1. Introduction – Different Microbiomes? – What is the Probiotic-Based Immune System?
The immune system has many names, and these days, the common term is the microbiome. Did you know that we have many microbiomes throughout the body?
The microbiome literally means the small living environment or domain. A microbiome is a small universe of living flora or bacteria in different parts of our body. It is specialized for the different areas and accordingly, it has different sets of flora to do different tasks. The key is a proper balance and abundance of friendly bacteria everywhere. Here are three main examples.
Skin Microbiome:
- The skin microbiome includes key bacteria such as Staphylococcus epidermidis, Propionibacterium acnes, and **Corynebacterium species**, which protect against pathogens and regulate skin health. Disruptions can lead to acne, eczema, and infections. The skin microbiome interacts with the gut and mouth microbiomes and influences mental health via the gut-skin-brain axis.
Gut Microbiome:
- The gut microbiome is a vast, living ecosystem of trillions of microorganisms—mostly bacteria, along with fungi, viruses, and spores—that inhabit your intestines. They work together to digest food, create essential vitamins, produce neurotransmitters, strengthen immunity, and maintain overall health.
- Key Microbial Groups:
- Bacteroides – Break down complex carbohydrates and plant fibers into short-chain fatty acids (like acetate and propionate) that nourish intestinal cells and support metabolism.
- Lactobacillus – Help digest lactose, produce lactic acid, and keep harmful microbes under control by maintaining an acidic environment in the gut.
- Lactobacillus plantarum – A particularly resilient species that helps protect the intestinal barrier, reduce inflammation, and support nutrient absorption, especially of amino acids and minerals.
- Bifidobacterium – Among the first microbes to colonize the infant gut; they digest oligosaccharides, produce B-vitamins, and strengthen immune tolerance while preventing infection by pathogens.
- Spore-based bacteria (e.g., Bacillus subtilis, Bacillus coagulans) – Form protective spores that survive stomach acid, aid fiber digestion, and help repopulate the gut after antibiotic use.
- Akkermansia muciniphila – Lives in the gut’s mucus layer, supporting barrier integrity, insulin sensitivity, and balanced weight regulation.
- Faecalibacterium prausnitzii – One of the most beneficial and abundant species; produces anti-inflammatory compounds and protects against disorders like Crohn’s disease and colitis.
- Saccharomyces boulardii (beneficial yeast) – A temporary resident that does not colonize the gut but helps restore balance after antibiotics, reduces diarrhea, inhibits pathogens, and strengthens the gut barrier.
- Functions of a Healthy Gut Microbiome:
- Digestion – Breaks down fibers, starches, and proteins into absorbable nutrients and short-chain fatty acids that fuel intestinal cells.
- Immunity – Trains the immune system, prevents infections, and balances inflammation throughout the body.
- Vitamin Production – Synthesizes vitamins B1, B2, B6, B12, and K, which are vital for metabolism, nerve health, and blood function.
- Neurotransmitter Production – Gut microbes produce key brain chemicals such as serotonin (mood and calmness), dopamine (motivation and pleasure), GABA (relaxation), and acetylcholine (memory and learning). These communicate with the brain through the gut-brain axis, influencing mood, sleep, and cognition.
- Gut-Brain Axis – Enables constant two-way communication between the gut and brain through the vagus nerve, hormones, and microbial metabolites — forming the biological basis for the “gut feeling.”
- Whole-Body Balance – Interconnected with the skin and oral microbiomes, helping regulate inflammation, nutrient flow, and immune strength across the body.
- When Things Go Wrong:
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Disruption of this delicate ecosystem — caused by poor diet, chronic stress, toxins, or antibiotic overuse — can lead to inflammatory bowel disease, obesity, insulin resistance, skin disorders, and even depression and anxiety due to disrupted neurotransmitter balance.In essence:
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The gut microbiome is like an inner rainforest — diverse, self-regulating, and essential to life. When it thrives, your entire body and mind flourish.
Mouth Microbiome:
- The mouth microbiome includes Streptococcus mutans, Porphyromonas gingivalis*, and Fusobacterium nucleatum, which maintain oral health and initiate digestion. Disruptions can lead to dental caries, gum disease, and systemic infections. The microbiome interacts with the gut and skin microbiomes and affects overall and brain health via the oral-gut-brain axis.
- Remember, with a healthy mouth microbiome and nutrition, 70% or more of cavities fix themselves
70% of our immune system is in the gut, and that is our first line of defense against pathogens, and each microbiome has its job, but that is the most important.
We also have immune cells for pathogens or infections. The infrastructure that produces immune cells production and transport, is in the blood and the bone marrow. such as the red and white blood cells and the platelets. These cells are produced in the bone marrow.
2. Interconnections and Brain Relation – the Gut-Brain Axis
All three microbiomes (skin, gut, and mouth) are interconnected, influencing each other’s health and the body’s overall well-being through immune modulation and metabolic pathways. These microbiomes communicate with the brain. The gut communicates by way of the the vagus nerve, thereby performing immune signaling. A healthy balance in these microbiomes is crucial for maintaining not just localized organ health but also systemic and neurological health, reflecting the intricate web of interactions within the human body.
Fermented Foods
3. Seven Advanced Points to understand, for Supporting our Microbiomes
1. Taking medical antibiotics kills all the flora in the gut, and compromises your immune system long-term.
2. Doctors suggest not taking probiotics when taking antibiotics since they will neutralize them. But, if you take spore-based probiotics, a special advanced probiotic, they do not negatively impact the antibiotics and will work to balance the gut even when taking antibiotics. Natto fermented foods and specific spore-based products from microbiomelabs.com are excellent sources and choices.
3. The best way to boost the immune system is with natural fermented foods since they are loaded with live probiotics, just like the ones in our own gut. And, even if there are only a few strains in the probiotic food, it still enhances the health of the microbiome and increases the diversity even beyond the consumed strains.
4. Some bad flora hide in their particular microbiome to avoid being detected. They create a biofilm. For the reproductive area, to combat persistent UTI infections, I recommend a 3-part natural remedy that addresses the microbiome and the biofilm issue. It is uqora.com and I have used it successfully with patients for many years.
5. Fiber is the food of probiotics. Therefore, the more fiber you eat, the more you feed your microbiome, the less inflammation you have, and the less disease you have, since 70% of disease is caused by inflammation
6. Sunlight is good for the microbiome. I recommend that people with gut issues expose their belly to the sun.
7. Improving the gut microbiome can improve mood and positively benefit depression since the gut creates neurotransmitters and happy hormones like serotonin, which are transferred to the brain by way of the gut-brain axis.
In a 2019 study, women with low vitamin D levels who received UVB light therapy showed increased gut microbiome diversity. The gut bacteria composition shifted to resemble that of hunter-gatherer populations with frequent sun exposure.
If you do take antibiotics, there is one group of probiotic products you can take even when you take antibiotics. These are spore-based bacteria such as Bacillus subtilis, Bacillus coagulans and others. They form protective spores that survive antibiotics, stomach acid, aid fiber digestion, and help repopulate the gut after antibiotic use.
