10 Common Misconceptions About the Human Microbiome

man-woman-microbiomeThe human microbiome has received a lot of attention lately, both in the scientific literature and in the mainstream press. Unfortunately though, not all of the information about gut health and human-associated microbes that is floating around is of high quality. The microbiome field is very young, and there is still a lot we don’t know about the trillions of microbes that colonize our bodies; hence, it’s not surprising that some untruths and misconceptions about the microbiome have been allowed to spread and gain foothold among the public. In today’ article I thought I’d take a look at 10 such common misconceptions. 

1. The womb is a sterile place

A longstanding dogma in medicine is that the womb is a sterile place, and by implication, that babies are not exposed to microorganisms prior to birth. This dogma is not based on solid science, but rather on assumptions. Over the past decade, it has become increasingly clear that the womb is not a sterile place and that the first seeding of the microbiome likely occurs prior to birth (1).

2. Of all the nutrients that make up the human diet, only dietary fibers affect the gut microbiota

Dietary fibers have received a lot of attention within the health/nutrition community lately, in large part because many of them have a profound impact on the microbial communities that colonize our bodies. What is often forgotten though, is that fiber is not the only type of nutrient that interacts with our microbiomes. Far from it. Many other nutrients, including simple sugars and fats, are also capable of modulating the human microbiome (2, 3, 4). For example, the consumption of simple sugars changes the microbiota of the upper gastrointestinal tract (3, 4), something that could have ripple effects down into the colon.

There are primarily two ways that a food substance can change the microbiota: 1) Microbes can break down and/or utilize the substance in question in their metabolic processes. 2) The substance in question can change the environment of the gut, thereby altering the microbial communities that are present there.

3. The human microbiome is slow to change

A common assumption is that it takes many days, weeks, or even months for the human microbiome to change following a perturbation by outside forces. I suspect that the main reason why some people think this is the case is that we, as a society, tend to view the human body as a fairly static structure. We assume that our genes are set in stone. This assumption doesn’t completely miss the mark when the genome in question is the human one (although epigenetic factors and mutation rates have to be taken into account); however, it’s very much incorrect if we’re talking about the human microbiome. The microbial communities that colonize our bodies change rapidly if their environment changes (5, 6). For example, if you apply an antibacterial lotion to your skin, that will alter the composition of the microbial community that resides there. This change can occur quite rapidly.

4. Yoghurt and probiotic supplements (the ones that are on the market today) can repair a degraded, damaged gut microbiota

Some people seem to be under the belief that a damaged gut microbiota can be repaired by yoghurt and/or probiotic supplements that contain a handful of strains of lactic acid bacteria. There are probably several reasons why this common misconception about the human microbiome has taken hold within the general population. First of all, food producers and probiotic manufacturers have put a lot of effort into constructing clever marketing campaigns and convincing the public that the products they sell are very healthy. Second, some physicians tell their patients to take probiotics and eat fermented dairy foods such as yoghurt following antibiotic use and seem to be under the belief that these nutritional products are capable of repairing the damage that antibiotics cause. Third, yoghurt and probiotic supplements have been touted a highly beneficial products in the general press and the health/fitness community.

The thing that eludes a lot of people is that yoghurt and probiotic supplements (the ones that are on the market today) only contain a very narrow range of bacteria. They primarily contain Lactobacillus spp., which only make up a very small portion of the gut microbiota of a normal person. Trying to repair a degraded microbiota with these products is analogous to trying to rebuild a burnt-down rainforest that was once home to hundreds of species of plants and animals with just a couple of different plant seeds and/or a few animal species.

5. Each person should eat a diet that is specifically tailored for his/her microbiota

No two people carry a completely identical microbiota. We’re all unique in that we all carry a unique mix of microbes. This has led some people to think that we should all be on different diets. This is a flawed assumption. Yes, it is true that we are all unique with regards to the types of microbial communities we harbor; however, that doesn’t mean that we should all eat different diets. The composition of your microbiome is constantly changing. Your microbiome doesn’t look exactly the same today as it did 1, 2, or 3 years ago. It has changed as a result of your behaviors: what you’ve eaten, where you’ve travelled, the drugs you’ve used, and so on. By itself, this should make it pretty clear that the assumption that we should tailor our diets to our individual microbiotas is erroneous.

The microbial communities you harbor in your gut change in accordance with changes in your diet, meaning that you can change your microbiota by changing what you eat. One shouldn’t assume that the microbiota is a static structure that only matches well with one specific type of diet. Furthermore, it’s important to point out that one can’t establish what a person should be eating simply from analyzing his microbiota.

Instead of trying to tailor our diets to our individual microbiotas, which is futile, I would argue that we should design our diets according to the evolutionary diet model. With that said, we should obviously pay attention to our microbes when we decide what we eat. Also, some people, in particular sick individuals who suffer from gastrointestinal disease, often harbor disturbed microbiotas and have special dietary needs.

6. The microbes that colonize our bodies can be classified into good and bad ones

A very common misconception about the human microbiota is that it is composed of good and bad microbes. It’s certainly true that some bugs are less friendly than others (from our perspective); however, it’s way too simplistic to label microbes as either good or bad. The human microbiota is a very complex community made up of trillions of microorganisms, all of which have their own unique place within the community.

Some microbes that are generally perceived as friendly, including various types of probiotics, can do us harm in certain situations. On the flip side, microbes that are generally perceived as bad can sometimes do us good. It all depends on the situation. If the community as whole is diverse and thriving, potentially problematic microbes are typically kept in check and are only present in small numbers, whereas if the community as whole is broken down, microbes that have the potential to do us harm may be able to rip off their shackles. The picture is further complicated by the fact that microbes evolve rapidly and are able to share DNA between themselves.

7. People who harbor a degraded, dysbiotic gut microbiota can fix their gut by eating healthy

Historically, the conventional nutritional community has paid very little attention to the bugs in our guts. It has long been assumed that all one needs to do to keep one’s gut microbiota in good shape is to eat healthy. This is an overly simplistic notion. A person who harbors a fairly diverse and resilient microbiota may indeed get away with just eating healthy; however, the same isn’t necessarily true for someone who harbors a microbiota that lacks diversity and resilience. This is particularly true if the diet in question is mostly composed of “clean”/sterile foods (e.g., cooked foods that harbor little or no live bacteria).

To illustrate this, let’s imagine that you have to go on a lengthy course of antibiotics and that the antibiotics you take wipe out substantial numbers of microbial species from your gut. A healthy diet of cooked meat, steamed veggies, berries, and nuts obviously won’t bring all of those microbes back into your gut.

8. Real, whole foods won’t cut it. One needs to use special nutritional products such as prebiotic supplements to build a truly healthy microbiota

Given the popularity of the human microbiome, it was inevitable that companies with financial interests would pick up an interest in the trillions of microbes that colonize our bodies. These days, you don’t have to look far and wide to find products that supposedly improve gut health and microbiota composition. Prebiotics, probiotics, and other microbiome-related products can be bought at every health food store. Is this a good thing? Not necessarily…

Most of these products don’t do much good. Many actually do a lot more harm than good. Prebiotic and probiotic manufacturers want us to think that we should be stuffing our bodies with lactic acid bacteria, psyllium husk supplements, powders rich in resistant starch, and so on. They don’t want us to know the truth, which is that one doesn’t have to use plenty of “special” nutritional products to be healthy. Actually, doing so may undermine one’s health. Real, whole foods are superior to supplements in that they contain a natural balance of different nutrients and other compounds; they don’t just contain very high concentrations of one or a couple of substances.

9. We need to locate and bring “ancient microbes” back into our guts

A very common misconception about the human microbiome is that we’ve in recent times lost ancient microbes from our microbiotas and that reintroducing these microbes into our guts is the key to improving our health. It’s certainly true that we, via our modern diet and lifestyle habits, have altered our microbiotas and that the microbiota of the western man is markedly less biodiverse than the microbiota of the typical hunter-gatherer. It’s also true that people who live or lived in non-industrialized environments often harbor microbes that are rarely found on the bodies of westernized people. What is important to note though is that it’s somewhat erroneous to classify some microbes as “ancient”. All organisms that are present on this planet change over time. Nothing remains static. This is particularly true within the microbial world, in which evolutionary processes occur rapidly. Over time, microbes evolve and adapt to their changing environments; they don’t remain in a standstill.

10. We all need to harbor x microbe to function correctly

A common belief is that each and every one of us needs to harbor specific strains of microbes if we are to function according to our evolutionary design. This is a somewhat erroneous belief. As pointed out earlier, microbes evolve at a rapid pace and are able to swap genetic material among themselves. Many different types of microbes are capable of carrying out similar functions (i.e., they can do similar things). Even a microbe that is not capable of carrying out a specific function may evolve an ability to perform that function. This is to say that there aren’t just one or two microbes that can let’s say break down a specific type of dietary fiber found in onions. It’s obviously important that we pay attention to what types of microbial species that are present in the guts of different types of people; however, we should avoid the pitfall of thinking that we all need to harbor x, y, and z microbes to be healthy.

Picture: Designed on the basis of pictures (1, 2, 3) from FreePik.


  1. I’m re-reading a book about microbes in all parts of life. I highly recommend it: ‘I Contain Multitudes. The Microbes Within Us and a Grander View of Life’ by Ed Young (2016), who is a science writer with The Atlantic, New Yorker, National Geographic and more. He gets us up to date on incredible changes inthe ability to obtain nformation on microbes and what they do. As the cover says ” allows us to see how ubiquitous and vital microbes are: they sculpt our organs, defend us from disease, breake down our food, educate our immune systems, guide our behavior, bombard our genomes with their genes, and grant us incredible abilities.” The book looks at humans and the general world around us. It’s really fascinating and highly recommend it.

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