Gut Microbiome: How the Gut Impacts Overall Health
15 min read

Gut Microbiome: How the Gut Impacts Overall Health

Updated Nov 13, 2019
Nate Martins

You’ve probably heard of the human gut microbiome.

This is a complex collection of microorganisms that lives inside our digestive tracts. In terms of pure numbers and diverse bacteria species, the group of bacteria in the stomach is the largest of anywhere else in the body. We can carry up to 2kg of microbes in the human gut and in these trillions of microorganisms, there can be thousands of species with millions of genes. About 2/3 of the gut flora is unique to that individual. It’s like a partial fingerprint of your stomach, identifying how you digest food, produce vitamins and potentially, your risk for disease and other health-related problems, including obesity.

This is a growing area of exploration, not only for researchers but also for the general public. It seems gut microbiome might act like a high school janitor, jangling keys attached to its hip, unlocking doors to metabolic health.

Before diving into how this complex gut ecosystem of microbes can help control weight, infection, immunity, or your chances of winning the lottery (not really), let’s investigate the power of the almighty gut.

The Gut as the Body’s Second Brain

Most people think the line of communication between the gut and the brain is a one way street: from the head down.

Think about all the idioms associated with this part of our body that we can’t really see or feel: gut check, gut instinct, gut feeling. Maybe they’re more than just metaphors. Funny we had those expressions even before we understood the connection between the gut and the brain.

Speaking generally, the gut and brain are connected by a maze of neurons and chemicals and hormones that constantly ping each other like supercomputers. Many emotional states were thought to have started in the mind and be felt in the stomach—but they may be generated in the stomach instead of just manifested there. That might be way the stomach is referred to as our “second brain.”

But how does the gut communicate with the brain, exactly?

There are almost as many nerves in the gut as in the brain: about 500 million neurons, more than either the spinal cord or peripheral nervous system.

This enteric nervous system (in our gastrointestinal tract) controls our gastrointestinal system, all the way from end to end (nose to tail, so to speak). This system interacts with our brain and the central nervous system via the autonomic nervous system (specifically the sympathetic and parasympathetic arms), which involuntarily controls heart rate, breathing and digestion. This system regulates the transit of food into the gut, amount of secreted stomach acid, and production of mucus in the intestines. The brain and stomach also communicate through the hypothalamic-pituitary-adrenal axis, or the HPA axis, helping control digestion via activation of hormones.

The circuit board of connected neurons, hormones and neurotransmitters sends messages to the brain about our gut, even allowing the brain to directly control the gut’s function.

Studies have shown the strength of the connection between mind and gut. One study showed that gut microbes influence behavior, even impacting cognitive function and mental health.1 Another notes the potential for treating the gut and its influence on certain psychiatric and neurological disorders.2 It seems the gut has a mind of its own, communicating with other parts of the body through the nervous system.

Research in the area is increasing and exciting, but this is what’s clear: the gut and the brain are linked in ways we’re only beginning to understand, and that link might be due to the bacteria living in our gut.

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Bacteria Background

So, where’s all the bacteria in the gut come into play?

Traditionally, scientists assumed we got colonized by bacteria at birth.3 But some scientists have found evidence of bacteria in the placenta, amniotic fluid and meconium, which has led researchers to think that the microbiome could be colonized before birth. Regardless of when human microbiome is colonized, it happens in very early life, so bacteria is a crucial part of who we are.

In short, your gut microbiome is comprised of trillions of microorganisms (and their genetic material) that live inside the intestinal tract. Many consider these bacteria critical to human health and wellbeing. They digest food. They help absorb and synthesize nutrients. But their reach extends far beyond the tummy. Growing research suggests they can influence metabolism, body weight, immune system, brain functions and even mood (more on these later).

Maybe because you’ve been told to wash your hands before dinner, then you might think all bacteria is bad. Confusingly, you’ve also been told that bacteria is everywhere, unavoidable, and even good. But bacteria is only good or bad depending on where it lives and the amount in which it’s present. For example, staphylococcus aureus is a bacterium that is often found in the human respiratory tract and on the skin—but if it gets under your skin, it can cause serious infections.

As mentioned, human gut microbiota compositions are individual. But like a blood type, there’s a theory that many of us belong to a certain enterotype—this is a way of separating people based on the types of bacteria that are present in their guts (however, this is still being studied).4 This might be a bit of an over-simplification, but it’s a start to understanding differences and similarities in this vast array of bacteria.

What likely determines our gut microbes is a web of factors: genes, age, gender, environment, hygiene, diet. Consider many variables when thinking about gut microbiome.

As we mentioned, our gut microbiome grows starting at, or a little before, birth. As we grow, the gut microbiome starts diversifying to include many different types of microbial species, and the microbiome changes both in response to, and in anticipation of, changes to the diet that occur as infants grow.

What are some of the first bacteria to develop? Makes sense it would be our ability to digest breast milk. Called “Bifidobacteria,” these help digest the healthy sugars in breast milk which are important for growth.

Gut Micriobiome’s Influence on Health

Bacteria are part of us. And just like any relationship with a living organism, how we care for them has an impact on the outcome of our relationship with them. It’s less about what our bacteria can do for us, and more like what we can do for our bacteria (to keep us healthy).

Let’s explore further how our gut microbiome plays an important role in overall health, from blood sugar to weight to even brain and heart health.

An illustration of the body with a stomach; lines are coming from the stomach showing how the gut affects overall health


They say you are what you eat. That’s definitely true when it comes to gut health. The microbes in our gut can affect how our bodies store nutrients, use sugar, control appetite and regulate weight.

At H.V.M.N., we’ve talked a lot about the standard American diet, also called the “Western Diet.” We want to change it through products targeted at metabolic health, like MCT oil and collagen powders. There have been numerous studies about its impact on weight gain and other metabolic disorders,5,6,7 pointing to how the consumption of carbohydrates, refined sugar and processed foods can negatively influence overall health. Part of the reason for that might be related to bacteria in the gut.

One interesting example is fiber. You’ve likely been told you need it to keep your bathroom trips regular and flowing smoothly. Some bacteria digest fiber, resulting in the production of short-chain fatty acids (like butyrate), which are key for gut health.8 Fiber can be an important factor in regulation of weight, and may even lower cholesterol.9,10 There’s a direct relationship between what’s consumed, resulting changes in the microbiome and the downstream effects of the microbiome on weight, metabolism and health.

Diet drastically changes out gut microbiome, and can contribute to negative health effects.11 One study notes the Western Diet promotes inflammation, which arises from changes in the gut microbiome.12 However, the mechanistic link between the Wester Diet, gut microbiome and obesity is largely unknown.

Despite those mechanistic unknowns, there are plenty of examples that show gut microbiome affects body weight, and affects everyone differently. Even two mice from the same litter (one who was obese, one who was a healthy weight) don’t share the same gut microbiome. This illustrates that differences in gut microbiome aren’t genetic.13,14

One study took the gut microbiome from both the obese mouse twin and its identical, healthy weight mouse twin, and transferred them to other mice. The result? Those mice that received the obese mouse’s gut microbiome gained more weight than those who received the gut microbiome of the healthy weight twin, even though all groups consumed the same diet.13

As more studies are done, we’re increasingly understanding that the presence or absence of keystone bacterial species are key to maintaining metabolic health and stable bodyweight.15 Things like prebiotics may help restore gut health and correct these imbalances (more on this later).

Diabetes and Blood Sugar

As you likely know, increased body weight is associated with an increased risk of diabetes; this points to the fact that the gut microbiome might be crucial in diabetes and blood sugar.

As a quick recap, insulin is a hormone that signals to our cells to take up glucose from our blood (among other things). Those with type 1 diabetes either produce very little insulin or don’t produce any insulin at all, and they’re diagnosed with the condition from a young age. Those with type 2 diabetes are insulin resistant (meaning they need to produce more insulin to have the same biological effect); this is much more common today, based on the body’s inability to process all the excess sugar in our diets.

Even though type 1 diabetes isn’t influenced by diet, there may be a role for the microbiome. One study looked at infants who had a genetic predisposition to developing type 1 diabetes. This study found that the diversity of gut microbiome greatly decreased before the onset of type 1 diabetes, also finding an increase in the number of unhealthy bacteria before the onset of the metabolic disorder.16

Regarding type 2 diabetes, emerging research illustrates its link with gut microbiome—and it may go back to the consumption of fiber.

One study showed that people who ate more fiber possessed more of an anti-inflammatory chemical in their blood called indolepropionic acid, a chemical made by the gut microbiome; these participants were less likely to develop type 2 diabetes.17 Interestingly, another study found that, in people who ate the exact same foods, blood sugar could greatly vary; the cause might’ve been the differences in bacteria in their stomachs.18

Of course, there are other ways to potentially reduce the risk of diabetes. Research has shown that low-carb, high-fat ketogenic diets (which trigger the production of ketone bodies) have potential uses in conditions such as diabetes and metabolic syndrome.19 And while achieving ketosis through diet or fasting can take days or weeks, ketone esters can get you into ketosis immediately, offering the benefits of ketosis without requiring adherence to the strict ketogenic diet.20

Ketone esters can also regulate blood sugar in the short term. But it doesn’t require weeks of dieting to get into ketosis, so the effects on blood sugar are fundamentally different, because the body can still consume carbs and be in ketosis with a ketone ester supplement. Studies have shown that ketone esters lower blood sugar and may even reduce the insulin spike if you consume carbs.21

We’re starting to understand how important gut microbiome is to metabolic diseases like diabetes, but further research is needed in order to figure out exactly how.

The Heart

You’ve heard the old saying: “the way to a man’s heart is through his stomach.” That connection between the gut and the heart might be stronger than we think, having an influence on cholesterol and chemicals produced in the gut.

Part of the reason for that connection are some of the chemicals produced by the microbes; some of these end up in our blood, and thus travel throughout the body. One of these chemicals is called trimethylamine N-oxide (TMAO). When we break down choline, lecithin and carnitine, (which are found in high-fat dairy products, meat and eggs), this process produces TMAO. Studies have shown that TMAO potentially increases risk factors for heart disease.22,23,24,25

On the flip side, another study showed that gut microbiome had a role in elevating HDL cholesterol (the good kind) and triglycerides.26 And other bacteria within the gut microbiome may help reduce cholesterol when taking with probiotics.27

While certain bacteria in the gut microbiome can result in the production of chemicals that could block arteries and cause heart disease (TMAO), others may help lower cholesterol and reduce the chance of heart disease. This is another example of the great unknown when it comes to the gut.

The Brain

We’ve discussed how the gut and the brain talk to each other—this is called the gut-brain axis. Even though you might just expect them to communicate about hunger, there’s much more to their relationship.

The brain contains about 100 billion neurons;28 the gut has about 500 million neurons, connected to the brain through the nervous system.29 Specifically, a major nerve bundle called the vagus nerve connects the gut and brain, sending signals from both directions like an information superhighway.30 The traffic on the highway can be directly influenced by bacteria, and some species can even help produce neurotransmitters—like serotonin.31 More and more, research is suggesting the gut microbiome may interact with brain function in ways that have a real and tangible impact on how we experience our day-to-day lives.32 Studies suggest that the gut microbiome may have a role in the development of anxiety, our mood, overall cognition and even pain.

Some of the scientific results are terrifying and awe-inspiring in equal measure.

In animals, alterations to the microbial composition of the gut can induce behavioral changes such as delirium, panic, anxiety and psychosis.33 Another study in humans demonstrated the link between bacteria in the gut and mood disorders like depression.34

Aside from a direct effect of bacteria on neurotransmission and brain function, the microbiome also has indirect effects on cognitive resilience.35 Bacterial type, and number are key to the bioavailability of polyphenols and antioxidants (which help protect against neuronal and cell aging), as they have a vital role in digestion of food substances. More research is needed to unpack these ideas, because dietary and lifestyle habits absolutely play a role in these cognitive disorders as well.

Even with modern scientific imaging techniques, the inner workings of the brain are somewhat of a black box to us. The gut and the critters inside appear to be equally difficult to understand, so unpicking how these two enigmatic systems interact is like exploring the depths of the ocean—we’re only starting to figure it out.

Immune System

Somewhat counter-intuitively, bacteria in the gut microbiome play a fundamental role in our immune system to defend us against attack. A healthy gut is important to overall health.

The immune system’s role is to detect and destroy pathogens that may cause the human body harm. Interestingly, it doesn’t attack the bacteria located in the gut. You’d think it would wage war on the bacteria we cohabit with daily.

Clearly this is not the case; our immune system has learned to work together with our gut bacteria in a mutually beneficial partnership. The bacteria in our gut are alive—we are their hosts. Rather than wipe them out, one study even says, “the immune system has largely evolved as a means to maintain the symbiotic relationship of the host with these highly diverse and evolving microbes.”36 So it makes sense that they influence our susceptibility to immune-related diseases and help regulate general immunity.37

From the minute we’re no longer sustained purely by our mother, we’re consuming foods that are not sterile, so the gut becomes our first line of defense. That defense starts with the layer of cells lining the gut, called epithelial cells. Here is where the bacteria start to contribute to the partnership—microbes living in the gut activate immune functions in these lining cells.38

Another cooperative interaction between gut bacteria and the human immune system is to even out the overall balance of inflammation in the body. Inflammation is a healthy function of the immune system. Essentially, signals from the gut microbiome maintain a balance between proinflammatory cells (that secrete immune-stimulating molecules) and anti-inflammatory cells (that reduce immune responses). Individual strains of gut microbes can change the inflammatory signature of the gut; multiple studies on mice have shown that if you can alter the microbiome, you can change the balance between proinflammatory T cells and immunosuppressive regulatory T cells.39,40

In more animal studies, mice without gut microbiome (meaning, germ-free) had vastly different immune reactions than mice with colonized with bacteria—they got intestinal infections more easily.41,42

As you once possibly saw Professor Snape as a villain sabotaging Harry Potter, upon further inspection, you realized he was actually helping Harry the whole time. The bacteria in our gut might be similar, forming an unlikely alliance that actually helps our immune system instead of hurting it.

Training and Reformulating Your Gut

Now that we’ve analyzed a few of the ways the make up of your gut microbiome has an effect on overall health, let’s look at how to make yours better (if you need it).

Several inputs, like diet, supplements, environment and lifestyle, offer ways to shift the cast of characters making up your gut’s bacteria.

An image of bacteria showing how to alter your gut microbiome

Perform a Fecal Transplant

Let’s get this one out of the way first: you can transfer gut bacteria buy consuming the feces of another person. But “re-poop-ulation,” as it’s known, isn’t that simple.

Our podcast guest and biohacker extraordinaire, Josiah Zayner, went through the dangerous process of doing this to himself (do we even have to say, “don’t try this at home”?) preparing a fecal sample in a pill and consuming it. After the experiment, he compared the bacteria in his feces to that of the fecal sampler. The result? He said, "The experiment actually worked."

We won’t dive into this too deeply, but wanted to let you know this is a thing that exists, and a thing that may yield results when used in a properly controlled medical setting. Fecal transplants have been used to successfully treat Clostridium difficile infection (which causes diarrhea and intestinal inflammation). Preliminary results also suggest it may help treat other conditions like inflammatory bowel disease, obesity, metabolic syndrome and functional gastrointestinal disorders.43

Eat Diverse Foods

Generally, a diverse gut microbiome is considered healthy. It’s kind of like a numbers game; the more species of bacteria that live inside your stomach, the greater potential they have to provide health benefits.44,45,46 How does one get a diverse microbiome? It follows that a diet of diverse foods leads to a diverse bacterial ecosystem.47,48

Of course, environmental factors play a huge role in the availability of diverse food. Studies have shown a greater diversity in gut microbiome in rural regions of South America and Africa, when compared to Europeans and Americans.49,50

So, what foods exactly should you be eating to increase the diversity of gut microbes?

Start with fruits and vegetables. These are high in fiber, which you already know is important for overall gut health. One study showed that a diet high in fruits and vegetables can help prevent the growth of some disease-causing bacteria.51 Beans and legumes are also great sources of fiber.

Try: artichokes, chickpeas, blueberries, and broccoli.

Whole grains are also part of a diverse diet, containing high amounts of fiber. Whole grains can encourage the growth of Bifidobacteria,52 which are considered a beneficial bacteria that may help prevent intestinal inflammation and enhance gut health.53

Feeling funky? Fermented foods may also play a role in gut health. Because the process of fermentation involved bacteria or yeasts, many of these foods are rich in lactobacilli, a bacteria that can be beneficial for health.

Popular sources of fermented foods include: yogurt, kimchi, and kombucha. Yogurt specifically has been studied, showing it can alter gut bacteria for the better.54,55 Be sure to read labels, though. Many flavored yogurts contain high levels of sugar.

Diversify your diet, diversify your gut microbes, and potentially improve your health.

Avoid the Artificial Sweeteners

Unfortunately, as we mentioned, the standard American diet isn’t all that diverse. It’s packed with carbohydrates and processed food and, the wolf in sheep’s clothing you gut health, artificial sweeteners.

So, on the one hand, you might think that cutting back sugar and replacing it with artificial sweeteners might help to avoid metabolic imbalances. Perhaps not—if these sweeteners take down your friendly gut bacteria. A paper published in the prestigious journal, Nature, demonstrated that feeding mice artificial sweeteners resulted in gut dysbiosis and metabolic abnormalities.56 Strikingly, these observations were recapitulated in human subjects. Another study fed mice artificial sweeteners, resulting in altered gut microbiome; they possessed high intestinal levels of Clostridium and Enterobacteriaceae, both bacteria associated with disease when present in high numbers.

But, despite these findings, the link between sweeteners and gut imbalance is not completely clear cut. A recent meta-analysis looked at 29 studies and showed that aspartame (a common sweetener) was not associated with worse outcomes in terms of weight gain, blood glucose control and other markers of metabolic health.57

Prebiotics, Probiotics and Polyphenols

Let’s quickly get some vocabulary out of the way.

Prebiotics are compounds in food (mostly in types of carbs [and mostly in fiber]) that induce the growth of beneficial bacteria. The good bacteria in your gut feed on this fiber.

Probiotics are live bacteria found in supplements or certain foods. They’re ingested with the idea to improve or restore gut bacteria.

Polyphenols are a category of chemicals that naturally occur in plants. They’re micronutrients that can induce the reduction of blood pressure, cholesterol levels, oxidative stress and cholesterol levels.58

So how the heck can these help diversify and improve gut health?

Studies have shown prebiotics can help promote the growth of healthy bacteria.

Certain foods with prebiotic properties can counteract the overexpression of host targets involved in the development of metabolic disorders and inflammation.59 And some prebiotics can reduce insulin, cholesterol levels, and triglycerides in obese people.60,61 In short, the promotion of the growth of certain bacteria may help reduce metabolic syndromes. Onions, leeks, garlic, asparagus and bananas are all good prebiotic food options.

Turning our attention to probiotics, these are mostly acquired through supplementation. They don’t permanently colonize the intestines, but they may help change the overall composition of gut microbiomes and support metabolism.62 But data is mixed on their efficacy. Results have shown less of an impact in the gut microbiome of healthy people; but in those with certain diseases some results have been more promising.63

Polyphenols, however, are digested by gut bacteria.64,65 Some of the larger polyphenol molecules can’t be digested by human cells, so they make their way to the colon when they’re feasted upon by the gut microbiome. Polyphenols can also increase the number of good bacteria; these changes can be associated with lower triglyceride and C-reactive protein levels, both markers of inflammation (in a study done on cacao-derived flavanols).66 It seems sources of polyphenols come from some of the best things in life: red wide, dark chocolate, almonds and blueberries.

In addition to a diverse diet, consider targeting foods or supplements rich in prebiotics, probiotics and polyphenols.

Gut Health for Better Overall Health

New discoveries are being made all the time that show the health and function of the gut can impact the health and function of the whole body. Even though we’ve made huge strides, there’s still a lot to learn.

Even before reading this article, you likely already knew the importance of eating a diverse diet and avoiding artificial sweeteners. Now you have some insight into why they’re so important, not only from a metabolic perspective, but also for overall health.

People often say that you should treat you body like a temple. Consider it more like a ship. You’re on a journey, and the living bacteria inside your stomach are the crew helping power the voyage.

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