Ask Eirik: Should I Get My Gut Microbiome Analyzed?

e.coli-bacteriaIt’s time for another edition of “Ask Eirik”, the series of blog posts dedicated to answering some of the questions I get about diet, health, and fitness. If you have any questions you’d like me to provide my two cents on, feel free to post a comment on the blog or use the contact form. The questions I choose to answer in these posts are those I feel deserve a lengthy reply and/or that revolve around topics I think a lot of people are interested in. I primarily choose to publish those that cover topics/problems I haven’t already written about, so before you shoot me a question, please take the time to use the search function in the sidebar.

For today’s post I’ll give my input on a recent question I got about microbiome sequencing…

Hi Eric.

I have a question that I would appreciate your input on.
I want to get my fecal matter tested and also vitamin and mineral content of my blood.
I subscribe to eating a diet that promotes good gut bacteria but I will only ever know if I am following the right diet once I get the right tests done.
I am serious about my health but I need the right information.

Thank you for all the great information you put out there.

Best regards


Hi Trayl!

A fecal microbiota analysis will provide you with information about biodiversity, pathogenic overgrowth, etc., but it will not tell you whether or not you harbour a gut microbiome that supports healthy digestion and immune function when matched with your diet/lifestyle. As I’ve pointed out many times on the blog, to achieve good health, you need to eat a healthy diet AND have a gut microbiota that is adapted to that diet.

Another problem with relying on gut microbiome analyses for determining the state of the microbial ecosystem in your gut is that these tests primarily give you information about the types of microbes that are present in your intestine, not the genetic capabilities of the microbiome.

Although we have learned a great deal about the trillions of microorganisms that occupy the human body over the last decade, there’s still a lot we don’t know. When it comes to establishing which types of microbes that enhance our health and which ones that undermine it, studies show conflicting results. Even probiotic strains of Bifidobacterium and/or Lactobaccillus may not all have an unequivocally beneficial impact on our health. For example, the use of high-potency probiotic supplements such as VSL#3 stimulates our immune system in evolutionarily novel ways and may block the development of a healthy adult gut microbiota.

As I’ve pointed out before here on the blog, many of the “probiotics” that are often considered to be key members of a healthy gut microbiota are not present in the guts of non-westernized, traditional people. For example, as you probably know, a recent study that investigated the phylogenetic diversity, taxonomic relative abundance, and the short-chain fatty-acid (SCFA) profile of the microbiome of the Hadza found that these hunter-gatherers have no Bifidobacteria in their gut (post-weaning) (1). This isn’t necessarily surprising, as the Hadza don’t consume milk or any other dairy products.

One of the main reasons it’s so difficult to determine how different types of microbes affect our health, is that genetic material is constantly swapped between microbes in the gut through horizontal gene transfer. This means that the critters in your gut can rapidly evolve new genetic capabilities, and that several different species of bacteria may be able to carry out the same functions (e.g., initiate the fermentation of various types of non-starch polysaccharides).

The key takeaways here are:

  • A lot of focus has been placed on trying to determine which microbial species and strains that enhance our health and which ones that undermine it. This strategy may not get us very far. We should probably focus more on the genetic capabilities of the microbes in our gut and the interaction between the microbiome and our diet.
  • What constitutes a healthy microbiota for you may not be a healthy microbiota for someone with a different diet and lifestyle.

Go ahead and get your fecal matter tested if you want. It will give you interesting information about what lives in your gut, as well as the biodiversity of your microbiota. All I’m saying is that you shouldn’t rely on the test as your main source of information about the state and health of your gut microbiota. Instead, I recommend that you start by doing an assessment of your current health condition. This should help you get an idea of how your gut is functioning. The following questions can help you get started:

  • Do you regularly experience digestive issues (e.g., bloating, loose stools, irregular bowel movements, food intolerance)?
  • Do you frequently get intense sugar and/or junk food cravings?
  • Do you suffer from any chronic health disorder that are characterized by perturbations of the gut microbiome?
  • Do you feel depressed and/or drained of energy?
  • Do you have low libido?

If the answer to one or more of these questions is yes, then chances are you have a dysfunctional microbiome. Hence, you need to work on improving your gut health. Use the questions above to track your progress. Fecal microbiome analyses can also be useful in this situation for detecting how the biodiversity and community structure of the microbiota are affected by the diet/lifestyle changes you make.

It’s important to note that my thoughts on this topic are constantly evolving as new research is published and I discover and explore different facets of the link between man and microbes. In other words, my perspective on these things may change somewhat over the coming years. This is really always the case when it comes to matters of nutrition, health, and medicine, as it’s important to be open to modifying one’s position as new research is published. That being said, the foundation usually stays intact; it’s the smaller things that sometimes need to be adjusted.

As for testing the vitamin and mineral content of the blood, some of the same limitations as I touched on above apply. These tests can be useful as they help reveal micronutrient deficiencies, but they don’t necessarily tell you much about whether you’re actually healthy. Moreover, the normal value ranges used for some of these tests may not be a good representation of a healthy or “optimal” range. With some potential exceptions (e.g., vitamin D), a nutrient-rich, whole foods diet coupled with a healthy gut microbiota should provide you with all the vitamins and minerals you need.

I hope this helps.

– Eirik

Picture: Creative Commons picture by NIAID. Some rights reserved.


  1. I perfectly agree. We still don’t have any actual causation factor but rather some clues that are in many cases controversial and mismatched. The posted study about critters able to metabolize lysine and produce butyrate is an example. Vegetarians have been beating the meat drum for a long claiming that meat produce nasty compounds. This is a further nail for their coffin…we have also studies that lactobacillus acidophilus may at best do nothing and at worse be very bad for you..probiotics, kefir etc. are full of such critter and other firmicutes. We only know that having a good matched microbiome is healthy but we don’t know what is a good microbiome. We are too biased by companies funded research that have mostly to do with their business. Now research is less and less funded by government and always more by who has got a huge interest to sell products and here’s the same. Keep your lifestyle matched with our evolutionary path as much as possible and you won’t need fecal tests.

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