The Other Microbiomes of the Body

Most people today have heard about the gut microbiome. But the gut is only one part of a much larger microbial ecosystem that protects and regulates the body.

A microbiome refers to the community of beneficial microorganisms—primarily bacteria, but also fungi and viruses—that live on and inside us. These microbes are not just passive passengers. They play essential roles in maintaining health and defending the body. While the gut microbiome receives the most attention, several other microbiomes throughout the body play equally important roles in protecting health.

When these microbial ecosystems become disrupted—a condition known as dysbiosis—the body becomes more vulnerable to infection, inflammation, and chronic disease.

The Skin Microbiome: Your Largest Microbial Barrier

The skin is the body’s largest organ and microbial habitat. It hosts billions of microorganisms that form a protective ecosystem on the skin’s surface and within hair follicles and glands.

A healthy skin microbiome helps:

• Prevent harmful bacteria from colonizing the skin
• Produce antimicrobial substances that inhibit pathogens
• Maintain the skin’s slightly acidic pH
• Support immune signaling and wound healing
• Strengthen the skin’s barrier against environmental stressors

These microbes essentially occupy the territory, making it harder for harmful organisms to gain a foothold.  However, the skin microbiome can be disrupted by modern lifestyle factors such as:

• Harsh soaps, skin products, and antibacterial products
• Excessive sanitizing
• Environmental toxins, chemicals, and pollution
• Antibiotics
• Highly processed diets

Using gentle skin care products and supporting overall microbiome health can help preserve this protective barrier. You can check out your products at the Environmental Working Group’s Skin Deep database here. (Also check out the apps called YUKA and Think Dirty in the App store)

The Oral Microbiome

The mouth contains hundreds of microbial species that help regulate oral health and protect against pathogens.

A balanced oral microbiome helps:

• Prevent tooth decay and gum disease
• Protect against harmful bacteria
• Support nitric oxide production, which influences cardiovascular health
• Maintain proper oral pH

Overuse of antibacterial mouthwashes and breath fresheners, high sugar intake, frequent snacking, and antibiotics can disrupt this balance.

Simple habits—such as good oral hygiene and limiting refined sugars—can help support a healthy oral ecosystem.

In case you missed it, here’s our short article for more information about the oral microbiome and consequences of oral/dental health issues.

The Vaginal Microbiome

The vaginal microbiome is typically dominated by Lactobacillus species, which produce lactic acid and maintain an acidic environment that discourages infection.

This microbiome helps:

• Prevent yeast overgrowth
• Protect against harmful bacteria
• Support reproductive health
• Reduce susceptibility to infections

Disruptions may occur due to antibiotics, hormonal shifts, douching, or chronic stress. Avoiding scented products and unnecessary antimicrobial treatments can help maintain balance.

The Urinary Microbiome

For many years, scientists believed urine was sterile. Research now shows that the urinary tract contains its own microbial ecosystem that helps protect the bladder.

A balanced urinary microbiome supports:

• Defense against urinary tract infections
• Bladder health
• Local immune function

Hydration, hormonal balance, and avoiding unnecessary antibiotics can help support this microbial environment.

The Nasal and Sinus Microbiome

The nasal passages contain beneficial microbes that act as a first line of defense against inhaled pathogens.

A healthy nasal microbiome helps:

• Prevent colonization by harmful microbes
• Regulate local immune responses
• Protect against chronic sinus infections

Environmental toxins, mold exposure, pollution, and repeated antibiotics can disrupt this protective ecosystem.

The Body as an Ecosystem

From a functional medicine perspective, the body’s microbiomes function as interconnected ecosystems. The gut, skin, oral cavity, urinary tract, nasal passages, and vaginal environment all communicate through immune signaling, inflammation pathways, and metabolic interactions. Because of this connection, disturbances in one area—especially the gut—can influence microbial balance throughout the body. When these protective microbes are depleted or imbalanced, the body’s natural defenses weaken, making it easier for inflammation, infections, and chronic health problems to develop.

Protecting these microbial partners is one of the most powerful ways to support long-term health.

Simple habits that support healthy microbiomes include:

• Eating a diverse, fiber-rich, whole-food diet
• Include fermented foods when tolerated
• Avoiding unnecessary antimicrobial and antibacterial products and prescriptions
• Supporting restorative sleep and stress resilience
• Staying hydrated and maintaining healthy oral hygiene
• Addressing environmental triggers such as mold or toxins

In many ways, we are not just human—we are a living ecosystem. Trillions of microbes inhabit our bodies, forming complex communities that help regulate immunity, defend against pathogens, and maintain the integrity of our protective barriers. In case you haven’t heard, 90% of our DNA is not our own! It belongs to all the microbes that live on us and in us.

When we protect these microbial ecosystems, they return the favor by helping protect us.

Be kind to your ecosystem. Be Well.

References

Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012.

Grice EA, Segre JA. The skin microbiome. Nature Reviews Microbiology. 2011.

Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nature Reviews Microbiology. 2018.

Nakatsuji T et al. Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus. Science Translational Medicine. 2017.

Chen YE, Fischbach MA, Belkaid Y. Skin microbiota-host interactions. Nature. 2018.

The Woodlands Institute for Health & Wellness - Mila McManus MD

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