Guts, Germs and Meals: what 37 microbiologist say about diet

Earlier this year (in 2012), U.S. News & World Report  reported its second annual list of the Best Diets, as ranked by a panel of  “22 nationally recognized experts in diet, nutrition, obesity, food psychology, diabetes, and heart disease.” The expert panel evaluated 28 diets including the well known Atkins, South Beach Diet, Biggest Loser Diet, and Paleo Diet, and the not so well-known Medifast and Cookie diets.

On a sliding scale of 1 to 5, the expert panel rated each diet on ability to “produce short-term and long-term weight loss, its nutritional completeness, its safety, and its potential for preventing and managing diabetes and heart disease.” While the Ornish Diet came out on top for best heart-healthy diet and Weight Watchers got the nod for best weight-loss, the DASH diet, which stands for Dietary Approaches to Stop Hypertension, took home the gold. Much to the dismay of its growing legions of supporters, the Paleo Diet was not popular among the panel experts, coming in at the back of the pack (see how it favored in questions 9 and 10 below).

The U.S. News & World Report Best Diets report got a lot of play in the media, and judging by the thousands who commented in a YES or NO to liking a particular diet on the list, the public is paying attention. The overall winner, the DASH diet, is built on the theory that a low-fat, low sodium strategy with a hint towards calorie restriction, is the healthiest way to go. But is it?

Given the avalanche of peer-reviewed studies linking the human microbiome (all our microbes and their genes) to everything from obesity, type 2 diabetes, heart disease, some cancers, autoimmune diseases, IBD – and the list goes on – it might be interesting to get the opinion of microbiologist of what might constitute a healthier dietary strategy, but from the view of the microbiome.

What if many of our acute and chronic diseases are an imbalance with the microbial world? While it’s a big what if, the 16 papers recently published as part of the Human Microbiome Project – not to mention hundreds of other papers published in the last few years alone – suggest that we need to start rethinking what makes us sick. Given what might be the proverbial writing on the wall, it’s probably not much of a stretch to suggest that dietary and lifestyle advice, which currently comes from a physicians, general practitioners and registered dietitians, will likely come from a microbiologist or related specialist working with the microbiome in the very near future. Or at a minimum, we are going to see GPs and RDs with increased training in “medical ecology” and evolutionary principles.

So with this in mind, I created a dietary questionnaire (below) and sent it to microbiologists who work with diet, disease, metabolism and so on in the context of the microbiome. Some of the researchers I knew, most I did not. And many opted not to participate. In some instances its frowned upon by institutions for their researchers to participate in such surveys. (For those that did, and could, its much appreciated). It is also acknowledged that some of the questions in the survey minimize the complexity of the interactions that are at play in linking the microbiome to a condition of interest – and that much of our understanding of the role of the microbiome in human disease is preliminary. There was no way around that while trying to keep the questions and answers understandable to a general audience. Its also acknowledged, that while the possibilities associated with changing or altering the microbiome for better health is within reach for some ailments, nobody wants to take the cake out of the oven too soon. So the scientists working in the field are optimistically cautious about their work.

Unlike some of the experts in the U.S. News & World Report survey, I don’t think many of the microbiologists have a horse in the race so to speak. They are interested in the microbiome and its modulation and impact on its host (you and me). Not a particular or popular diet or philosophy. This, of course, may be naive and short coming of the results presented here. But nevertheless, the microbiologist were all asked to consider the questions and their answers in the context of the microbiome without regard to a “named or labeled” diet plan. For this reason the questions were not about a specific diet plan, as was done in the U.S. News & World Report survey, but more “indirect” questions.

Below are the results from 37 microbiologists who had responded within 24 hours of sending out the survey. It includes researchers from all over the world from major research universities and organizations. Note the respondents were anonymous as I did not want them to receive a bunch of emails from individuals who may not have agreed with their answers. Again, another short coming of the survey, but it is what it is. The survey was limited to 10 questions in all (with several sub questions within questions). Without a doubt, more questions could have been asked and the questions asked could have all been worded differently – so shoot holes in it if you must.

The questions and the average answer on the sliding scale is provided. Brief comments are provided after each question and a take home summary is provided at the end. We would love to get your feed back on this and please share these results with others.


Q1. Does diet play a role in shaping the human gut microbiome?
(1 = strongly disagree and 10 = strongly agree)
Results: 8.9

The question was pretty straightforward and an average answer of 8.9 is consistent with the research that diet modulates gut microbiome composition. Some of the research can be found here, here, here, here, here – you get the idea.

Q2. Do you believe increasing diversity within the gut microbiome is important?
(1 = strongly disagree and 10 = strongly agree)
Results 7.4

The concept of diversity is best understood from an ecological perspective. Since our gut microbiome is an “inner ecosystem,” made up of thousands of species, increased species diversity within the microbiome is emerging as an indicator of potentially positive diet and lifestyle choices – and a hallmark of our evolutionary past. Click here, here, and here, and for general overviews of the concept.

Q3. Do you believe our ancestors had a more diverse inner ecosystem?
(1 = strongly disagree and 10 = strongly agree)
Results 6.4

Given the lifestyle of our ancestors it is hypothesized – though data is lacking – that our ancestral life exposed us to a greater diversity of micro organisms on a daily basis. This, coupled with the lack of antibiotics, which is known to impact diversity in our modern microbiome, suggests that our ancestral microbiome may have been characterized by greater diversity. Again, maybe. Future research is needed.

Q4. Do the following play a role in shaping the human gut microbiome? Sorry for the long list.
(1 = strongly disagree and 10 = strongly agree)

There were several sub questions in this question. Questions were:
Birthing method (c-section vs vaginal): Results 8.3
Length of breast-feeding (months, years): Results 8.0
Early childhood exposure to antibiotics: Results 9.3
Lifetime exposure to antibiotics (all sources): Results 9.2
(Hygiene) Lifetime exposure to animals, soil, etc: Results 9.1
Sodium in diet: Results 3.6
Taking vitamin supplements: Results 3.5
Organic vs conventionally grown vegetables: Results 4.7
Organic vs conventionally raised meat: Results 3.4

Mounting evidence suggests that how you enter this world (c-section vs vaginal) and whether or not you are breast-fed, and for how long, may have short and long-term effects on the composition of your microbiome. However, as one of the survey respondents indicated in a comments section, the long-term effects into adult life is “completely unknown.” Additional, long-term studies are needed. The idea that early childhood and lifetime exposure to antibiotics from medicine and our food supply is receiving a considerable amount of research attention – given that disruption of the microbiome by antibiotics is well documented. It’s long-term role in things such as obesity are currently being considered.  It’s clear from the low scores for sodium and vitamin intake, and whether or not you consume organic or conventionally grown foods, the survey respondents do not think that any of these has much of an impact on your gut microbiome.

Q5. Although accessibility by various bacterial groups will vary, do you believe in general that dietary fiber and resistant starch are beneficial for the microbiome?
(1 = strongly disagree and 10 = strongly agree)
Results 8.5

It is widely accepted that dietary fiber and resistant starch serve as substrates for bacteria growth in the large bowel (colon). Increasing the delivery of substrates to the residing bacteria results in greater short chain fatty acid production (SCFA) and reduction in colonic pH – both of which are desirable. And if those substrates include special dietary fiber known as prebiotics, it may also improve gut barrier function.

Q6. Do you believe the current USDA’s Dietary Guidelines for Americans were compiled with a clear understanding of the impact of dietary choices on the microbiome?
(1= Probably not, 10= Yes)
Results 1.3

A quick review of the panel of experts assembled to update the 2005 Dietary Guidelines for Americans to the current 2010 guidelines (myPlate), reveals a diverse group of distinguished researchers within their respective fields. But the omission of researchers who work with the gut microbiome is unfortunate. And unless I missed it, neither the 2010 dietary guidelines or the accompanying 1,375-page report from the Institute of the Office of Medicine, contain the word microbiome anywhere in the text. The respondents to this survey do not think much consideration was given to the microbiome either. Maybe next time.

Q7. Based on current research – and what research may reveal in the future – do you believe the microbiome may play a role in the following disease/condition?
(1 = strongly disagree and 10 = strongly agree)

There were several sub questions in this question. Questions were:
Colon cancer: Results 9.4
Obesity: Results 8.6
Type 2 diabetes: Results 8.6
Heart Disease: Results 8.3
IBD: Results 9.4
Autoimmune disease in general: Results 8.3
Metabolic diseases in general: Results 9.1
Select other cancers in general: Results 7.8
Autism: Results 5.3
Other cognitive disorders in general: Results 6.2
Gut permeability and systemic inflammation: Results 9.3

The results above were somewhat expected. You can Google the disease + microbiome and access published research associated with each. There are lots of it. For some, like obesity, the role of the gut microbiome is well-established, but much work remains to be done. For others, like Autism, there are only tantalizing hints that our gut bugs may play a role. With each, an underlying genetic susceptibility is required and then an environmental trigger. More often than not, that environmental trigger is diet related. What should be of great interest is the general consensus that is forming around the role of the microbiome and gut permeability – or leaky gut. Once an imbalance (dysbiosis) occurs, be it from diet, antibiotics or so on, a chain reaction occurs and things leak into the bloodstream which can lead to low-grade inflammation associated with obesity, type 2 diabetes and some other less desirable things. One condition that was inadvertently left off the list was the autoimmune disorder Celiac disease. Mounting research is linking the gut microbiome with the timing and onset of this debilitating disease.

Q8. General diet related questions.
(1= I have no idea, 10= strongly agree)

Would low GI foods be preferable?: Results 5.6
Would a raw food diet be less desirable: Results 4.6
Is a calorie a calorie? Or, is dietary quality more important than qty? Results: 7.5
Does source of protein matter (plant vs animal)? Results: 6.6

As a general rule – again, general – someone who follows are low glycemic diet (low GI), they will be consuming more “whole foods.” Translation: more minimally processed plants. Again, in theory, this would raise the amount of naturally occurring dietary fiber in the diet. This was a round about way of asking “nearly” same question I posed in Q5 above, which got an 8.5 average response apposed the 5.6 here.  Seems the raw food diet is not considered a big deal when it comes to the microbiome. May have something to do with the idea that cooking increases the energy density of the foot item and also cleaves the structure of the plants in such a way that make more of the material available for fermentation (i.e., less may pass out the other end). I threw in the calorie is a calorie question in light of the recent study published in the Journal of the American Medical Association that not all calories are created equal. As I was told, the “does the source of the protein matter” question could have probably been worded differently. I can only assume what the respondents thought I was getting at – so the 6.6 is middle of the road to slight agree, but for what I’m not sure. Maybe that plant protein is more interesting as it comes in a package that also delivers some fermentable substrates (fiber) along with it.

Q9. Do you believe a better understanding of the nutritional landscape (and lifestyle) of our ancestors (and remote, traditional communities today) may provide insight into the conditions that selected for our current human-associated microbiome?
(1= strongly disagree, 10= strongly agree)
Results 9.1

A recent study published in the journal Nature comparing the gut microbiome of U.S. citizens to individuals living in Malawi and the Amazonas of Venezuela, reveal differences. This study, and others among less westernized populations, suggest that our modern world and its highly processed diet may be changing our microbiome as well. But the jury is still out on whether its changing for the better or worse. The latter is more likely. Therefore, it may be prudent to better understand the nutritional and ecological landscape that selected for our modern human-associated microbiome.

Q10. Do you believe a high protein-fat diet, so long as it includes a significant amount and diversity of whole plants (fermentation sources) and minimal to no processed carbohydrates, is a strategy for a healthy microbiome?
(1= strongly disagree, 10= strongly agree)
Results 9.1

I threw this question in due the whippin’ that the Paleo Diet got in the U.S. News & World Report survey. The experts ranked it 24th overall. The theory behind the Paleo diet is simple: if our ancestors ate it, you should eat it. If they didn’t, you shouldn’t either. This means things like grains and dairy are out, and lots of meat and fruits and veggies are in. Even though the data suggest otherwise, some continue to be concerned that the high fat intake may have deleterious effects. In addition, the adherence does not seem to be an issue for the multitudes now following the paleo lifestyle. While the fat issue may be of concern when it comes to leaky gut and associated inflammation, it’s not when that diet includes a significant quantity and diversity of plants – which the diet proponents advocate. At an average score of 9.1, the Paleo Diet is line with a healthy microbiome.


In summary, I paraphrase Michale Pollan: Eat dirt, not too much, mainly with plants (and meat is ok, even with a little fat on it).

*I wish I could claim credit for coming up with Guts, Germs, and Meals – but I cannot. I borrowed it from an excellent article written about the association of gut bugs and type 1 diabetes (definitively worth reading).


23 Comments Add yours

  1. jerry curtis says:

    Very interesting Jeff. As a side note, I would like to see more independent, non biased ( funded by special interest entities),research on the impact of processed foods on humans. To me it seems logicial to think that the addition of hormones,antibiotics and a myriad of adulterants, would have a negative impact on us. The other issue related to this that should be of concern is genetically modified plants. the potential effects on biodiversity could be catastrophic. I would like to see mors support and awareness of seed banks, we may need them in the future. your friend Jerry Curtis, keep up the good work.

    1. Ryan says:

      Indeed, GMOs must be considered when talking microbiome. I’ve read a number or articles recently, not sure if based on peer-reviewed studies, that genetically modified organisms can alter the DNA of our gut flora. Not cool.

      1. thanks ryan. not aware of any studies with GMO foods and microbiome. however, not sure what the impact would be… if any. but…

    2. thanks jerry. good thoughts. jury still out on GMO. next few yrs will tell.

  2. vordo says:

    I recently read about a study that really looks at the relative value of a different types of calories effect upon diet and weight gain. paleo seems to well in this study except for the infamitory nature of high protein/high fat. a low glycemic diet seems to fair the best in the long run.

    1. yes, that was the JAMA study by Ebbeling et al (link – yes, the biomarkers of inflammation as a result of the high protein/fat diet is a well-documented phenomenon. i’ve written about here

  3. Thank you for this…and for exploring the topic of microbiomes and their importance relating to human health. I feel that our hunter-gatherer family members on this planet are really struggling. And, the the wild part of our hearts…they are being squeezed out by lines, boundaries, profit-margins, and bottom lines. I feel these people are very important to protect. I see a lot of folks raising money for the habitat, of say — giraffes. However, when it comes to the dwindling land available for proper living of the hunting-gathering lifestyle…that is not protected. These humans live in dynamic balance with their surroundings and move according to the seasons and weather. They have a delicate and beautiful rhythm with the planet…of what I understand. I hope your research will show us how important their lifestyles are to human health…and the importance to protect their territories from further encroachment from ‘civilized’ peoples.

  4. A very interesting survey. It may be an idea to hold similar surveys with other specialists. Specialists and working scientists may well have other opinions as generalists and scientists closer to politics who organise the funding for their profession.

    Still, I have one critical comment on question 6.

    Q6. Do you believe the current USDA’s Dietary Guidelines for Americans were compiled with a clear understanding of the impact of dietary choices on the microbiome? (1= Probably not, 10= Yes) Results 1.3

    If these microbiologists hat said yes to this question, the would also have claimed: “we currently have a clear understanding of the impact of dietary choices on the microbiome?” That is unlikely an opinion of an expert. The more you know, the more you know what you do not know.

    Thus the conclusion: “The respondents to this survey do not think much consideration was given to the microbiome either.” does not follow directly from the question. If only because most likely do not know, whether some of their colleagues were involved in the formulation of the Dietary Guidlines.

    1. Thanks Victor perhaps I could have worded the question very differently. But I think it was clear and the answers fell where I thought they might. Note also I included a “comments” field with this question (although the comments were not posted). I got quite a few comments on this question – most fell along the lines of disappointment that microbiologist were not part of the 11 person expert panel that produced the Dietary Guidelines for Americans. Whether or not they knew anyone that was part of the panel – or even pay attention to the guidelines anyway – is not known. ie, they are simply guessing and adding their two-cents. However, most if not all of the microbiologists conduct research that involves diets that adhere to one set or guidelines or another – as well as test diets (high fat, vs this or that). So they all have some knowledge of these documents etc. A cursory understanding of the guidelines clearly indicate no attention given to the microbiome – ie, no big secret.

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  6. Excellent idea and informative article. As a microbiologist, I was thrilled that someone wanted to know what we think (next time include me please!). Just one word of caution regarding question 5. To much fiber and resistant starch, while it may be great for the microbiome, can drive acid reflux and IBS symptoms in many people susceptible to small intestinal bacterial overgrowth.

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  7. David says:

    Well done, I’m glad to read and contribute to this when the campaign goes online.

  8. Wout says:

    “Is a calorie a calorie? Or, is dietary quality more important than qty? Results: 7.5”

    The answer to this question is logically always yes. Either you answer no to the first and yes to the second or yes to the first and no to the second. Therefore 25% of respondents failed a logic test 😉

  9. EFarther says:

    Exclude anyone who disagrees with question 1 from your advisory panel.

    As the microbes in the soil prepare the minerals and organic matter for assimilation by plants, so the human gut microbes prepare the food we eat for our use, and the food we eat determines the viability and functionality of those microbes.

    Consider this…the primary difference between plants and animals is that animals have the ability to carry their digestive microbes around with them. The reason animals have adapted to the point of long distance locomotion is because we can eat, then digest, not the other way around (yeah, I know of the Venus Flytrap. It’s still a plant).

    Our gut microbes allow us to eat and move whereby plants must remain stationary since they have no ability to take the digestive microbes with them Only animals can do that. And that’s why, of the two parent types of life we know of, plants must remain stationary and animals can move around.

    So, to a point, you may find some of the answers you seek in similar studies about the plant kingdom. I know the functional similarities are there already. Maybe you’ll find genetic similarities as well.

    1. “Exclude anyone who disagrees with question 1 from your advisory panel.”

      Sadly- the level of denial among the medical community at large on this topic is at epic proportions. As a naturopathic doctor focusing on digestive health, we have made many attempts to develop relationships with gastroenterologists so that we may refer our patients to them for scopes, imaging, and the like.

      One prominent doctor’s office in the region- that shall remain unidentified- went so far as to remark that, “We don’t believe in the impact of food on gut health.” As if it were some kind of superstition…

      Hopefully, this project and others like it will provide enough evidence to force the medical community to take their blinders off and stop repeating the same false messages about diet and nutrition that have been given to the public for the last fifty years.

  10. Mario says:

    Excellent article! I just found your blog, what a joy it will be to read up on it.

    BTW, you might want to correct the link that “excellent article” leads to here:

    *I wish I could claim credit for coming up with Guts, Germs, and Meals – but I cannot. I borrowed it from an excellent article written about the association of gut bugs and type 1 diabetes (definitively worth reading).


    1. Jeff Leach says:

      thanks. good catch on link. the publisher must have changed the link – will track it down and re-link.

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