary lipids, endogenous endotoxins and metabolic inflammation.” Biochimie 93(1): 39-45.

      Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, et al. Metabolic syn- drome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010; 328:228-31; PMID:20203013; ence.1179721.

      1. Denise says:

        I’m just so curious – (first off let me say I too love this project) – because the Amish don’t get diseases like diabetes at the same high levels as the rest of the population in America, and yet they eat full fat and higher fat diets. They also don’t eat the adulterated foods of the SAD – but I wonder – like the other post – is it the type of fat? Things like corn oil and raw butter to me seem polar opposites. And also, the quality of the foods that surround those fats seems to affect the outcome – hamburgers and processed foods around fat – versus – greens, healthy meats, veggies, some unrefined grains.

        1. Jeff Leach says:

          Thanks Denise. While the qty and type of fat matter in a lot of things – i think the point here – at least in these studies – is not about the fat, but the absence of substrates for the beneficial bacteria to grow on. ie, it’s their reduction or absence in the diet that shifts the microbiota to an unhealthy state not the presence or type of fat per se. but much left to learn.

  5. Superb article! Will forward within my network.
    In Health,
    Stella Metsovas B.S., CCN

  6. Rebecca says:

    I think it’s very important to keep in mind that it’s the reduction in fiber and not the fat per se. Many of these hunter-gatherer tribes prize animal fat and eat it in large amounts whenever it is available. I assume the many and varied fibrous plant materials that they forage balance this out.

  7. Kristen says:

    There are so many things that I dislike about this article.
    #1 the title is totally misleading. What are we supposed to eat? We still don’t know.
    #2 The study was done on RODENTS. When do rats eat a high fat diet? Why am I reading about rodent guts on the human food project blog?
    #3 If we were to follow this logic then Inuits would have completely disrupted guts. I am no scientist and even I know this.
    #4 All this speculation can be misleading.

    1. Jeff Leach says:

      thx kristen. valid points. you are correct, a microbiome eaters guide is not more valid than any eaters guide. we all still don’t know what to eat. the studies mentioned – and it was just an example of some dietary work (there are lots of others) – were also done on human subjects (see references above). good question on Inuits. would be interesting to see their microbiome. folks who follow an atkins-like diet might be an easier population to study – and somewhat analogous to your Inuit. hopefully we will get some atkins folks in our American Gut project. as for all this being speculation and misleading.. the point is to be honest and not definitive about the work. there are very absolutes in dietary advice when it comes to disease. that is, everyone wants their pony in the race to be causative, when most or just correlative. folks are just know beginning to understand the role of the microbiome in health and disease. but the writing is on the wall – should be an exciting and interesting next couple of years. as for your microbiome, the single best thing one can do is eat as many species of plants as you can in a week, stop worrying about fat and protein coming from animals (its OK), think twice about taking an antibiotic you might not need, get your hands and feet dirty from time-to-time, eat more dirt, open some windows and improve your home microbiome, get a dog and kiss them and their microbiome a little more often (the mouth end that is), and stop hyper-cooking food – let your stomach do a little of the work. but what do i know, i think Willie Nelson should be president.

      1. Kristen says:

        Love it! For the record the only horse I have in this race is a healthy gut. Now I’m going to go make out w/ my dog.

      2. Emily says:

        You mention atkins folks being possible analogous to inuit guts- I hesitate on this, because personally, I eat FAR more veggies (fermentable substrate) than I ever did on a SAD. To be fair, I’m “paleo”(ish), so I eat more g carbs/day than most atkins folk, but not by much. I do leafy greens, broccoli, and asparagus. That’s my primary veggie intake. (and I eat a lot). So even though my diet is very high fat (300%RDA of saturated fats, holla!), it is also very high in fermentable substrate.

    2. Janice Osborn says:

      Kristen, I too, was looking for a “list”. But then to learn that its th gut health in EVERY animal, e.g mice, humans etc. that influences the over all physical health, or at least cause or resistance to disease, was very enlightening and informative .

  8. Lori R says:

    I know in the comments I keep reading, it’s not the fat, per se”, but with the line “So, if you change your diet (higher fat in this case) you can reduce your SCFA production…”, or this line “Some interesting studies in mice and humans have shown that a high fat diet can shift your gut microbes which in turn has the knock on effect of low-grade inflammation as measured by circulating levels (in your blood) of a plasma endotoxin known as lipopolysaccharide (LPS).” in the article, it makes it difficult to keep the per se in mind. But I’m no scientist, and I’m not attacking. I’m just a lay person trying very hard to understand.
    I find it very interesting that even the info provided by Jenny M (above) lists the fat as corn oil and lard, and presumably this lard would come from pigs fed corn and soy. I think what I’m trying to point out is that there may be a differentiation between the aforementioned fat (corn and lard) and the fat that Rebecca is talking about, with hunter-gatherer tribes prizing large animal fat.
    So yes, I hear the Rajun Cajun, “It’s the fiber, stupid!” I would love for the studies to really pinpoint that it is the reduction of fiber that changes the gut bacteria. But how can someone utilize these studies when they have introduced a substance (being inflammatory, GMO’d, vegetable, non-pastured fat) that has not been controlled for in the study. Am I crazy? Maybe just stupid. Thanks Rajun Cajun:)

    1. Jeff Leach says:

      great comments lori. i think the thing to keep in mind is that these studies are not designed with normal chow, in the case of mice – but are so with human subjects. in other words, most folks who (and mice) would never follow such a diet. the researchers are using extreme diets to get the swings they after. however, in some cases they will dial down the ‘macro’ nutritient of concern (some of those references i listed above). the take home – in my opinion – is not focus on the type or quality of fat (or even the qty), but rather when you ‘remove’ fermentable substrates from the diet (in this case, that’s things like dietray fiber [non starch polysaccharides, resistant starch etc]), you remove a significant energy source from the bacteria. in these same studies, patrice cani (who is also on our American Gut team), held things like fat constant – that is, levels that were high and resulted in elevated levels in LPS in serum (ie leakey gut) – but then added in prebiotic fiber from chicory roots that elevated the levels of bifidobacterium (even in the presence of high fat diet) and the levels of LPS and thus the inflammation dropped. the point being the bifido bacteria are protective. as for you being crazy – we are all crazy 🙂 – great questions, keep them coming…

  9. Amanda says:

    A little off the topic but why do the Otjhimba women paint their bodies with ground up ocher and animal fat? Is it for sunscreen or fashion or something else? Do they do it every day?

    1. Jeff Leach says:

      Amanda – my understanding – and i could be wrong – is that the red ochre (and animal fat) are thought to keep the women clean.

      1. Eleanor Snyder says:

        so what DID you buy at the grocery store?

        1. Jeff Leach says:

          hah. good question. lots of whole plants, and various meats. avoided highly processed foods (we don’t eat much bread or pasta). nothing sugary (unless you count the 750ml bottle of jose cuervo!). onions, garlic and leek are of specific interests. frozen veggies.

          1. Emily says:

            I think we have similar diets! Sulferous veggies, leafy greens, aliums, and well-sourced meat? Are you paleo/primal and hiding it? 😉

          2. Leslie says:

            What is the impact of freezing vegetables on fiber?

            Dr. Robert Lustig (UCSF) has talked about the need for intact cellulose for it’s role in digestion, forming a lattice structure to hold soluble fiber, so 2 types of fiber work together. He compares the structure’s function to a plastic “hair catcher” in a drain.

            So, for example, he recommends whole grain European style bread rather than whole grain bread from ground grains or even whole grain pasta.

            The idea that if you grind whole grains, their insoluble fiber can’t perform its function.

            Doesn’t freezing vegetables break up the cells and disrupt the cellulose’s ability to form the structure, similar to grinding grain or juicing vegetables or fruit?


      2. PatrikD says:

        Interesting! Would be great to look at their skin microbiome, and how it differs with “unpainted” individuals (men? kids? young girls?) Should be a huge difference there.

  10. Sharon says:

    What type of fiber? Soluble, insoluble, or both? The benefits of soluble are derived mostly in the small intestine and the benefits of insoluble mostly in the large intestine. How similar or different do we want the gut flora to be in the small vs the large intestine?

    1. Jeff Leach says:

      Hi Sharon – I typically find that most discussions around soluble vs insoluble are driven by folks who are taking supplements etc. There is no need to consider the %’s of this vs that if you are eating a diversity of plants. It matters no more than your % of cellulose to hemicellulose etc. And yes, some fibers – depending on ‘degree of polymerization’ as the lab coats like to say – determines how rapidly and slowly (and thus proximal or distal in your gut) a substance is fermented – or if it all. However, I would say that our modern diet and cultural preferences have greatly reduced the amount of cellulose and other poorly fermented substrates in our diet. In other words, we usually don’t eat the butt end of the asparagus – too fibrous. But we should. This hard-to-chew-and-digest structural parts ‘extend’ bioactivity into the distal reaches of our gut. That is, because they are so poorly fermented, they literally last until the end! During this journey, the microbes are still chewing away and producing short chain fatty acids – which in turn promote intestinal health and reduce pH – all a good thing. At the end of the day, sky rocketing rates of colorectal cancer may have a lot to do with our reduction on poorly fermented fiber (ie, not enough distal activity). Or maybe it has nothing to do with it. But in any case, the microbial community plays a role in colorectal cancer etiology.

  11. Diane Smith says:

    Hi Jeff!
    I’m super-duper excited about your study!! All the old idioms..”It’s inside what counts”, “Listen to your gut”, and “The answers lie inside of us” are ALL going to take on a new meaning!
    🙂 YEP, you’re on it, Jeff! And I’m with you all the way with your work on this. I am currently working (volunteering) to change school food, and the first implementation was bringing in grass-fed beef! It is now on the menu in our entire school district, although only one day a week, but it’s a start! I’m all about educating people about what we need to eat, i.e. coconut oils, lard from grazing animals, grass-fed meats, fiberous veggies, and fermented foods, oh, the list goes on! Are you familiar with Weston A. Price? Surely you are as you are also studying isolated human groups to learn from them what it means to BE healthy and have a healthy gut!~ Bless you in your work, Jeff! This is the beginning of some very important work you are taking on, and I really want to be a part of it!
    A Kombucha Cheers to you!
    Diane Smith

    1. Janice Osborn says:

      AMEN to ALL of that Diane! A resounding, I SECOND!! Than you as well, Diane. YOU keep you the good, an very necessary work in the name of our kids.

  12. Gail says:

    I am glad that Diane brought up WAPF. You should study some of us! We follow a high fat, low carb diet, making sure that we eat unprocessed fats and that we process the grains we eat before we consume them so that they don’t interfere with our nutrient absorption! I will be interested to watch your findings on fat. Another concern I have is there is no mention, by you, of GMO’s and what microorganisms they are introducing into our guts. I think that they are wreaking way more havoc than anything else we are consuming (besides antibiotics) … Thanks for your study, it’s awesome being able to follow it.

    1. Jeff Leach says:

      Thanks Gail. As for GMOs, the issue that most freaks people out is ‘horizontal gene transfer’ (HGT) from the GMO food or critter. In short, HGT has been happerning throughout human evolution. That is, in the case of our gut microbiome and ots 3 million plus genes, the bcteria are swapping genes all the time – same goes for plants etc – see – so, for me at least, I’m not concerned about HGT – its who we are, one big shape shifting gene machine (at lest with our gut microbiome). As for GMO labeling, it’s a right-to-know issue. Even if we pass GMO labeling laws in the US – and I hope we do – the nonGMO foods (all foods) already possess HGT genes.

      1. PatrikD says:

        Definitely have to agree with Jeff on this one. From a scientific perspective, there is no reason to believe that eating a tomato that carries a fish gene is any more dangerous to your health than eating a fish-and-tomato meal. Or that the glyphosphate resistant enzyme used in “Roundup-Ready” strains is any more dangerous than the homologous glyphosphate sensitive protein found in all plant foods. I would be far more worried about the possible ecological and societal consequences of GMO’s, including the accumulation of the actual herbicides in the environment.

        1. Maureen says:

          I wouldn’t be so sure that eating a genetically engineered tomato whose DNA has been modified to carry fish DNA is the same as eating fish and tomato together. Plant microRNA act on human microRNA inside our cells. Our own microRNA combines with the microRNA of the foods we eat. When the two microRNA do not match up one can only imagine that we are not getting the nourishment that we would have otherwise gotten and who knows what effect it has on our genes. Genetically cross breeding species is an experiment unleashed on the both the human and animal populations without the scientific evidence to prove its safety. If you are not familiar with Seralini’s study on GMOs, I suggest you read about his results.

      2. I came across this study on the effects of glyphosate on poultry microbiota. Unfortunately, I don’t have access to the full text to evaluate it more thoroughly:

        Shehata AA, Schrödl W, Aldin AA, Hafez HM, Krüger M. The Effect of Glyphosate on Potential Pathogens and Beneficial Members of Poultry Microbiota In Vitro. Curr Microbiol. 2012 Dec 9. DOI: 10.1007/s00284-012-0277-2

        “The use of glyphosate modifies the environment which stresses the living microorganisms. The aim of the present study was to determine the real impact of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro. The presented results evidence that the highly pathogenic bacteria as Salmonella Entritidis, Salmonella Gallinarum, Salmonella Typhimurium, Clostridium perfringens and Clostridium botulinum are highly resistant to glyphosate. However, most of beneficial bacteria as Enterococcus faecalis, Enterococcus faecium, Bacillus badius, Bifidobacterium adolescentis and Lactobacillus spp. were found to be moderate to highly susceptible. Also Campylobacter spp. were found to be susceptible to glyphosate. A reduction of beneficial bacteria in the gastrointestinal tract microbiota by ingestion of glyphosate could disturb the normal gut bacterial community. Also, the toxicity of glyphosate to the most prevalent Enterococcus spp. could be a significant predisposing factor that is associated with the increase in C. botulinum-mediated diseases by suppressing the antagonistic effect of these bacteria on clostridia.”

        Personally, I’m much more concerned about glyphosate-resistant (Roundup-ready) crops than other forms of GMOs. Unfortunately, they all get lumped together in the media.

        At the end of the day, it’s buyer-beware when it comes to the food marketplace. History proves time and again that we cannot rely upon government agencies to keep the public safe from potential food hazards.

  13. CC says:

    As an off-and-on raw foodist for many years, may i respectfully recommend that you reconsider your basic language that less-cooked foods require more work from your digestive system…?

    I understand that you’re working off the knowledge that cooking breaks down some complex carbs, and generally renders things more rapidly assimilable, but describing raw foods in that way reinforces the mistaken impression that it’s true on an experiential level. Cooking certainly makes some things easier to digest (e.g. a potato) and in some foods can make available some nutrients that are otherwise unavailable (though i think it’s clear that this is the exception), but most raw foodists’ experience is that the overall “work” of digestion is much reduced when (appropriate) foods are not cooked. Indeed, one of the main propaganda points of the raw food advocates is the ease of digestion resulting in less energy required for it. Anyone that has eaten that way will attest that food leaves your stomach and goes through your GI tract faster. Even if the digestion is technically using “more work” from some limited chemistry perspective, it’s not the case on an overall human level, and describing raw foods in such terms doesn’t increase the odds that people are going to eat them. 🙂

    My armchair theory is that one reason many people associate raw foods with digestive trouble is indeed the microbiome… you eat something you never eat, you have a little gas or feel uncomfortable, and you assume it’s “hard to digest”. Since 99.9999% of Americans eat no raw meals, ever, it’s no surprise that this is the received wisdom. Eating salad a couple times a week is not sufficient research to know how your body handles raw food.

    Raw kale is about the most digestible thing I can imagine (and helps the digestion of other foods, not to mention being ridiculously healthy to eat), yet people are often surprised that you can eat it raw at all. Craziness. And I think this comes down to the spirit of your language that eating raw foods is somehow “toughing it” or giving your digestive system a “workout”… we really need to shake off that association! Call it what it is: giving your digestive system a “break”, letting it “take it easy”, etc. At the human level, I believe this is much more accurate and useful, even if somewhere in your ileum there’s an extra molecular step involved (and i’m kinda skeptical even on that level.)

    I’m excited to see what results the American Gut produces for raw foodists (if you can find more than 2 of them to sign up.)

    1. Jeff Leach says:

      Thanks for the comment(s) – good stuff. However, cooked food does require less digestion than raw – in general – but there are a handful of exceptions – but again, its a gnrl rule. Starches and carbs – as well as denaturation of proteins – is helped along with cooking. But I would add that our modern lifestyle cook foods a bit to much – which also goes to heart of the problem of an over processed food supply. For me, i think about these issues from an evolutionary and physiological perspective – its not a political or lifestyle issue for me – ie, not my wheelhouse of interest. Clearly we ate raw and cooked foods throughout history (only cooked once we figured out how to control fire on a regular basis). And the evidence that 1) cooked food was on the menu for a long time; 2) cooked foods are more easily digested; 3) cooked foods are preferred by most animals when given the choice over raw (lots of fascinating studies on this) and; 4) the easier digestion also equals greater energy and nutrietn harvesting from a given unit of food are all things that are covered by an extensive body of peer-reviewed literature. But people should be able to select how and what they eat – period. Yes, would be great to get a number of raw food folks in the American Gut study – I know a few have already signed up – the more the better – and the more interesting.

      1. CC says:

        Thanks for the reply. Re-reading your original post I see that I over-reacted, sorry. My comments weren’t an attempt to make an argument for Raw as a lifestyle, however sympathetic I may be. 🙂

        I’ll respond just because it’s an interesting subject: I was taking issue with the language describing the of eating raw foods as being “a workout” for the digestive system — while it may be true at the biochemical level (and I understand that this blog is all about that level, so, fair enough) it’s not the human-level experience of all of the raw foodists I’ve ever known or read about or heard about. (The skepticism re: digestion of cooked foods I mentioned above is my unscientific suspicion that the numbers would come out differently if you studied a raw foodist… and that such studies tend to focus on generalities like bioavailable calories and not overall health, etc., but again, that’s a different subject.)

        In my under-educated, unbid opinion, it goes back to the basic dialectic between civilized and wild… we have a cultural notion that raw foods are the province of nasty/brutal/short-lived animals that eat roughage and sleep in the rain, and cooked foods are better because they score higher for a couple of macronutrients (I’m setting aside the actual science here and talking about the cultural perception of the situation). White rice and white wheat flour fit most of your bullet points pretty well if compared to brown, yet characterizing brown rice as “challenging your body” or “giving your digestive system a workout” wouldn’t seem helpful or even particularly accurate on a human level, however true it may be in the gut… that was my only real quibble (and it was basically unwarranted, I now realize, having re-read your post). When we talk about such a food as brown rice in relation to white, we describe it in the more appropriate terms of “healthful”, “nurturing”, “more balanced”, “easier on your system”, etc. In other words, glucose pills would qualify terrifically for points 2 through 4, but that doesn’t mean we should cast real food in terms of deprivation. 🙂 All the unexperienced people I’ve made raw food dishes for are rather shocked that the meal isn’t an exercise in joyless bark-eating, and I think our habitual language that frames raw foods that way is responsible for this phenomena.

        There is something subversive in the recent microbiome interest, no? A gradual overturning of an order? As far as I can tell it is a needed wake-up call to the scientists of the world that long ignored the microbiome, sterilized it, etc. Given all that we’re still learning about digestion, it seems to me that we should expand that circle of humility to include other long-standing assumptions we hold. I’m sure that as scientists you are all professionally open to those possibilities, and I trust that you wouldn’t let bullet points 1-4 alone constitute a sufficient argument for eating cooked vs raw, since, true though they may well be, they are the same type of generalities that helped lead us to be over-paranoid about infectious germs, avoid breastfeeding, overuse c-sections, or ignore our gut biome. We’ve overturned a lot of those perspectives, to varying degrees. It’ll be interesting to see if the cooking of nearly all our food is ever seriously called into question as well.

        I’d be interested in references for point 3), above. Any handy?


  14. Diane Smith says:

    Thanks for this, Dr. Matthew! No need for the full text, the first line said it all, and the rest supported this finding. GMO’s ARE the ‘lead cups’ of yesteryear. This study of Jeff’s will blow the lid off conventional medicine! I agree that it’s the Round-up Ready crops that are the most damaging to our human microbiome, but any and all GMO’s must be stopped…the latest is GMO Salmon which the FDA is considering for approval. All of us can put in our 2 cents about this creepy practice if you log on to The Institute for Responsibile Technology and let the FDA know what you think of their ‘franken fish’.
    Anyway, thanks to all who are contributing to this extremely important microbiome work! Our kids’ generation is counting on us to find the answers for so much of what ails us today, and find them we WILL!

    1. I agree these investigations into the gut microbiome will blow the lid off of conventional medicine. In a way- they already have only most practitioners have their noses buried too deep in their respective specialties to notice, and as for the institutions, well they are notoriously slow to change.

      No plans to be eating any “Frankenfish” here. Just saying that oversimplification of these kinds of issues by the public makes it all too easy for the food/medical establishment to “strawman” their way into ignoring public outcry.

      The problem with making public appeals to agencies like the FDA is that they tend to respond to the most vocal opposition rather than the more well-articulated views. We see a similar thing with the CAM arm of the NIH. IMO- they spend too much of their research money investigating claims that never had much weight behind them in the first place- except for that they somehow took hold in the mass consciousness, and so are the most in their face.

  15. Tatjana says:

    Hi, i know how odd this may sound…I have a lot of pets and have found that vets have all the info before ‘human’ doctors have them. That is because most pet owners want something that works and will try even outlandish suggestions, because they dont have to explain it to the patient, or justify it in front of a ‘family’, neighbors etc. So when my guinea pig had serious issues with diarrhea, the best solution we came up with is to syringe-feed him a solution of feces from his healthy brothers. It seems natural that we should be able to locate people with a predominantly good gut flora and do fecal transplants, probably through the lower end of our plumbing, through an enema. Considering that both autism and diabetes are linked to gut bacteria not functioning, I can freely say that the work on these questions is the most important medical work done right now, in my opinion.

  16. Sharon Downes says:

    Love this project. Has anyone tried selecting for resistance to certain common antibiotics in “good” bacteria so that if/when it is necessary to take antibiotics they only kill the “bad” bacteria?

  17. Kerin Norris says:

    I have many questions…
    Do we acquire microbes from the fruit and vege or do we need to have the microbes already there to be fed by the fiber.
    And if we acquire the microbiome from veggies and fruit do they have any specifics to live properly?
    We live in a western society, I nutri bullet my juices, does over blitzing kill anything or is it all good because its full of fiber?
    Does microwaving meals cause any problems (if not overly cooked)
    What about freezing and how about fridge left overs.
    I have read that probiotics in tablets don’t colonize they just stay for a visit and leave, if this is correct is there anyway to help them colonize?
    Really trying to get my head clear of what I need to be doing to create the best gut that I am able to.
    Many thanks for your article, looking forward to finding the follow up studies.

  18. Alice says:

    Hello Jeff, I live in the UK and am attempting to learn more about the links between gut biome, stomach problems, allergies and depression (suffer all three). I’d love to find a doctor or researcher or organisation over on this side of the pond who is respected at the front of research. Would you have any leads of where I might start? I particularly hope to find someone to help guide me through healing my stomach by supporting me adjust my biome and diet.
    Thank you in advance.

  19. Diane says:

    Hi Alice,
    Give Dr. Natasha Campbell McBride a try, here is her website:
    She understands all about our gut and how to heal it so we heal!
    There is a book in that link I highly recommend reading, so look around on the site.
    Best to you,

  20. Diane says:

    ALSO, the best foundation bar none is The Weston A. Price Foundation.
    Dr. Natasha has been a key speaker for this foundation, and there is an incredible amount of information that is spot on for what to eat, what to NOT eat, and how to nourish yourself and your family.

  21. Sarah says:

    Hi! Not sure if you will be reading/replying to these comments, but I have a question about the overall project. As far as I can tell, you are mostly looking at percentages of different types of bacteria, not total quantities. (For example, I could have a healthy level of diversity, but a small quantity that prevents sufficient production of SCFA, etc.)

    The reason I got started on this question was that I recently had some testing done through my integrative doctor that says I have low SCFA, so I should eat more fiber and take probiotics. (On the probiotics front, I am currently experimenting with SBOs.) I am also upping my prebiotic fiber intake both through food and Biotogen. However, it seems unclear to me how much low SCFA in the stool would be related to production and how much would be related to absorption–if someone had increased absorption of SCFA in the colon leading to lowered excretion, for example.

Leave a Reply