What Is the Microbiome?

By: Dr. Naika Apeakorang

You may have heard of the term microbiome before. You may have even heard about how important it is for your health. But do you know what it is and why it’s so important? 

Let’s dive in!


What is the microbiome?

The microbiome is a diverse, complex, and essential community of trillions of microorganisms in your body that are mostly symbiotic (a mutually beneficial relationship between two groups). Your microbiome profile is determined by your genetics, birth process (babies get more immediate microbe exposure when they pass through the birth canal), environment, diet, and more. 

So, each person’s microbiome profile is unique. The microbiome is actually composed of not just bacteria but also fungi, parasites, and viruses, which all work together to regulate and support a variety of health functions in your body. 

Your microbiome supports everything from your immune health to your digestive health to your vaginal health and even your nervous system health (via the gut-brain axis). The microbiome primarily resides in your gut, but it also makes it home in a couple of other places, including your skin and genitalia.


Why is the microbiome important?

For starters, there are more bacterial cells in your body than human cells, so that’s pretty major! While newer research suggests that babies may come into contact with gut microbes inside the womb, the relationship between the microbiome and a human gets established at birth, with the most activity occurring in the first three years of life. So, this is a life-long relationship we’re talking about! 

The microbiome is important because it stimulates and supports your immune system, defends your body against “bad bacteria,” creates key vitamins, and breaks down foods (including dietary fiber, which humans can’t break down). 


What Are the Signs That Your Microbiome Health Is Lacking?

When there’s an imbalance or disruption in the microbiome (aka dysbiosis), the body becomes more susceptible to disease. And when that happens, a slew of not-so-wonderful symptoms are likely to follow suit — let’s unpack them:


Gastrointestinal Glitches

When your microbiome is off balance, your gut is the first to throw up the red flags. Symptoms like bloating, gas, diarrhea, and constipation aren't just your body being finicky. 

They're clear indicators that your gut bacteria might be in a bit of turmoil, trying to tell you that the balance between beneficial and harmful bacteria is out of whack. It’s like when your favorite playlist gets jumbled with tracks you don’t vibe with — nothing feels right.


Sugar Cravings on Steroids

Ever find yourself longing for sweets more than usual? When your gut microbiota is out of balance, those microbes that thrive on sugar start having a rave, demanding more of that sweet, sweet energy. This can lead to an intense craving for sugars and carbs, pushing you towards a dietary spiral that only feeds the bad guys down there.


Perpetual Fatigue Syndrome

Feeling like you're running on empty even after a full night's sleep is a classic sign your microbiome might be sending SOS signals. An unbalanced microbiome can significantly impact your body's ability to absorb nutrients, leading to a lack of energy. It's as if your body's engine is trying to run on fumes — because, in a way, it is.


Mood Swings and Mental Fog

Our gut is often called our second brain, for good reason, thanks to the gut-brain axis. An imbalance in the gut microbiota can lead to mood fluctuations, stress, and a general feeling of mental cloudiness. If you feel more down or anxious than usual, or if decision-making suddenly feels like navigating through a fog, your microbiome might be calling for help.


Unexpected Weight Changes

Whether it’s unexpected weight gain or difficulty losing weight, changes in your weight without significant changes in your diet or exercise routine might stem from your microbiome. Certain gut bacteria profiles can influence how your body metabolizes food, how fat is stored, and even regulate your appetite, playing a role in obesity and weight management issues.


Skin Irritations and Flare-Ups

Your skin is a mirror reflecting your gut health. A number of skin conditions can flare up when your microbiome is disrupted. It's all about that internal ecosystem — if it's stormy in your gut, you might just see the effects on your skin.


Frequent Illnesses

Finding yourself catching every cold and flu around? Your microbiome plays an important role in your immune system. An imbalance can weaken your defenses, making you more susceptible to pathogens, recurrent infections, and even autoimmune conditions. Not good. 


So, What Exactly Disrupts the Microbiome?

Believe it or not, there are a number of things that can tip the balance from harmonious to chaotic. Here's the lowdown on what can send your microbial communities into a tailspin.



Think of antibiotics as the big reset button for your gut microbiota, sweeping through your intestinal tract with the might of a tiny antibiotic army. While they're heroes in the fight against pathogens, they don't discriminate, often wiping out beneficial gut bacteria in their campaign. It's a textbook case of "you've got to crack a few eggs to make an omelet," but at what cost to your gut ecosystem?


Dietary Decisions

Our daily menu is a direct pipeline to the bustling world of the gut microbiota. Indulging in a diet heavy on processed carbohydrates and low in fibers doesn't just mess with your waistline — it's like throwing a gastronomical gala for the less savory characters in your microbial communities. 

On the flip side, a plate piled high with diverse, fibrous foods acts as a garden party, encouraging the growth of beneficial gut bacteria. It's a delicate balance, moderated by the enzymes and metabolites these microbes produce, playing an important role in everything from breaking down lipids to modulating immune responses.


Lifestyle Factors

Ever notice how stress ties your stomach in knots? It's not just a feeling — stress can actually alter your gut bacteria, leading to gastrointestinal issues and beyond. The same goes for poor sleep habits, which can disrupt your gut microbiome balance, affecting everything from your immune responses to your mental health.


Environmental Factors

Exploring the great outdoors around us impacts our inner universe of microbes more than we think. Fresh air, pure water, and, yes, a bit of grime are champions for our microbiome. 

Picture your childhood adventures in the mud or that puppy you couldn't resist — those weren't just fun and games but a hardcore training camp for your gut buddies. Yet, our modern life's clean freak habits, indoor binging (we see you, Netflix), and city living are kinda snubbing essential microbial meet-and-greets. It's about finding a balance — less sanitizer, more nature.



Did you know that your genetic makeup can reveal a fascinating blueprint for the microbial communities thriving within you? Yup, it’s true — through the magic of metagenomics and microbiome research, scientists are uncovering how our genes lay out the welcome mat for specific microbial settlers. 

It's not so much a formal dance but an inclusive party thrown by our DNA, inviting a mix of microbes that just 'click' with us. This blend of genetics and microbiology isn't just about cohabitation — it's a symbiotic interaction essential for our health and well-being.


What is the relationship between the microbiome and the vagina?

A substantial portion of your microbiome exists in your genital tract. When the vaginal microbiome is compromised, other microorganisms get the opportunity to colonize and take over the vaginal environment, which can lead to infections such as bacterial vaginosis (aka BV), urinary tract infections (UTIs), yeast infections, and more. 

The vaginal microbiome maintains a balanced environment by keeping the vagina at a healthy pH and by maintaining its population numbers so that other harmful microorganisms don’t get the chance to take over. 

It’s important to note that your vagina actually does an incredible job of self-regulating and self-cleaning, which means that you do not and should not have to douche.


What Happens When The Vaginal Microbiome Isn't Balanced?

When the vaginal microbiome isn't balanced, a cascade of not-so-great things can happen, impacting everything from your comfort to your overall well-being. 

Let's break it down:

  • Off-Kilter pH Levels: A balanced vaginal microbiome helps maintain an optimal pH level. When imbalanced, pH levels can swing, making the environment more welcoming to unwanted guests (think: pathogens and other bacterial species that don't belong).
  • Discomfort and Odor: An imbalance often leads to discomfort, itching, or an unusual odor, signaling that not all is well in the land down under.
  • Increased Risk of Infections: Without the protective barrier of a balanced microbiome, the risk for infections other than BV, UTIs, or yeast infections goes up. This can include more obscure, less talked-about infections — such as trichomoniasis — that are just as troublesome.
  • Compromised Reproductive Health: Long-term imbalances can impact reproductive health, affecting everything from your ability to conceive to the risk of preterm labor.


What can you do to support your microbiome?


Eat a diverse range of food

A more diverse diet means a more diverse and healthier microbiome, which means more support for all of the amazing health benefits that microbiome provides. Aim to eat a balanced diet with plenty of fruits, vegetables, healthy fats, healthy grains, and your preferred protein source (ideally lean meats, fish, or plant-based protein).


Incorporate prebiotic and probiotic foods into your diet: 

You can support your gut microbiome by eating both prebiotic and probiotic foods. Prebiotic foods feed the microorganisms in your microbiome, while probiotic foods supply your body with even more health-supportive microorganisms (aka “good bacteria”). 

Some examples of probiotic foods include miso, tempeh, kombucha, kefir, kimchi, sauerkraut, and cultured yogurt. Some examples of prebiotic foods include asparagus, artichokes, garlic, onions, legumes, apples, bananas, and oats, which are all rich in fiber. 

Some foods to cut back on that compromise your microbiome include processed foods, high-sugar foods, artificial sweeteners, and red meat.


Supplement With probiotics

Probioticsupplements contain live active bacteria that support digestive health by increasing the number of microorganisms in your microbiome, improving the function of gut bacteria, supporting your metabolism, and restoring your microbiome to a more balanced state. 

While current research shows that healthy folks might not need to supplement with probiotics, it is well documented that folks with certain medical conditions (such as digestive disorders) can significantly benefit from probiotics. It’s also important to be intentional with probiotics after antibiotic use since antibiotics can compromise the state of your microbiome.


Take care of your mind-body health

Both stress and suboptimal sleep can impact both the composition and function of your microbiome. So, practice sleep hygiene and try some pre-slumber mindfulness practices like meditation or journaling to welcome a more restful sleep. 

Exercise can also support your mind-body health. Studies show that physically active people actually have a more diverse and healthier microbiome. 

Lastly, there’s some pretty interesting research showing that gardening — yes, gardening — exposes you to beneficial microorganisms in the soil. So, if it’s spring or summer where you are, this is your sign to take up gardening this year, or at least to get your hands in some soil while you set up your house plants.


The Bottom Line

At Honey Pot, we're all about embracing the naturally derived, plant-powered goodness that supports the thriving universe within you. Understanding the microbiome, from your human gut to the universe of microbes calling your human body home, is key to unlocking an aspect of human health that often goes unnoticed. 

But here's the thing — caring for this complex ecosystem isn't just about scientific terms like genome or bacterial species. It's about simple, daily actions that honor and nourish your body's innate wisdom.

Whether you're choosing our soothing washes or supporting your wellness with a probiotic boost, every choice is a step towards harmony within. After all, your body's balance isn't just about the absence of discomfort — it's about the presence of well-being in every sense. 

So here's to living in tune with your body's unique rhythm, one day, one meal, one mindful moment at a time


About the Human Microbiome | NIHHuman Microbiome Project

10 Signs of an Unhealthy Gut | Frederick Health

Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms | NIH | National Library of Medicine | PMC

Vaginal microbiome | PubMed | NIH