The Problem With Gut Microbiome Testing

bacteriaHave you gotten your gut microbiome analyzed? If so, then you’re not alone. Over the most recent decade, the number of companies conducting fecal microbiome analyses has grown progressively, due in large part to increasing demands for microbiome sequencing services. My impression is that many of the people who send in fecal samples to these companies for analysis think that they will get a document in return that tells them “everything” they need to know about the trillions of microbes living in their guts, as well as answers the key question they want answered: “Do I have a healthy gut microbiota?”

These people are usually let down when they get the results of the analysis and realise that there’s really only so much one can learn about one’s microbiome from conducting a fecal microbiome analysis. A microbiome analysis will give you an overview of the bugs that are living in your bowels, as well as an indication of how diverse your gut microbiome is; however, it won’t give you a conclusive answer to the question posed above. It won’t tell you everything you want to know about your microbiome. In this article, I thought I’d briefly discuss why that is the case.

Our microbiomes are constantly changing

Microbes are active creatures; they don’t just stand around doing nothing. The critters that colonize your body are constantly alert and “fight” against each other, competing for limited resources. If you suddenly decide to change your diet, take a new drug, or adopt a new, intense exercise regime, the environment in your gut will change, and as a result, your gut microbiota will also change. (1, 2, 3) Those microbes that do well under the new conditions flourish, while those who don’t do so well wither.

If you’ve been paying attention to how your body functions and what goes on inside your gut, you’ve undoubtedly noticed that these types of changes can occur rapidly. It doesn’t take weeks or months for things to happen. A lot can happen in a matter of hours or days. You’ve undoubtedly noticed that your energy levels, bowel movements, and state of mind vary from day to day. This is partly (largely?) because your gut microbiome changes in accordance with your diet and lifestyle.

If your environment and lifestyle don’t change from day to day or week to week and you are fairly healthy, your gut microbiome will most likely remain quite stable over time. However, if you’re sick and/or are constantly exposing yourself to new foods and antimicrobial drugs, your microbiome will most likely be in a constant state of flux.

Most people find themselves somewhere in the middle of those two ends of the “microbiome dynamicity spectrum”. Their diet and lifestyle practices change somewhat from day to day and week to week, but some core elements are always retained.

All of this is to say that a single gut microbiome analysis will only provide you with a snapshot of your microbiome. If you were to do another analysis at a later time, you wouldn’t necessarily get the same results as the ones you got from the first analysis. The similarity of the two sets of results will largely depend on what you’ve been doing in the period between the two tests. If you’ve been changing your diet, have been sick, or have started using a new drug, your microbiome has likely changed quite a bit; whereas if not much interesting or dramatic has happened, your microbiome has probably remained fairly unchanged.

This doesn’t mean that it’s necessarily a waste of time and money to conduct a fecal microbiome analysis; however, it’s certainly something one should be aware of. Another thing that it’s important to be aware of is that microbiome sequencing companies analyze the microbial components of feces, not the microbial components of guts per se. The microbiota of a fecal sample may not perfectly represent the microbiota of the large intestine from which the fecal sample originated. This is particularly true if a lot of time passes between the collection of the fecal sample and the microbiome analysis.

Many different microbes are capable of carrying out similar functions

My impression is that some people think that they need to harbor x, y, and z microbes in order to be healthy and that one can tell from looking at a document describing a person’s gut microbiome whether that person carries a healthy microbiota or not. That’s not necessarily correct.

Microbes evolve at a rapid pace. They are constantly changing in order to adapt to their environment. Many different microbes are capable of doing similar things. This helps explain why we humans don’t depend on a specific set of microbes to be healthy. Two healthy people don’t necessarily have similar microbiomes. Their microbiomes may differ in several respects. One of them may for example harbor a lot of Bifidobacteria, whereas the other person has none of those types of bacteria. Associations have been found between certain gut microbes and various health parameters; however, that doesn’t necessarily mean that one needs to carry the microbes in question in order to be healthy.

All of this is to say that it’s a mistake to think that you will know, from getting your microbiome analyzed, whether you harbor a microbiota that matches well with your biology. The analysis will likely give you an indication of what the current state of your microbiota is – whether you harbor a lot of pathogens, if there are many lactic acid bacteria in your gut, and so forth; however, it won’t give you a clear idea of whether you harbor a resilient, stable microbiota.

This leads us over to the last thing I wanted to talk about in today’s article…

You can learn a lot about your microbiome by paying attention to how your body looks and functions

It’s certainly interesting to find out what types of bugs that live in one’s gut; however, as pointed out earlier, there’s really only so much one can learn from a microbiome analysis. If you want to find out whether you harbor a healthy microbiota or not, the first thing you should do is not to go online and look for a company that can analyze your fecal microbiome; rather, the first thing you should do is assess how your body functions.

Do you have stable energy levels? Do you experience any gut issues? How are your bowel movements? Do you frequently feel depressed?

Your answer to these questions can tell you a lot about the state of your microbiota. Microbiome dysfunction goes hand in hand with gut dysfunction, inflammation, and cognitive impairment (4, 5, 6). In other words, if your microbiota is in a sorry state, you don’t have to get your feces analyzed to find that out.

By paying attention to how your body functions and how you feel, you can “hack” your way towards a more resilient and diverse microbiota. You can certainly get your microbiome analyzed as well, but don’t expect it to revolutionize your understanding of your health.


  1. Any insights in how the microbiome is impacted when fasting?
    So does fasting select for specific strains? I wonder because fasting seems to me a recurring pattern in the human diet in ancient times.

    • Hi riesjart,

      That’s a great question. Unfortunately, it’s not a question that scientists have paid much attention to. Not yet at least.

      With that said, I shared some of my thoughts on the matter in this recent article. It’s by no means a detailed exploration of the topic, but I think you may find it informative.

Leave a Reply


Get every new post delivered to your Inbox

Join other followers: