Microbiome and Meat: Let the Silly Season Begin

I’ve been meaning to get this one out of the way. As the microbiome and the importance of our gut microflora composition begins to get more attention, it will become, as all things do, subject to preconceived notions and biases about health. And perhaps nothing is as preconceived and biased in the world of diet and health as the idea that intake of meat and its associated saturated fat are inherently unhealthy.

Case in point. A writer for The Guardian reports on having his gut bacteria sequenced and drops a couple of misconceptions that really need to be cleared up:

At the broadest level, the phylum level, my microbiota, in common with everyone else’s, was dominated by two types: firmicutes and bacteroidetes. The western diet, by which we tend to mean the North American diet, is high in fat and protein. In this diet bacteroidetes usually make up more than 55% of the gut microbiota, and sometimes, in North America itself, as much as 80%. In Europe, the average numbers vary from country to country. In my case I had 34%.


Again these were positive results. Lachnospira degrade pectins and ferment dietary fibres and I have three times more than typical. And bacteroides are often associated with meat-based, high-protein, high-fat diets, just as alistipes tend to be more present in people who eat less plant-based food. In sum that meant my gut – the lack of six-pack notwithstanding – was probably in good shape.


But by then he had managed to make a blind prediction of my diet that was uncannily accurate. He saw very little evidence of meat-eating – I haven’t eaten meat for 30 years.

Where to even start? The idea that specific colonic bacteria are enriched by meat and fat consumption is reflective of having missed a third grade lesson on anatomy. Meat and fat are, by and large, absorbed in the small intestine. Non-digestible carbohydrates — fiber — pass into the large intestine to be fermented by bacteria. In the context of diet, the composition of your microflora will be a reflection of the amount and type of fiber ingested.

Tell me how, exactly, one would see “evidence” of high or low meat consumption in this scenario. High meat and fat consumption and high plant consumption are not mutually exclusive. In fact, there is an entire diet devoted to this eating pattern. I forget the name.

To make it even clearer, I’ll once again highlight the evidence that I talked about in this post, showing what plant fiber — and plant fiber alone — can do to your gut microbiome:


Notice what doesn’t change in this experiment? Meat and fat consumption. Because it doesn’t matter. While it’s true that, on a personal level, your decision to eat meat and fat may lead you to eat less plants, that is a personal decision. And this may in fact explain the oft-cited correlation between high meat (red meat, specifically) intake and diseases like heart disease and colorectal cancer. In other words, “high meat & fat” may have really been “low fermentable plant fiber” all along. But again, these are not mutually exclusive eating patterns. Sure, at a certain point, meat and fat intake can begin to “crowd out” plant consumption to a level that is not optimal for gut health. But that is a far cry from saying that meat and fat themselves cause disease. Advice like that could lead one to cut meat and saturated fat out of one’s diet, and instead increase their intake of sugar, processed grains, and industrially-processed oils. Theoretically. Failure to make important, nuanced distinctions could, say, lead us down a 40-year road that results in no improvement in disease prevalence.


Of course, our diet-nutriton-health industrial complex can’t allow for such a nuanced idea. It’s all a one-or-the-other, good vs evil, science-illiterate holy war, isn’t it?

It’s the omnivore’s dilemma.

— Heisenbug

Update: An exchange in the comments led me to realize a further piece of evidence showing how useless it is to focus on meat & fat: the chart above shows that a high meat + fat + plant fiber diet produces MORE Firmicutes and LESS “meat & fat loving” Bacteroidetes than the author of the Guardian piece reports for himself. He reports 51% Firmicutes and 34% Bacteroidetes. From the chart above, it looks like high meat/fat/fiber produces around 75% Firmicutes, and less than 25% Bacteroidetes. I’m willing to bet that the Actinobacteria (good guys, Bifidobacteria) in that chart are much higher than in our intrepid reporter as well.


23 thoughts on “Microbiome and Meat: Let the Silly Season Begin

  1. Hmmm. This article, while it doesn’t make a great distinction between increasing meat consumption and decreasing fiber, does note that increasing meat consumption does increase bile production, and there are “bile-loving bacteria” that would increase.

    “…microbes that “love bile” — the Bilophila — started to dominate the volunteers’ guts during the animal-based diet. Bile helps the stomach digest fats. So people make more bile when their diet is rich in meat and dairy fats.”


    • My point exactly: what is notable about the “animal based diet” is not that it contains animal foods, but that it is devoid of plant fiber. As experiments testing this show, simply adding fiber reverses the effect.

  2. ‘Bile helps the stomach digest fats’

    Anatomy lesson required here. Bile enters the digestive tract at the duodenum, which is south of the stomach. You’ll only get bile into the stomach if you are very sick and vomit repeatedly when the stomach is empty. Bile does not belong in the stomach.

    Anyone who knows anything also knows that proper functioning of the gall bladder is important for good health. The gall bladder stores only as much bile as the liver produces. It is natural and necessary for the gall bladder to eject its contents on a regular basis.

    Bile enters via the common bile duct which is also the duct whereby pancreatic enzymes enter the GI tract. Blockage of the bile duct by infection or stones or sand will also result in pancreatitis.

    If certain bacterial type are encouraged to grow in the presence of bile, then this is right and correct. It does not mean these bacteria will over balance the other types of bacteria found in the colon from the digestion of plant fibres/resistant starch/fructo-oligosaccharides and so on. To each their own.

    Heisenbug, I caught the fallacy when I read this article earlier this week. Am glad you brought it to the attention of people. The author is one of those self stroking twits.

      • Yeah, lots of science and health reporters don’t know the basics. I canceled my Time magazine subscription after it was reported that malaria is caused by a virus. 😦
        That was the last straw.

    • Gabriella, first let’s not call people twits here.

      Second, your statement of “If certain bacterial type are encouraged to grow in the presence of bile, then this is right and correct. It does not mean these bacteria will over balance the other types of bacteria” is proven incorrect in the thousands of cases of biophila overgrowth in humans in documented literature.

      I’m not a meat hater – eat it regularly. And yet I read studies about overgrowth of various kinds of bad bacteria — because I have an open mind. Overgrowth does happen, not just from eating meat, of course, but it does. And it’s not “right and correct”.

      It must be nice to live in the idealistic place you live.

  3. MH and GK: I guess I’m still not clear. If meat increases bile production, then won’t that increase “bile-loving bacteria?” I’m not saying whether that’s good, bad, or indifferent. I thought MH said bacteria was ONLY affected by fiber. Doesn’t this say that meat consumption will increase said bacteria?

    • It isn’t that they love bile, it’s that they grow in an alkaline, less acidic environment. Bile makes your GI less acidic. But does it really make sense to cut off two out of three macronutrients out of your diet, in order to decrease bile production? Why on earth do our bodies produce bile, then? So yeah, eating meat & fat promotes alkalinity. So does eating nothing. Fiber fermentation, or the lack of it, is the relevant factor.

      • Bile is ejected when fat is detected.

        The liver produces a given amount of bile per 24 hours. This accumulates in the gall bladder until cholecystokinin stimulates it to squish it out. (Somatostatin keeps the muscle of the gall bladder ‘in shape’ so to speak.) Cholecystokinin is produced in response to the presence of fat.

        The protein portion of food begins to be digested and broken down in the stomach by acid and pepsin. It is further digested by the enzymes produced by the pancreas. Protein needs to be digested to a given extent before the stomach releases it to the rest of the digestive tract. Some proteins are more difficult to process than others, so they spend more time in the stomach. The stomach’s ability to selectively move various types of foods into the pylorus and then through the sphincter at the duodenum is amazing.

        Usually protein food sources also contain fat. So there is a nice harmony of activity on both the parts of the gall bladder and the pancreas. But if you down a shot glass of excellent olive oil, your gall bladder will respond.

        If you have ever vomited bile, you’ll know how utterly bitter and disgusting this is. (Actually Thai and Filipino cooking uses raw beef bile in a soup recipe. Just 1 tablespoon. And even that will make a pot of soup quite bitter. These people take the concept of nose to tail to extreme levels! Yeah, there are containers of frozen raw beef bile in the supermarket by me, right beside the containers of frozen pig blood. So it behooves the curious to find out what on earth it is used for.)

        Apparently it only takes about 5 to 10 grams of dietary fat per day to initiate gall bladder contraction. Coincidentally I checked this out earlier this week.

    • Also, take a look at the chart — a high meat + fat diet, with a lot of plant fiber, produces more “plant-loving” bacteria, and less “meat/fat-loving” bacteria, than the author of the Guardian piece reports for himself.

    • I think another, simpler way to put this is: what’s promoting the growth of those bacteria isn’t the presence of meat/fat, it’s the lack of plant fiber. If they devised a non-animal, low plant fiber diet, they would have found a similar result I’m betting. That’s why, again, experiments show the effect is reversed when plant fiber is added to an “animal based” diet. Why they didn’t have a third group consuming a mix, I do not know. Or a low fiber, non-animal diet. Or a fasting group. Those would have all been informative.

  4. I’ve recently read this article: Impact of diet in shaping microbiota revealed by comparative study in children from Europe and Central Africa. (http://www.pnas.org/content/107/33/14691.long)

    In this study, the African children on their traditional “Neolithic” type diet (mostly all plant) had higher Bacteroidetes compared to Italian children’s diet producing more Firmicutes. I realize this is in children, but I was struck by the high Bacteroidetes in the African children despite their plant diet. You may not have time, but if you do, would you maybe think about why this is the case and how this may relate to what this post and a few others touch on (Firmicutes high in diets high in plants.). The African children also had high short chain fatty acids compared to the Italians.

    I have an interest in butyrate as it applies to GI motility and intestinal permeability so I’ve started following along. Thank you for your articles.

    Take care. ~~Terri

    • Hi Terri. I’m familiar with the study — these African children consume a diet high in grains, which is known to lead to an abundance of Prevotella, a genus within the Bacteroidetes phylum. In people with Bacteroidetes predominance, it’s either Prevotella or Bacteroides that are the dominant genus. Again, grain consumption seems to lead to Prevotella dominance.

      As for the SCFAs, this is tricky. They seem to have determined SCFA production by looking at fecal SCFA. But from my understanding, this isn’t a particularly good way to measure actual SCFA production. Fecal SCFA is just a measure of how much is excreted. It just indicates absorption efficiency and transit time.

      However, if we are to accept that the African children do produce more SCFA, there’s a good explanation. Prevotella seem to be especially good at extracting energy from polysaccharides in whole grains. Given the lower overall energy density of the food that the African children are consuming compared to the EU children, it’s a necessary symbiotic adaptation. Not a huge surprise that they’d be producing more SCFA as a matter of necessity. Especially given that they are probably consuming a lot more fiber too.

      It’s unclear what other consequences (ie, downsides) there are to having an abundance of Prevotella. Studies show a strong connection between HIV infection and Prevotella abundance.


      • Since you brought up the HIV thing, Peter Piot http://en.wikipedia.org/wiki/Peter_Piot several years ago came up with a statement that healthy, well nourished people can be exposed to HIV and their immune system will fight it off.

        Basically in places where AIDs really takes off are where people have several things going against them: malnutrition, parasite load, poor living conditions.

        There are conditions which weaken the immune system and make it easy for HIV. (of course there are 4 different major strains of HIV, each with its own characteristics)

        So possibly the relatively low nutrient density of the diet in these Burkina Faso children (and the high prevotella) will make them more susceptible to the infection if exposed to the virus.

        It would be interesting to find studies on how various other viruses affect the intestinal microbiome, because they certainly do. And, remember all that stuff about vaccines and autism? Those allegations were directed at the thimerosol. Of course the clincher on disproving the thimerosol hypothesis was the Danish data.

        I wonder what impact the vaccines themselves have on the developing gut biome.

        Has anyone checked babies’ poo before and after the various vaccines they are given?

  5. Gabriella I thought it was mainly the mercury part of the thimerosal that was suspect. For the same token that the kids in Burkina Faso would be susceptible because of poor nutritional condition, wouldn’t it be reasonable to expect that kids here in good physical health, with no underlying low level inflammation etc. be able to fight off any kind of environmental assault?
    Thanks again MR Heisenbug for an interesting post. I think I am going to get Omnivore’s Dilemma back out of my library. Read up on my botany of desire 🙂

    • I’m just wondering. Autism is now being ‘diagnosed’ retroactively much earlier. There was a study done of younger siblings of autistic children. The brain studies indicated that growth and development were different in those that developed autism at only a few months of age.

      Autism is supposedly a genetic ‘propensity’. Sort of like celiac. You can have the genes but something has to happen to get the disease.

      Anything can potentially trip the immune system with celiac. An infection, an antibiotic, ? a vaccine…….?

      I’m wondering if the challenge to the immune system of anything, vaccine, virus infection, antibiotic can trip the genes in babies who then develop autism. The Danish study involved an entire population of children, half of whom were immunized, half were not. The incidence of autism was not different between the two populations. But that doesn’t mean there isn’t an environmental stimulus that triggers the genes which modify the brain growth and development.

      That’s my point. Perfectly healthy babies can get a bad cold (they do) and this can disrupt something and there you go: autism.

  6. Hi Mr. H., great post!
    I know I’m going off topic here, but I was wondering, if you are planning on inquiring into the effects of alcohol on the microbiome? From my personal experience, I’ve noticed that when drinking north of 3 servings of alcohol, my immune system tends to weaken. I notice that inflammation goes up (My teeth and gums become very sensitive, i start having mild aches on my hip and wrist), it really messes with my energy levels and I start having problems with bowel movements.
    You already found a great connection between gut bacteria and smoking, I was thinking that alcohol consumption, considering it’s so widespread, was another thing worth looking into :)! Cheers

    • Thanks, Wilbur. This very well COULD support the idea that it’s fiber that’s the factor. But unfortunately this study is the same old stuff — epidemiological data that doesn’t control for other lifestyle factors (among many other lifestyle factors) and draws speculative conclusions based on conventional wisdom. Too bad.

  7. I was doing some reading on Bacteroidetes and Firmicutes. Many articles have stated leaner individuals have higher proportion of Bacteroidetes than obese individuals. In one case, a mother took a fecal transplant from her daughter. Daughter who was fat had more Firmicutes. Mother then gained significant weight and became obese. Fasting increases Bacteroidetes according to one source.

    I would love to get one of these tests done; I have plenty of money. I don’t think my diet is very typical–lots of veggies (mostly greens and onions), meat, fat and a lot of dairy. I eat a lot of greens, onions, eggs, beef, pork, lamb, salmon, mussels, oysters, liver, butter, milk, cheese, kimchi, sauerkraut, avocados, yogurt, dark chocolate, etc. How do you think I would turn out?

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