Top to Bottom Microbiome Testing: A Holistic Guide to Whole-Body Health
When people think about the microbiome, the gut usually takes center stage. But at Aya Naturopathic Medicine, we look top to bottom—from the mouth to the gut, and even the vaginal and nasal ecosystems. This approach, known as top to bottom microbiome testing, helps us understand how microbial balance (or imbalance) affects inflammation, cognition, hormones, and immunity across the entire body.
Whether you’re struggling with chronic sinus infections, digestive distress, or fatigue that doesn’t match your lifestyle, microbiome mapping can reveal the unseen contributors to your symptoms—and help guide individualized care from the inside out.
The Microbiome as an Ecosystem
Your body isn’t just a collection of organs—it’s a living ecosystem. Trillions of microbes live within and on you, influencing digestion, immunity, mood, and even memory. When these communities fall out of balance, inflammation and chronic disease can follow.
Top to bottom microbiome testing allows us to see this full picture by evaluating microbial activity at key entry points of the body:
- Oral microbiome: Influences cardiovascular and brain health.
- Gut microbiome: Affects digestion, hormones, immunity, and metabolism.
- Vaginal microbiome: Plays a role in fertility, infection resistance, and overall inflammatory tone.
- Nasal microbiome: Impacts respiratory health and sinus resilience.
Testing these interconnected ecosystems helps us identify where imbalance begins—and how it cascades through the rest of the body.
Why We Start with the Mouth
At Aya, we often begin top to bottom microbiome testing in the mouth. Why? Because the oral microbiome often reflects—and predicts—what’s happening further downstream.
A healthy mouth supports more than fresh breath and strong teeth. It influences:
- Brain health: Oral pathogens like Porphyromonas gingivalis have been linked to Alzheimer’s-related inflammation.
- Cardiovascular function: Chronic gum disease increases risk of heart disease.
- Systemic inflammation: Oral bacteria can enter the bloodstream, affecting immune balance.
When we see cognitive shifts, persistent fatigue, or unexplained inflammation, oral testing often provides the first clues.
When and Why to Consider Microbiome Testing
Top to bottom microbiome testing isn’t necessary for everyone—but it becomes a valuable tool when symptoms persist despite lifestyle changes or basic functional testing.
We may recommend microbiome analysis if you experience:
- Recurrent sinus infections or nasal congestion
- Ongoing digestive distress (bloating, constipation, or IBS)
- Hormonal imbalance or unexplained pelvic inflammation
- Brain fog, mood changes, or cognitive decline
- Chronic inflammation or immune dysregulation
Each test helps us answer three key questions:
- Is there microbial imbalance or overgrowth in a specific region?
- Are there signs of inflammation, leaky barriers, or immune stress?
- Which natural interventions—herbal, nutritional, or lifestyle—best restore balance?
How We Use Results in Personalized Care
Once we identify patterns through top to bottom microbiome testing, treatment becomes far more precise. For instance:
- Oral imbalance: We may collaborate with a biologic dentist for oral detoxification or targeted antimicrobial rinses.
- Gut dysbiosis: We use herbal antimicrobials, probiotics, and dietary strategies to restore microbial harmony.
- Vaginal microbiome issues: We focus on rebalancing estrogen metabolism, immune support, and microbial restoration.
- Nasal microbiome imbalance: We may recommend saline herbal rinses, immune modulation, and anti-inflammatory nutrients.
This data-driven yet holistic approach aligns with the naturopathic principle of treating the whole person—not just symptoms.
Oral Health and Cognitive Wellness
Our recent case studies remind us how the mouth and brain are deeply connected. In one patient, heavy metal exposure from old fillings correlated with cognitive decline. In another, early periodontal disease signaled increased neuroinflammatory risk despite an otherwise healthy lifestyle.
These examples show why top to bottom microbiome testing can be so powerful—especially when prevention and early intervention are the goals.
Curious to learn more? Our partners in biologic dentistry—like Dr. Judith Whitcomb in Nashua and Dr. Tamatha Johnson in Epping—offer advanced oral microbiome testing and whole-body dental care.
The Naturopathic Perspective: Small Choices, Deep Impacts
Your microbiome reflects your daily choices—what you eat, how you breathe, the stress you carry, and even your dental care routine. When we honor these systems as part of a single ecosystem, healing becomes more intuitive and sustainable.
If you’re curious about top to bottom microbiome testing or wondering whether oral or gut imbalance might be affecting your energy, digestion, or focus, we’d be honored to guide that process.
👉 Book a free discovery call to explore your personalized testing options.
References
- Kilian, M., et al. (2016). The oral microbiome – an update for oral healthcare professionals. British Dental Journal, 221(10), 657–666. https://doi.org/10.1038/sj.bdj.2016.865
- Sampson, T. R., & Mazmanian, S. K. (2015). Control of brain development, function, and behavior by the microbiome. Cell Host & Microbe, 17(5), 565–576.
- Hajishengallis, G. (2015). Periodontitis: from microbial immune subversion to systemic inflammation. Nature Reviews Immunology, 15(1), 30–44.
- Integrative and Functional Medicine Testing Guidelines. Institute for Functional Medicine. (2023).
- Genco, R. J., & Borgnakke, W. S. (2020). Risk factors for periodontal disease. Periodontology 2000, 83(1), 9–13.
