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Your Unique Microbiome (And How it Influences Your Ideal Diet)

primal nutrition, gut health, microbiome, lean muscle

By Kelley Herring

Today, we continue our series of articles on why there is no “perfect diet” for all people… but there may be a perfect diet just for you! In my last post, we discussed biochemical individuality and how your genes influence your personal nutritional needs. We also covered nutrigenomics and how you can actually influence your genes (in a positive or negative way) with food choices you make and the nutrients you consume.

But there is another factor – and one that is equally important – that impacts whether specific foods contribute to health or disease in your body.

microbiome, gut health

Your microbiome!

As I’m sure you’re aware, your microbiome is defined as the collection of microbes that live in your body and on your skin. These populations number in the trillions and their diversity is spectacular. A 2010 study showed that Europeans carry at least 160 bacterial species, with more than 536,000 bacterial genes between them. That’s over 20 times the human gene count![i]

Your individual microbiome is affected by the foods you eat, the activities you engage in (gardening, for example) and the environment that surrounds you. And as anyone who has ever had food poisoning or a “gut bug” can attest, it can change on a daily or even hourly basis.

Your microbiome exerts a powerful influence on every aspect of your well-being, including:

  • Immune System: The types of immune cells you produce and their activity is greatly influenced by your microbiome. A healthy microbiome is also especially important for preventing autoimmunity, as it helps train the immune system using cells called toll-like receptors (TLRs) to differentiate between “self” and “non-self”.
  • Nutrient Absorption: An overgrowth of certain types of bugs can prevent nutrient absorption and lead to deficiencies, while other microbes actually boost nutrient absorption directly or by converting compounds in your food to nutrients your body needs.
  • Digestive Function: Healthy populations of microbes (in the right places in your gut) is important for healthy digestion, assimilation and elimination.
  • Brain Health & Mood: The types and balance of the microbes in your gut influence brain health, memory and mood via the gut-brain axis. This is a bidirectional communication system between your central nervous system (located in the brain and spinal cord) and your enteric nervous system (found in the gut). This links the emotional and cognitive centers of your brain with your intestinal functions.
  • Metabolism: Certain microbes (like those known as Firmicutes) promote fat storage. Others (like gasseri) promote leanness.

Of course, this is just a very basic list of the functions affected by your microbiome. The list goes on and on!

gut health, microbiome,

Microbiome Individuality: A Key Factor in Your Personalized Diet

There is no “one-size-fits all” approach creating and nurturing a healthy microbiome. Just as we are all genetically unique, we are also unique in the composition of our microbiome.

For example, consider this study on thiamine deficiency…

In this study, researchers examined a group of healthy young males between 16 and 23 years old. The subjects, who were on a controlled diet, were given 1 mg of the B-vitamin thiamine per day. This amount was gradually reduced until deficiencies were observed. Among the subjects that did NOT develop a deficiency, the researchers discovered about 20 times more free thiamin in their waste (compared to those who showed symptoms of deficiency).

The difference was due to the ability of particular microbes in their gut to synthesize thiamine.[ii]

The takeaway is that each one of us has not only genetic variations that impact our ability to absorb and assimilate nutrients… but also variations in our “inner ecosystem” that influence our individual nutritional requirements.

The trillions of organisms that make up your microbiome each produce different substances and have unique activities and abilities. That’s why one of the biggest factors in YOUR ideal personalized diet is the health, diversity and composition of your individual microbiome.

This is also why you should be VERY cautious of “one-size-fits all” advice when it comes to gut health and your microbiome, such as:

  • Eat more fiber to “feed the good bugs” and reduce constipation
  • Resistant starch is healthy – it boosts immunity and promotes weight loss
  • If you don’t eat enough carbs, you will “starve” your microbiome

For example, there are countless so-called health “experts” who practically worship dietary fiber as a universally necessary and supremely healthy substance. They praise its ability to “feed” populations of bacteria in the gut and promote healthy regularity.

And while that might be the case for some people, fiber can also cause bloating, gas, extreme digestive discomfort and constipation for others. And the more you eat – as we are often encouraged – the worse the symptoms become!

What’s more, certain strains of bacteria that are prevalent in one population might be completely absent in another. That means there is no such thing as a universal “healthy” microbiome.

Take a look:

  • Bifidus is Healthy, Right? You’ve probably heard of Bifidobacterium, the “beneficial” strain of probiotics found in almost every probiotic supplement and one of the primary species found in most people. But the lean and healthy tribe of African hunter-gatherers, the Hadza, have no Bifidobacterium in their guts![iii]
  • Does Your Microbiome Like Carbs? Populations that live closer to the equator typically consume more carbohydrates (and less protein and fat) than northern populations. Accordingly, these groups also have very different microbiomes. That means that research conducted on one group is often not relevant to the other populations when it comes to gut health, food choices and the microbiome.[iv]
  • Constipation Cause… or Nutrient Saver? An overgrowth of the bacteria M. smithii is known to cause bloating, constipation and gas. In fact, if you have methane-dominant Small Intestinal Bacteria Overgrowth (SIBO), this is the predominant culprit of your constipation and digestive distress. Overgrowth of this bug has also been shown to cause high cholesterol, elevated blood sugar and even weight gain in Western populations.[v][vi][vii]But as you might guess, smithii isn’t a problem for everyone. In fact, the highest levels are seen in African hunter-gatherers (and no, they’re not constipated or overweight). In these populations, the bug confers a survival advantage during lean times, by slowing the transit of food through the intestines and allowing more time to extract nutrients.[viii]

Dr. Michael Ruscio, DC author of the new, eye-opening book – Healthy Gut, Healthy You – says:

“This reinforces the notion that we can’t treat every ecosystem the same. Your gut ecosystem is different from an African hunter-gatherer and your Paleolithic ancestors. To improve your health, we have to create the environment that is ideal for your ecosystem.[ix]

What’s more, unlike your relatively “fixed” genetics, your microbiome is constantly changing in response to your diet, stress, sleep, and environment. And according to research published in Nature, significant changes can occur within days of a big shift in what you eat.

Dr. Lawrence David, assistant professor at the Duke Institute for Genome Sciences and Policy and one of the study’s authors, says:

“We found that the bacteria that live in peoples’ guts is surprisingly responsive to change in diet… Within days we saw not just a variation in the abundance of different kinds of bacteria, but in the kinds of genes they were expressing.”[x]

Improve Your Microbiome, Improve Your Health

The first step you can take to improve your microbiome – and overall health – is to take a look at your current state through testing.
How is your microbial diversity? Do you have an overgrowth of any specific bacteria, yeast, fungi, archaea or parasites?

To answer these questions, I recommend a service like Viome. Unlike other microbiome testing companies, Viome sequences the RNA of the microbes in your sample. This gives you a clearer picture of the organisms that inhabit your gut, their specific activities and byproducts. This is called metatranscriptomic analysis and it is far superior to other testing methods.

Additionally, if you experience digestive disturbances or have been diagnosed with “IBS”, it is important to get evaluated for small intestinal bacterial overgrowth (SIBO). In fact, studies show that SIBO is the underlying cause of IBS in up to 84% of those who suffer.[xi] The three-hour lactulose breath test is the best diagnostic test on the market today.

In both cases, your testing results can provide valuable information as to the specific foods to enjoy – as well as those you should avoid – to improve the health of your microbiome and your overall wellness.

Have you tested your microbiome? If so, how did the dietary recommendations you were given impact your health? Do you find that certain foods, which cause no issues for other people, cause digestive distress for you? We’d love to hear from you…

kelley herring


Kelley Herring is the author of the brand new book Keto Breads – which includes more information you need to know about why it is so important to avoid wheat and grains in your diet, plus how to use healthy replacements for these foods to create all the breads you love… without the gluten, carbs and health-harming effects. Click here to learn more about Keto Breads


[i] Qin J1, Li R, Raes J, Arumugam M, et al. A human gut microbial gene catalogue established by metagenomic sequencing.Nature. 2010 Mar 4;464(7285):59-65. doi: 10.1038/nature08821.

[ii] Najjar Va, Holt Le. The Biosynthesis Of Thiamine In Man and Its Implications In Human Nutrition. Jama. 1943;123(11):683–684. Doi:10.1001/Jama.1943.02840460017005 https://Jamanetwork.Com/Journals/Jama/Article-Abstract/264821

[iii] Stephanie L. Schnorr, Marco Candela, Simone Rampelli, et al. Gut microbiome of the Hadza hunter-gatherers. Nature Communications volume 5, Article number: 3654 (2014)doi:10.1038/ncomms4654

[iv] Alexander Ströhle, Andreas Hahn, Anthony Sebastian; Latitude, local ecology, and hunter-gatherer dietary acid load: implications from evolutionary ecology, The American Journal of Clinical Nutrition, Volume 92, Issue 4, 1 October 2010, Pages 940–945,

[v] Basseri RJ1, Basseri B, Pimentel M, Chong K, Youdim A, Low K, Hwang L, Soffer E, Chang C, Mathur R.Intestinal methane production in obese individuals is associated with a higher body mass index.Gastroenterol Hepatol (N Y). 2012 Jan;8(1):22-8.

[vi] R. Mathur, M. Amichai, K. S. Chua, J. Mirocha, G. M. Barlow, M. Pimentel; Methane and Hydrogen Positivity on Breath Test Is Associated With Greater Body Mass Index and Body Fat, The Journal of Clinical Endocrinology & Metabolism, Volume 98, Issue 4, 1 April 2013, Pages E698–E702,

[vii] Mbakwa, C. A., Penders, J. , Savelkoul, P. H., Thijs, C. , Dagnelie, P. C., Mommers, M. and Arts, I. C. (2015), Gut colonization with methanobrevibacter smithii is associated with childhood weight development. Obesity, 23: 2508-2516. doi:10.1002/oby.21266

[viii] Stephanie L. Schnorr, Marco Candela, Simone Rampelli, et al. Gut microbiome of the Hadza hunter-gatherers. Nature Communications volume 5, Article number: 3654 (2014)doi:10.1038/ncomms4654

[ix] Ruscio, M. Healthy Gut Healthy You. Publisher: The Ruscio Institute, LLC (February 15, 2018). ISBN-10: 0999766805

[x] Scientific American. The Gut’s Microbiome Changes Rapidly with Diet. December 14, 2013.

[xi]  Pimentel M, Chow EJ, Lin HC. Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome. a double-blind, randomized, placebo-controlled study. Am J Gastroenterol. 2003 Feb;98(2):412-9.