10 Things You Should Know About the Link Between Gut Bacteria and Obesity

feet-on-scaleI’ve been thinking a lot about the microbiome’s involvement in the pathogenesis of obesity lately. A couple of years ago, I wrote a lengthy paper in which I took an in-depth look at the scientific research pertaining to the link between gut microbes and body fat regulation. Back then, I was convinced that microorganisms play a key role in regulating the appetite and body fat levels of macroscopic organisms. This belief has only strengthened in the years that have passed.

In today’s post, I’m not going to take another in-depth look at the science on this topic. Rather, I wanted to summarize some of the key things we’ve learned about the microbiome-obesity connection over the past two decades, as well as share some of my current opinions, thoughts, and ideas on this topic.

Established facts: Some of the key things we’ve learned about the microbiome-obesity connection over the past two decades

1. Obese people harbor a microbiota that differs from that of lean individuals

There doesn’t seem to be a clear pattern as to the specific differences, but there is definitely a difference (1, 2, 3). Some studies have found that “obese microbiota” lacks biodiversity when compared to “lean microbiota” (3, 4).

2. An overweight phenotype may be transferred from obese animals to germ-free animals via transfer of microorganisms

Studies have shown that germ-free mice that are infused with lean microbiota stay lean, whereas germ-free mice that receive microbiota from obese mice gain weight (5).

3. FMT can improve the metabolic health of obese humans

A recent study found that transfer of microbiota from lean to obese humans improves insulin sensitivity in the latter (4). Significant changes in body weight were not observed, however, which isn’t really surprising, given that the microbiota that is already established in the intestine of the recipients may partly inhibit the colonization of the infused critters.

4. The microbiota affects how much we eat, what we eat, how much energy we expend, and how much fat we carry

The microbiota can affect appetite regulation, eating behavior, and body fat regulation through several different mechanisms (6, 7, 8). Gut bacteria produce a long range of hormones and neurotransmitters that reach various organs in the human body, including the brain, and they regulate the immune system and the permeability of the intestinal barrier, something that affects the inflammatory status of the body, and hence, sensitivity to metabolic and adipostatic hormones, energy expenditure, and appetite.

The following statement by Dr. Art Ayers, one of my favorite professors/researchers, helps describe the role microbes play in regulating body fat levels in humans.

I think that the extra fat that we carry is regulated by our gut flora and a change in energy consumed and expended alters our gut flora to maintain our fat storage. Increased consumption of calories and stored fat alters the gut flora to produce more bacteria/poop and less contribution to fat. Starvation does the opposite. (9)

5. There’s still a lot we don’t know

There are thousands of scientific papers out there that cover topics related to the connection between the human microbiome and obesity. We’ve learned a lot over the past couple of decades. That said, there’s still a way to go before we have an in-depth understanding of this topic.

Taking it a step further: My theories, opinions, and current understanding

In the previous section, I listed five scientific facts pertaining to the role gut microbes play in the regulation of body fat levels in humans. Now, I’ll move on to summarize some of my current thoughts, opinions, and hypotheses related to this topic; all of which are based on a combination of everything I’ve read about microbes and obesity, my own experience and thought processes, and the observations I’ve made over the years.

6. All obese people carry a “suboptimal” microbiota

There are two main reasons why this must be true. First, with the exception of monogenic obesity, you have to eat unhealthy foods to become obese. It’s virtually impossible to become obese if you eat a healthy, species-appropriate diet. An unhealthy diet, particularly one that’s rich in highly processed food, selects for a microbiota that is poorly matched with human genetics.

Second, a healthy microbiota would not “allow” its host to accumulate the amount of fat mass that is present in obesity. Obesity is characterized by impaired leptin and insulin sensitivity, low-grade inflammation, abnormal eating behavior, and an elevated body fat set-point (10, 11, 12). These derangements would not have occurred, at least not to that extent, if a healthy microbiota was present. I want to make it very clear that it’s not just obese people who harbor a microbiota that is poorly matched with human genetics. Many lean individuals do as well.

7. Obesity is partly caused by a genome-microbiome mismatch

Antibiotics and other pharmaceutical drugs, c-sections, highly processed foods, and many other microbiota-disrupting factors associated with our modern way of life have caused a conflict between the human and microbial parts of our bodies, something that has undoubtedly contributed to driving the progression of the obesity epidemic.

8. Gut bacteria are largely to blame for undesirable food cravings

Obesity is characterized by excessive eating and cravings for unhealthy food. A lot of people, both obese and non-obese, find it almost impossible to stay away from sugary junk food. I strongly suspect that gut microbes are largely to blame for the undesirable cravings these people experience.

Gut bacteria can exert control over their host’s eating behavior and appetite (6, 7). The microbes that proliferate following the consumption of highly processed food probably affect their host’s eating behavior in such a way that he/she craves more of the foods these microbes depend on for their survival and reproduction.

I think we as a society overestimate the amount of control we have over our actions. The vast majority of obese people want to lose weight and eat healthier; however, they find it very difficult to do so, because the systems in their body that are involved in the regulation of appetite and body fat levels are compromised. If the body is “screaming” at you to eat crap and avoid exercise, willpower and self-discipline may not be sufficient to lose weight.

9. The microbiotas of the obese can be categorized into a couple of different categories

“Obese microbiomes” can be classified into at least two main categories. In category one, you’ll find obese people who harbor a disordered, severely dysbiotic microbiota. These are the individuals who find it almost impossible to stop eating and have a completely deranged metabolic system. In the other category, you’ll find those who carry a microbiota that is fairly stable, but not healthy. The microbiota of these individuals is typically matched with an imprudent diet. I know people from both categories. Keep in mind, my understanding of this issue is constantly evolving. In other words, my theories may change somewhat as new evidence comes to light.

10. Therapies aimed at manipulating the microbiome should be included in the treatment of obesity

Obesity can’t be solved with a magic pill or a single lifestyle change; it requires a multifaceted approach. We have to get away from old, simplistic ideas about calories in vs. calories out, and acknowledge that human beings are biological systems; systems that have their own integrated ways of regulating energy expenditure and energy intake. Ultimately, it’s the energy equation that determines whether we lose or gain weight, but that doesn’t mean that simply telling an obese person to “eat less and move more” is good advice. In order to combat obesity, we have to consider what’s causing us to overeat and store fat in the first place, and how our diet and lifestyle choices affect the microbial communities we carry with us.

Now I want to hear from you: What are your thought about all of this? Do you have any comments or additions to the lists?


  1. https://www.youtube.com/watch?v=U1hbPXooB1U
    Documentary – Why Are Thin People Not Fat?
    Ande Terix.- Publicado el 24 jul. 2015
    Why Are Thin People Not Fat? Horizon, 2008-2009 Episode 7 of 17
    The world is affected by an obesity epidemic, but why is it that not everyone is succumbing? Medical science has been obsessed with this subject and is coming up with some unexpected answers. As it turns out, it is not all about exercise and diet. At the centre of this programme is a controversial overeating experiment that aims to identify exactly what it is about some people that makes it hard for them to bulk up.
    Comentarios • 63


    Eneko Landaburu enekolan@gmail.com

  2. We surely overestimate our power.
    Since we can be controlled by our fellows, how can we have control over the evolutionary forces that created us and everything around us.
    Anyway, cravings have also to do with esorphins and caseomorphins from grains and dairy, that work together with the biochemical signals from gut microbes.
    I agree that it’s about the mismatch between our genome and the microbiome and the microbiome diversity is associated with healthier outcomes.
    Nevertheless, I’m not convinced that comparing our microbiome with the microbiome of the Hadza is the definitive response. At this regard, I found interesting the talk by Dr. Ruscio at the AHS16 that made me think.
    Outside Africa we expect less microbial diversity and less plant foods, indeed archeological analysis show that our ancestors who lived in british islands were almost carnivores like the arctic fox.
    We have “healthy” hunter gatherers diets from the Equator to the Pole with a wide array of foods and maybe microbial diversity.
    Of course I think that now we have an absolutely lack of natural diversity even given our nordic descendants, but touting to compare a microbiome of a nordic man with an african tribe is not the definitive way to go for me.
    Furthermore, we should consider what may happen if we try to push hard a new ecosystem into an untrained immune system of a western raised person.
    We don’t know how his immune system is going to respond with such overstimulation.
    We should be very careful to push probiotics and prebiotics a go-go, considering where we are coming from (a scandinavian is meant to be matched to a different microbiome than an african) and how we raised up (breastfeeding, city or countryside, natural birth, early antibiotic use, etc.).

  3. kyle barichello says:

    Unfortunately, the medical industry has convinced us of the “benefits” of antibiotics when in reality, these are often the root cause of a poor gut micro biome. Overtime, societies obsession with nuking our system to rid ourselves from modern discomfort has led many to overlook the importance of this microbial makeup. If instead we chose to suck it up, our bodies would do what they do best, adapt and overcome and foster a better microbial environment. Yet, so many are convinced by the modern medicine that the best solution is to remove the disease/organs and treat symptoms as opposed to fixing the source with a more natural lifestyle. Hugely important topic and discussed very well in the article!

  4. Do you happen to know anything about Dr. Art Ayers? I haven’t seen a single post, tweet or coment from him since August 2015. Almost two years by now….

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