2 Free Articles Remaining (through 06/11/21)

At this point, we don’t know exactly what characterizes the obese microbiome. However, it could be argued that we don’t really need to establish exactly which phyla and species of microbes that play a key role in obesity. Certainly, having more knowledge about the obese microbiome and the role of specific gut microbes in obesity would help us develop probiotics (beneficial bacteria), prebiotics (food ingredients that boost the growth of beneficial bacteria), synbiotics (combination of prebiotics and probiotics), and other products that can modulate the gut microbiome. However, we already have a lot of the knowledge we need to target and treat the obese microbiome.

First, we know that gut microbes play an essential role in regulating fat storage (1,2). They are definitely not the only factor involved, but they seem to be important.

Second, we know that manipulating the gut microbiome can promote changes in bodyweight (3,4).

Third, we know that hunter-gatherers and some traditional populations that are unaffected by western lifestyle are lean, virtually free from diseases of civilization, and have vastly more diverse microbiomes than westerners (However, more studies in this area is needed) (5,6,7). Archeological data also suggest that the modern cosmopolitan lifestyle leads to a significant change to the human gut microbiome (8).

Just like our human genome was forged in the ancestral natural environment, the human microbiome is probably also healthiest when we live in a way that is somewhat in consistence with the hunter-gatherer human lifestyle. This is supported by studies which show that factors associated with the western lifestyle (e.g., antibiotic use, refined diets, c-sections) have a negative effect on the gut microbiome, while factors associated with the hunter-gatherer and traditional human lifestyle (e.g., diets rich in nutritious whole foods, microbial exposures, no access to antimicrobials) promote a healthy microbiome (4,9,10,11) .

Treating the obese microbiome

As both the obese microbiota and obesity itself largely result from a gene-environment mismatch, reconnecting with the natural human environment is the obvious way to retake our health. This doesn’t mean that we have to abandon all aspects of our modern lifestyle and move into the wild, it simply means that we should consider the impact our lifestyle has on our microbial inhabitants. From a practical perspective, studies have shown that avoiding antibiotics (unless they are absolutely necessary), eating fermented foods, avoiding highly processed foods, eating more fermentable substrates, breastfeeding your child, and performing a natural birth are some of the key things you can do to promote a healthy, lean microbiome (12,13,14,15,16). Also, while we need more studies to say for sure, it’s likely that part of the hereditary component of obesity involves the transfer of microbial DNA from mother to child. This means that taking care of your own microbiome is probably a good idea not just for your own benefit, but also for the sake of your children. In combination with new types of advanced microbiome modulators that target specific disorders, these general lifestyle changes will hopefully be enough to rewild our bodies and retake our health.

Some plant food, such as green bananas, are especially rich in prebiotic fiber. Source: http://www.freeimages.com

Some plant food, such as green bananas, are especially rich in prebiotic fiber.
Source: http://www.freeimages.com

A way to go

Before we can accurately determine the role of the gut microbiome in obesity, we have to learn more about the connection between microorganism and obesity and develop effective strategies for treating the obese microbiota. Large corporations, such as Second Genome, have already begun the development of advanced microbiome modulators that could be used in the treatment of obesity, type-2 diabetes, and other conditions that are characterized by an altered gut microbiota. But do we really need modern science to figure out how to beneficially manipulate the microbiome?

Humans have lived for millions of years without advanced probiotics and prebiotics, and we can probably learn a lot by studying populations that are free from diseases of civilization and seem to maintain diverse and robust microbiomes. However, we don’t know whether lifestyle changes are enough to treat conditions that are characterized by moderate-severe dysbiosis. Also, it could be that we’ve lost some key microbial species, which are either lost forever or can only be replenished with specific probiotic supplements.

Lifestyle and environment have a profound impact on the balance of microbes that live in and on our bodies, and it’s therefore difficult to determine exactly what a healthy microbiome looks like. Since most people in industrialized nations have taken antibiotics sometime during their life and generally maintain several aspects of a western-type lifestyle, it seems unlikely that we can determine what a healthy microbiome looks like by studying westerners. This is also something a lot of researchers have taken into account, as studies of hunter-gatherer populations, such as the Hadza, and rural populations, such as children in Burkina Faso, have now been carried out. More research on the microbiome of non-westernized populations – especially ancestral cultures that live in an environment that closely resembles that of our paleolithic ancestors – will help us learn more about the natural, unperturbed state of the human microbiome. While these studies will reveal a large degree of difference between populations, as microbiome structure largely depends on the environment we live in, they can help us establish a framework regarding what a healthy microbiome probably looks like.

In terms of obesity, it will be interesting to see more comparative studies of the lean and obese microbiome, as the results from these trials can help us understand more about the exact species and microbial DNA that play a role in the obesity epidemic.

Time to start considering our microbial inhabitants

What we’re now learning is that although modern technology and science come with many benefits, they have also allowed us to create products, living conditions, etc. that negatively impact the microbial ecosystems in and on our bodies. One example of this is antibiotics, which have helped save many lives and allowed us to combat many types of infectious diseases, but widespread use of these drugs have also resulted in the development of antibiotic resistant superbugs, loss of microbial old friends, and dysbiosis.

The fact that microbes are transferred between humans through birth, breastfeeding, social interactions, etc. and that we pick up bacteria from the natural environment suggests that we’ve seen rapid changes in the human microbiome over the last decade and that this trend could only continue unless we change the way we live in the modern world. If a woman has taken several courses of broad-spectrum antibiotics throughout her life, eaten a highly processed western diet, and/or been extremely hygienic, her child will probably receive a less than optimal mix of bacteria. This ecosystem damage could then be further enhanced by the child’s lifestyle choices and affect future generations. The fact that so many aspects of our modern way of life have now been scientifically proven to perturb the human microbiome could help explain the rapid rise in inflammation-driven diseases in industrialized nations.

Going forward, we shouldn’t just consider our human genome when we determine the optimal human environment and lifestyle, but also the human microbiome.


Obesity rates have increased dramatically over the last couple of decades, and this fat epidemic is thought to result from a combination of genetic and environmental factors . The fact that obesity is almost unheard of in hunter-gatherer populations and some non-westernized societies has led to the definition of obesity as a disease of civilization.

Recent discoveries about the trillions of microorganisms that live in and on the human body are now changing the traditional perspective on human health and disease. In terms of obesity, we’re learning that it’s not just heredity and gene expression related to our human genome that play a role, but also the trillions of microorganisms that make up the vastly larger (in terms of unique genetic material) second genome in our body, the human microbiome.

The idea that the gut microbiome plays an important role in the obesity epidemic is supported by the following observations:

1) Obesity is characterized by an obese microbiome, which is different from the microbiome of a lean person.

2) The western lifestyle is a master manipulator of the microbiome, and recent studies indicate that the microbiome of hunter-gatherer populations and some non-westernized cultures where obesity is unheard of are very different from that of the so-called westernized microbiome. This is consistent with the idea that obesity is a disease of civilization that results from a gene-environment mismatch.

3) The gut microbiome plays an important role in body fat regulation, and manipulating the microbiome can promote fat gain or fat loss. It’s still unclear exactly how gut microbes are able to affect body fat regulation, but one prevailing hypothesis is that the gut microbiota controls the inflammatory milieu in the body and thereby sensitivity to key metabolic hormones such as leptin and insulin. The food reward hypothesis, which states that highly rewarding and calorie-dense processed foods are the primary driver of the obesity epidemic, and the microbiome hypothesis, which states that alterations in the bacterial communities in the gut drive weight gain, are now two of the leading hypotheses of obesity. Both of these hypotheses are based on the idea that fat gain is a vicious cycle, where diet and/or other lifestyle factors impacts dietary preferences and appetite.

While more studies are needed to determine the exact role of the microbiome in obesity, we already know that prebiotics, probiotics, and other types of microbiome modulators can cause fat loss in both animals and humans. The gut microbiome is an important emerging field in obesity research, and in the future there will most likely, and should, be even more focus on the treatment of the obese microbiome.

Read more
Part I: The Second Genome
Part II: Ancestral vs. Westernized Microbiome
Part III: Two Emerging Hypotheses of Obesity
Part IV: Wrapping It Up




Like this article? For more great content, delivered right to your door (and tablet, phone & computer!) subscribe to Paleo Magazine now!