Deep dive into the gut microbiome
Gut health and its relationship to overall health has become quite the hot topic lately, and for good reason. Scientific research into this area of the human body has exploded, and with it, the number of supplements and “gut health” branded foods on the market. This can lead people to be a bit confused about what the microbiome really is and if they should actually be paying attention to it. When things get “trendy” it’s easy to dismiss it as just the latest nutrition fad (trust me, if this is you, you are not alone). So let’s dive into it! This post is going to be all about the gut microbiome and why everyone should care about theirs, I promise this is not just the latest trendy nutrition fad!
So what is the gut microbiome? A microbiome is the community of microorganisms living in a particular environment. The gut microbiome is the most studied and well-known, but many organ systems in the human body have their own specific microbiome community. It is estimated that the human body houses up to 40 trillion bacteria with bacterial genes actually outnumbering our human cells, so technically we are more bacteria than we are human. Research increasingly shows that these microbes play an essential role in maintaining normal organ function and overall physiological balance.
Before we dive into the good stuff, lets talk anatomy so you have a good understanding of where all these bacteria live. Our gut bacteria live in our gut, makes sense. But what is our “gut”? Our digestive tract runs from our mouth to our anus and is essentially one long hollow tube whose primary role is to break food down into nutrients that can be absorbed and used by the body. Simple right? Not even close. Our digestive tract is one of the most intricate and complicated organ systems in the body (I will get more in depth in a later post for anyone interested). Each area of the digestive tract has its own unique set of bacteria; these bacteria are essential, because we now know each strain has very important jobs when it comes to keeping that organ healthy and functioning.
MOUTH: We have ~700 bacterial species living in our mouths, a majority of them are categorized as “good” bacteria, “neutral” bacteria, and “bad” (pathogenic) bacteria. The good bacteria perform essential duties to keep our mouth and teeth healthy; they support the immune system and help prevent overgrowths of pathogenic bacteria, while some others are able to metabolize lactic acid produced by other bacteria, converting it into less harmful substances to protect tooth enamel. The pathogenic bacteria feed on sugar/starch, then produce lactic acid which breaks down tooth enamel and cause cavities. Some of these pathogenic bacteria can even cause periodontitis, a severe gum disease, by destroying gum tissue and bone from the toxins they produce.
STOMACH: The number of bacteria in the stomach is much lower due to the very acidic nature of the environment. But, the bacteria we do have in our stomach have very important jobs. Some aid in digestion by producing lactic acid that helps digest complex carbs, produce vitamins, and contributes to the immune system. We also have a group of bacteria that protects against harmful pathogenic bacteria we may consume through our food. There is also a very well known bacteria living in the stomachs of two-thirds of the world’s population called h. pylori. This bacteria lives in the stomach lining and can sometimes cause issues like low stomach acid and ulcers, but many people live with this bacteria and have no idea.
SMALL INTESTINE: The number of bacteria living in the small intestine is much lower than the colon, researchers previously believed there were no bacteria living in the small intestine, but we now know these bacteria play vital roles in digestion and absorption of nutrients. Some of their functions include: lowering pH to prevent growth of pathogenic bacteria, aiding in breaking down carbohydrates, and interacting with immune cells to promote gut tolerance and repair.
LARGE INTESTINE: The bacteria in our large intestine/colon are the stars of the show. It is currently estimated that there are 39 trillion bacterial cells in the large intestine weighing roughly 2-4 pounds. These bacteria play a vital role not only in the health of the colon itself, but also in overall human health and longevity.
So now we know what the microbiome is and where it lives inside the body, but what do these bacteria do all day? In short, the bacteria in our colon eat what we eat and they feel what we feel (again, more on that one later). They spend a lot of the day breaking down the fiber and other plant compounds that we humans cannot break down and digest; then something amazing happens. When they breakdown and consume this fiber they produce potent metabolites that influence human physiology in several ways. Certain gut bacteria contribute to the production of B vitamins and vitamin K, adding to the body’s overall nutrient pool. Disruptions in this ecosystem may influence nutrient status, particularly in vulnerable individuals. Vitamins are not the only thing they create; the most significant metabolites are short-chain fatty acids (SCFA). SCFA directly nourish colon cells and support a healthy colonic environment, which has been associated with reduced risk of colorectal disease. Not only that, but SCFA have been found to have very potent anti-inflammatory properties that influence inflammatory signaling throughout the body.
Why Diversity Matters:
We’ve covered that the microbiome in the colon consists of hundreds of bacterial strains (good and bad), but why are there so many different strains and does that matter? Greater microbial diversity is consistently associated with better metabolic and immune health, while low diversity has been linked to several chronic diseases. Think of the bacteria in your gut like a lush rain forest; each animal plays an integral part of the entire ecosystem. It’s the same for your gut bacteria. When you have a wide, diverse community of bacteria in your gut, that increases your gut’s resiliency; it is able to quickly bounce back from disturbances like antibiotics, infections, or dietary changes. More diversity in the gut also means more species that are producing those beneficial metabolites, like SCFA, which can lead to enhanced metabolic function. Lastly, the beneficial bacteria in a diverse microbiome are able to outcompete harmful bacteria for resources which helps prevent them from establishing themselves in high numbers in the gut.
What our bacteria control:
Digestion- The gut microbiome helps break down fibers and plant compounds that human enzymes cannot digest. In doing so, it produces short-chain fatty acids that support colon health, nutrient absorption, and bowel regularity. When microbial balance is disrupted, symptoms like bloating, constipation, and food sensitivities often follow.
Immune system - A large portion of the immune system is housed in the gut. The microbiome helps train immune cells to respond appropriately; defending against pathogens while preventing excessive inflammation. Imbalances in gut bacteria are linked to increased infection risk, allergies, and autoimmune activity.
Brain and mood - The gut and brain communicate constantly through the gut–brain axis. Certain bacteria influence neurotransmitters like serotonin and GABA, which affect mood and stress response. Changes in the microbiome have been associated with anxiety, depression, and altered stress regulation.
Metabolism and blood sugar - The microbiome influences how the body processes carbohydrates, regulates blood sugar, and extracts energy from food. Differences in gut bacteria may help explain why individuals respond differently to the same diet and why microbial diversity is linked to better metabolic health.
Hormones - Gut bacteria help regulate how hormones, especially estrogen, are metabolized and eliminated. Disruptions in microbial balance or slowed digestion can alter hormone clearance, potentially contributing to PMS, irregular cycles, and other hormone-related symptoms.
Inflammation - Healthy gut bacteria support the integrity of the intestinal lining and help regulate immune signaling. When the microbiome is disrupted, increased intestinal permeability and chronic low-grade inflammation can develop, contributing to long-term disease risk.
How the microbiome develops
So it’s pretty clear based on what we now know about the gut microbiome (remember, research has acknowledged that what we “know” is probably a very small fraction of what these bacteria do for us) that these bacteria play a vital role in our overall health and longevity. So how is our microbiome formed? Previously researchers believed that we are first colonized with bacteria in the birth canal (if you were born vaginally) or in the case of c-section, colonized with bacteria living on the skin. However, emerging science suggested we are colonized much sooner, in the uterus of our mothers and that a mother’s diet and microbiome have a direct impact on our own. By the time we turn two years old our microbiome appears very similar to a fully grown adult, which likely means those two years of microbiome development are very important. Each person’s microbiome is constantly being remodeled throughout their lifetime based on their lifestyle and diet.
What happens when the microbiome is disrupted?
Every gut, no matter how healthy, has pathogenic (bad) bacteria and beneficial (good) bacteria. Ideally these bacteria live together in harmony, each strain having their own function and role to play in the community. However, when this community of good and bad bacteria become disrupted this is called “dysbiosis” meaning the balance between these bacteria has been altered. There are many causes of dysbiosis, which I will cover with more depth in a future post, but the most common causes are chronic stress, poor diet low in fiber and high in ultra-processed foods, antibiotics, and poor digestion. The symptoms associated with dysbiosis is wide and varied; bloating, nausea, constipation, diarrhea, fatigue, skin rashes, increased allergies, and anxiety/depression.
We’ve discussed the numerous beneficial metabolites that are produced by our beneficial bacteria, but what about the pathogenic bacteria? Pathogenic bacteria, especially when overgrown, produce harmful metabolites that induce inflammation in the gut which can then lead to permeability of the gut barrier (AKA “leaky gut”). When the gut barrier is more permeable this allows food particles and bacterial toxins to enter the bloodstream and cause immune activation and inflammation. Dysbiosis has been linked to several chronic health issues like diabetes, cardiovascular issues, obesity, and inflammatory bowel disease.
How to support a healthy microbiome:
At this point, you may be wondering what you can do to support this ecosystem. Our lifestyle, diet, living environment, stress levels, and sleep quality all play significant roles in keeping our microbiome in good shape. Supporting your microbiome largely comes down to increasing diversity and minimizing unnecessary disruption. I will dive much deeper in a future post, but essentially focusing on the following will support microbial diversity and metabolic function:
Eating an adequate amount of fiber each day (~25-30 grams, more if tolerated)
Including fermented foods in your diet (sauerkraut, kimchi, kefir, yogurt, kombucha)
Prioritizing stress management and restorative sleep
Emphasizing a variety of fruits, vegetables, whole grains, and nuts/seeds in your diet
Avoid unnecessary antibiotic use
These foundational habits create an environment where beneficial bacteria can thrive and maintain resilience over time.
Whew! I applaud you if you have made it this far! I know this post covers a lot of information, but I do want to leave you with this concept to remember; microbes metabolize what we don’t, and their metabolic byproducts feed back into our human physiology in extremely beneficial (or potentially harmful) ways. You’re not just feeding yourself. You’re feeding a biochemical ecosystem that talks to your liver, pancreas, immune system, and brain. Our bacteria depend on us for survival, and mounting evidence suggests that long-term health depends on them as well.
