Commensal and Keystone Bacteria: Why They Matter for Gut Health and How to Balance Your Microbiome

Your gut is home to a diverse community of trillions of bacteria that work together to keep you healthy. Supposedly there are more microbes in your gut then there are stars in the Milky Way! 

Among these, some of the most essential gut bugs are the commensal and keystone bacteria species. These beneficial bacteria are crucial for maintaining a balanced gut environment, supporting digestion, influencing your immune system, and even impacting your mood through the gut-brain axis.

In this post, we’ll chat about what commensal and keystone bacteria are, why they’re important for overall health, what happens when they’re out of balance, and how lifestyle changes can support a thriving gut microbiome. By the end, you’ll have a deeper understanding of your gut’s inner world and how to nurture it for better health.

If you're curious about what's going on in your gut- reach out and let me know! 

What Are Commensal and Keystone Bacteria?

Commensal bacteria are the beneficial microorganisms that naturally reside in your gut, forming a complex ecosystem essential to your health. Keystone bacteria are a specific subset of commensal bacteria that play particularly crucial roles. For example, bacteria like Akkermansia muciniphila and Faecalibacterium prausnitzii are known to be key contributors to gut barrier integrity, nutrient absorption, and balanced immune function.

These bacteria are essential for maintaining a balanced gut environment. Commensal bacteria help extract nutrients from food, produce necessary vitamins (like biotin and vitamin K), and protect against colonization by harmful pathogens. When these beneficial bacteria are in balance, they contribute to your overall health and resilience.

Why Are These Bacteria Important?

The commensal and keystone bacteria in your gut play several key roles in maintaining your health:

1. Gut Barrier Integrity: Keystone species like Akkermansia muciniphila help maintain the gut lining by consuming mucin, which encourages mucin growth and strengthens the lining. This process is essential in preventing leaky gut syndrome, where harmful substances can pass through the gut lining into the bloodstream, causing inflammation.

2. Nutrient Absorption: Commensal bacteria aid in the breakdown of complex carbohydrates, proteins, and fats, allowing your body to absorb nutrients more efficiently. They also produce short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate, which provide energy for epithelial cells and promote a healthy gut lining. 

3. Immune System Regulation: These beneficial bacteria communicate with the immune system, helping it distinguish between harmless and harmful substances, which prevents overreactions and reduces the risk of autoimmune conditions.

4. Gut-Brain Connection: The gut-brain axis is a communication system where the state of your gut directly influences your mental health. Commensal bacteria produce neurotransmitters like serotonin and GABA, essential for mood regulation. A well-balanced microbiome supports positive mood, cognitive function, and stress resilience.

What Happens When There Are Too Few or Too Many Commensal Bacteria?

An imbalance in gut bacteria, known as dysbiosis, can occur when there are too few beneficial commensal bacteria or an overgrowth of certain bacteria. This imbalance can lead to various health issues:

Too Few Beneficial Bacteria:

• Leaky Gut: A deficiency in keystone species like Akkermansia muciniphila can compromise the gut lining, leading to increased intestinal permeability ("leaky gut"), which allows toxins and pathogens to enter the bloodstream and trigger systemic inflammation.
• Digestive Issues: Low levels of beneficial bacteria such as Bifidobacterium spp. can lead to symptoms like bloating, cramps, and IBS.
• Reduced Immunity: Low levels of beneficial bacteria can compromise mucosal health, reducing the body's ability to protect against harmful bacteria like E. coli and pathogens.

Too Many Bacteria (Overgrowth):

• Small Intestinal Bacterial Overgrowth (SIBO): Overgrowth of bacteria in the small intestine can cause symptoms like bloating, gas, and abdominal pain. GI-MAP testing can reveal specific bacterial patterns associated with SIBO, including an overgrowth of hydrogen and methane-producing bacteria.
• Inflammation: High levels of commensal bacteria like Enterococcus spp. and Lactobacillus spp. can indicate inflammation, maldigestion, and constipation. Elevated Akkermansia muciniphila levels may also be associated with high carbohydrate and sugar intake and imbalances related to metabolic syndromes.

How Can You Improve Your Commensal Bacteria Population?

To support a healthy and diverse microbiome, focus on lifestyle changes that nurture commensal and keystone bacteria. Here are some strategies to incorporate today:

1. Eat a Diverse, Fiber-Rich Diet:

   • Why: Fiber is the primary fuel for gut bacteria, especially keystone species like Faecalibacterium prausnitzii and Bifidobacterium spp. These bacteria thrive on a variety of prebiotic fibers, including foods like bananas, asparagus, garlic, onions, and oats.
   • How: Incorporate a range of plant-based foods to promote diversity and balance within your gut microbiome.

2. Include Probiotic and Fermented Foods:

   • Why: Probiotics introduce beneficial bacteria into the gut, while fermented foods support a healthy environment for existing commensal bacteria.
   • How: Add foods like yogurt, sauerkraut, kefir, and kimchi to your diet. For broader support, supplementing with diverse probiotics (250-450 billion CFUs/day) may help replenish gut flora and improve low commensal bacteria levels.

3. Limit Sugar and Refined Carbohydrates:

   • Why: High sugar intake can disrupt the balance of beneficial bacteria and promote the overgrowth of harmful species.
   • How: Focus on complex carbohydrates and fiber-rich foods, which feed beneficial bacteria without causing imbalances.

4. Support the Gut Lining with Nutrients:

   • Why: Nutrients like L-glutamine, fish oil, and polyphenols can support mucosal health and the growth of keystone species like Akkermansia muciniphila.
   • How: Consider adding L-glutamine, polyphenol-rich foods (e.g., apples, berries, cocoa, green tea), and prebiotic fibers to your daily routine to promote a balanced microbiome.

5. Manage Stress and Sleep:

   • Why: Chronic stress and poor sleep can negatively affect gut microbiome diversity and balance.
   • How: Implement mindfulness practices, regular physical activity, and proper sleep hygiene to support the gut-brain axis and maintain a balanced gut environment.

Curious About Your Gut Microbiome?

Your gut health is unique to you, and understanding what's happening inside your microbiome is the first step toward better health. GI-MAP testing provides detailed insights into your gut's microbial balance, including levels of keystone bacteria, potential overgrowths, and markers of digestive dysfunction.

If you're experiencing digestive discomfort, mood swings, or unexplained fatigue, it might be time to explore your gut's health through functional testing. Book a consultation with me today, and together, we’ll uncover the root of your symptoms and create a personalized plan to restore balance to your gut microbiome.

References:

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3.  Iannone LF, Preda A, Blottière HM, Clarke G, Albani D, Belcastro V, et al. Microbiota-gut brain axis involvement in neuropsychiatric disorders. Expert Rev Neurother. 2019 Oct;19(10):1037-1050. doi: 10.1080/14737175.2019.1638763.
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6. Rinninella, E., Raoul, P., Cintoni, M., et al. (2019). What is the Healthy Gut Microbiota composition? A Changing Ecosystem across age, environment, diet, and Diseases. Microorganisms, 7(1), 14. https://doi.org/10.3390/microorganisms7010014
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