How Your Gut Microbiome Shapes Your Health

Did you know that your body is home to trillions of tiny organisms that play a crucial role in your health? This bustling community, known as your microbiome, is a complex network of bacteria, viruses, fungi, and other microbes that live primarily in your gut.

In recent years, scientists have begun to uncover the profound impact that these microscopic residents have on everything from digestion and immunity to mood and metabolism. Let's dive into the fascinating world of the gut microbiome and discover why it's so vital to our well-being.

In fact, the more research that is done it seems that there is no area of health that is not influenced by your gut microbiome.

Meet Your Inner Ecosystem: The Gut Microbiome

Imagine a bustling city, teeming with diverse inhabitants, each playing a unique role in the city's functioning. That's a bit like what's happening in your gut. This 'city' is home to an estimated 100 trillion microbes, belonging to more than 1000 different species.

Each person's gut microbiome is as unique as their fingerprint, but there are some commonalities at the broader levels.
A healthy gut microbiome is like a well-balanced ecosystem, with a diverse range of bacteria, a rich population, and minimal harmful pathogens.

Your Microbiome: The Unsung Hero of Your Health

  1. Guardian of the Immune System: Your microbiome helps protect against allergies, boosts your immunity, and even 'trains' your immune system to respond effectively to threats.
  2. Nutritionist at Work: It synthesizes essential vitamins and aids in the absorption of vital minerals.
  3. Master of Metabolism: Your microbiome plays a key role in managing your blood glucose levels, insulin sensitivity, mood, and even the aging process.
  4. Protector Against Pathogens: A healthy microbiome can help prevent harmful microorganisms from taking up residence in your gut.
  5. Energy Provider: It produces short-chain fatty acids (SCFAs), which serve as energy sources for your body and help maintain gut health.
  6. Enhanced GIT motility: The presence of healthy gut microbiota has been found to impact gastric emptying, small intestinal transit, and colonic transit. Interestingly, 'normal' GIT propulsive activity is determined to a significant degree by the presence of a healthy microbiome.

The Mighty Microbiome: Unleashing the Power of Short-Chain Fatty Acids

Did you know that the tiny microbes in your gut are hard at work producing substances that play a crucial role in your health? One of their most important products is short-chain fatty acids (SCFAs).

These little molecules play a massive role when it comes to your well-being, from boosting your digestion to protecting your colon. Let's explore the fascinating world of SCFAs and the microbiome.

The SCFA Superpower: Fueling Your Health

The top benefit of a healthy microbiome is the production of SCFAs. When you take probiotics and prebiotics, it's their influence on bacteria that produce SCFAs that gives you the health benefits.

Digestion Boosters: How Your Microbiome Helps You Absorb Nutrients

A healthy microbiome is like a well-oiled machine, helping to improve your digestion and nutrient absorption. It does this by converting unabsorbed carbohydrates in your colon into SCFAs. These SCFAs not only help regulate the absorption of essential minerals like calcium and magnesium but also have a positive impact on gut health.

Vitamin Factories: Your Microbiome's Role in Nutrient Production

Your microbiome is a little like a vitamin factory, involved in the production of essential B group vitamins and vitamin K. These vitamins are produced in forms that your body can easily absorb. Plus, your microbiome interacts with nearly 95% of ingested polyphenols – compounds found in many plant foods – modifying them into more effective and absorbable forms.

The Magic of SCFAs: How They're Produced and What They Do

SCFAs are produced predominantly through the fermentation of unabsorbed carbohydrates by your gut microbiome. The three main SCFAs are butyrate, propionate, and acetate. But what do these SCFAs do? Here are some of their key roles:

  1. Maintaining a Healthy pH: SCFAs help lower the pH in your colon, promoting overall colon health.
  2. Supporting the Intestinal Barrier: SCFAs play a role in maintaining the integrity of your intestinal barrier.
  3. Protecting Against Colon Cancer: SCFAs have been shown to provide protection against colon cancer.
  4. Stimulating Small Intestine Growth: SCFAs have beneficial effects on the small intestine.
  5. Aiding Regular Bowel Movements: SCFAs may help maintain regular bowel movements.
  6. Enhancing Blood Flow: SCFAs support blood flow to the colon and liver.
  7. Boosting Mineral Absorption: SCFAs assist in the absorption of essential minerals.
  8. Reducing Inflammation: SCFAs have anti-inflammatory effects.
Top Foods to increase butyrate

When Gut Microbiome Goes Out of Balance: Dysbiosis and Your Health

Imagine a bustling city thrown into chaos by a sudden influx of unruly visitors. That's a bit like what happens in your gut when dysbiosis occurs.

Dysbiosis refers to an imbalance in your gut microbiome, either due to a lack of beneficial bacteria or an overgrowth of harmful ones, or a parasitic infection.

Also Read: GI Map Test, Opportunistic Bacteria, and Dysbiosis

This imbalance can trigger inflammation and lead to various health issues.

The Ripple Effect: How Dysbiosis Impacts Your Health

Dysbiosis doesn't just affect your gut. It can have far-reaching effects on your overall health, contributing to a range of conditions from gastrointestinal issues like irritable bowel syndrome and Crohn's disease to non-GI conditions like depression, obesity, and even Alzheimer's disease.

Factors such as modern diet, lifestyle, and the use of pharmaceutical drugs have led to disruptions in the normal intestinal microflora and its activities, resulting in dysbiosis.

This dysregulation often leads to an overgrowth of potentially pathogenic microorganisms, altering the metabolic activities and byproducts of the gut ecosystem.

Diseases Associated with GI Dysbiosis

Gastrointestinal Conditions:
  • Alcoholic liver disease
  • Antibiotic-associated diarrhea
  • Chemotherapy-associated diarrhea
  • Clostridium difficile-associated disease
  • Coeliac disease
  • Crohn's disease
  • Diverticular disease
  • Irritable bowel syndrome
  • Liver cirrhosis
  • Non-alcoholic fatty liver disease
  • Radiotherapy-associated diarrhea
  • Small intestinal bacterial overgrowth (SIBO)
  • Ulcerative colitis
Non-GI Conditions:
  • Alzheimer's disease
  • Anxiety
  • Asthma
  • Atopic eczema
  • Autism
  • Chronic Fatigue Syndrome
  • Chronic kidney disease
  • Depression
  • Kidney stones
  • Metabolic syndrome
  • Multiple sclerosis
  • Obesity
  • Parkinson's disease
  • Rheumatoid arthritis
  • Type I and II diabetes
The Microbiome's Role in Specific Conditions

Let's take a closer look at how dysbiosis can contribute to specific health conditions:

  • Ulcerative Colitis: In people with ulcerative colitis, dysbiosis often involves decreased populations of certain beneficial bacteria and an increase in harmful ones.
  • Kidney Stones: The presence of a specific bacteria in your colon can reduce the risk of kidney stones. However, antibiotic therapy can disrupt this beneficial bacteria, increasing the risk of developing kidney stones.
  • Obesity: Early exposure to antibiotics has been identified as a risk factor for childhood obesity.
  • Depression: Several studies have shown an increased risk of depression with antibiotic use, which can disrupt the balance of the microbiota.
  • Mitochondrial Health: Certain microbial byproducts, such as SCFAs, can improve mitochondrial function and overall health.

Restoring Balance: Strategies for Improving Dysbiosis

So, how can you restore balance to your gut microbiome? Here are some key strategies:

  1. Feed Your Microbiome: Incorporate a wide variety of whole plant foods, polyphenol-rich foods, and resistant starch-rich foods in your diet.
  • Wide Diversity of Whole Plant Foods: Incorporate a range of fruits, vegetables, whole grains, legumes, nuts, and seeds. These foods support the growth of different beneficial microbes.
  • Polyphenol-Rich Foods: Polyphenols are bioactive compounds found in many plant-based foods. They act as prebiotics, stimulating the growth of beneficial bacteria in the gut. Include foods such as berries, dark chocolate, green tea, and colorful fruits and vegetables.
  • Resistant Starch-Rich Foods: Resistant starch is a type of dietary fiber that resists digestion in the small intestine and serves as food for beneficial gut bacteria. Examples of resistant starch-rich foods include green bananas, cooked and cooled potatoes, legumes, and certain whole grains like oats and barley.
Gut microbiome enhancing foods
2. Boost Your Intake of Prebiotics and Probiotics: Include prebiotic-rich foods and probiotic-rich foods in your diet. Consider low-level introduction of probiotic supplements to prevent symptoms like bloating and increased gas.
  • Prebiotics are specific types of dietary fibers that selectively feed beneficial gut bacteria. They promote the growth of probiotics and help establish a healthy microbial balance. Foods rich in prebiotics include onions, garlic, leeks, asparagus, artichokes, bananas, and whole grains like wheat bran.
  • Prebiotic supplements include PHGG, Galactooligosaccharides and lactulose - it is important to introduce these at low levels to prevent symptoms such as bloating and increased gas.
  • Probiotics are beneficial live bacteria or yeasts that can be consumed through certain foods. They help restore the balance of the gut microbiota. Include fermented foods like yogurt, kefir, sauerkraut, kimchi, tempeh, and kombucha in your diet to introduce beneficial probiotics.
3. Make Lifestyle Changes: Regular exercise, spending time in nature, stress reduction, and activities like gardening can all help support a healthy microbiota.
  • Exercise: Regular physical activity has been associated with a more diverse and balanced gut microbiota. Engage in aerobic exercises, strength training, or any form of physical activity that suits your preferences.
  • Gardening and Exposure to Nature: Spending time in nature, such as gardening, provides opportunities for microbial exposure. Working with soil and being surrounded by green spaces can introduce beneficial microbes to your body.
  • Stress Reduction: Chronic stress can negatively impact the gut microbiota. Practice stress management techniques like meditation, yoga, deep breathing exercises, or engaging in activities you enjoy.
  • Time in Nature: Spend time outdoors and engage in activities like hiking, walking, or picnics in nature. Exposure to diverse outdoor environments enhances microbial diversity on the skin and can influence the diversity of the gut microbiota indirectly.

When to Seek Further Help

If you've been following these strategies but still experiencing digestive issues, it may be time to consider further diagnosis and tests for gut health.

You can book your appointment with me. Just click on the button below and you'll be directed to the page where you can book your consultation.

Advanced stool tests like my favourite stool test the Gut Zoomer Test OR GI Map test can help identify whether the main issue is high levels of pathogenic bacteria, yeast or parasites, or a lack of the “good guys” and this can guide treatment strategies.

SIBO testing is another option to rule out Small Intestinal Bacteria Overgrowth, a good indication of whether this is a problem is if you find yourself getting more gas and bloating from increasing the foods that are beneficial for your microbiome, too much fiber can be problematic for SIBO.


Restoring balance to your gut microbiota isn't just about taking a pill or eating a particular food. It's about adopting a holistic approach that includes a diverse, plant-based diet and a healthy lifestyle. By nurturing your gut microbiota, you're not just improving your digestive health – you're enhancing your overall well-being.

Was this article helpful?

Affiliate Disclosure

This website contains Amazon affiliate links, which means we may receive a percentage of any product or service you purchase using the links in the articles or advertisements. You will pay the same price (or get a discount) for all products and services, and your purchase helps support Planet Naturopath’s ongoing research and work. Thanks for your support!

Planet Naturopath Editorial Policy