Oral Health & the Microbiome: Your Mouth as the Metabolic Front Porch [Facilitated: Episode 35]

The Facility Denver
2 days ago
8 min read

Most people think of oral health as brushing, flossing, and avoiding judgment from their dental hygienist. In reality, the mouth is a metabolic hotspot. It’s the starting point of the gut tube, the airway tube, and a major neighborhood of your immune system. The oral microbiome is a rich ecosystem of bacteria lining every surface. It sits upstream as a command center for digestion, nitric oxide production, inflammation, and cardiovascular function. When this community is balanced, it behaves like a quiet, competent homeowner’s association. When it’s disrupted, the neighborhood gets rowdy fast.

One of the biggest players is an unassuming pathway that runs from your salad to your saliva to your stomach. Greens, beets, and other nitrate-rich foods only contribute to nitric oxide if the bacteria living on your tongue can convert nitrates to nitrites. Once swallowed, those nitrites turn into nitric oxide—a molecule that keeps blood vessels flexible, helps mitochondria make energy efficiently, and regulates immune signaling. When you knock out those nitrate-reducing bacteria with antiseptic mouthwash, your nitric oxide production drops for the next 12 to 24 hours. Blood pressure ticks upward. Mitochondria get a little grumpy. It’s one of those physiological chain reactions that feels unfair but is completely predictable.

So what lives at the center of this story? Daily choices at the bathroom sink.

A deep dive into the habits that can turn your oral routine from a quiet troublemaker into one of your strongest metabolic allies. ahhhhh

Listen to Episode 35

OUR PERSONAL ORAL HEALTH GO-TO PRODUCTS AND RECOMMENDATIONS

Our favorite toothpaste: Fygg Flouride-Free Prebiotic Toothpaste or David's NanoHydroxyapetite

Our favorite oil pulling blend: Oliveda i88 Microbiome Oil

Go-to tools: WaterPik Flosser , HumbleCo Floss Picks , Fygg Tongue Scraper

(Splurge-worthy) electric toothbrush: Oral B iO Series7

<< Shop our Amazon Storefront for other oral health faves >>

Coffee brewing setup to maximize coffee benefits for health

Toothpaste, Mouthwash, and the Oral Microbiome

Hydroxyapatite has become our go-to for patients. It’s a mineral structurally similar to your enamel and does something wonderfully practical: it fills microscopic weak spots and supports remineralization without torching the microbiome in the process. Fluoride can be helpful in the right setting, but hydroxyapatite tends to be gentler for people with dry mouth from mouth breathing, sleep apnea, or medications.

There are also a few things worth keeping off your countertop. Sodium lauryl sulfate, the classic foaming agent, is great at producing bubbles and terrible for your mucosa. It irritates the tissue, worsens canker sores, and for some people, creates a cycle of inflammation that never fully calms down. Triclosan is another no-thanks ingredient. It’s an aggressive antimicrobial that bulldozes beneficial species far more than modern oral care routines need.

And while we’re here, let’s talk mouthwash. Even the alcohol-free antiseptic versions disrupt nitrate-reducing bacteria like Neisseria and Haemophilus. If you rely on them regularly, you’re essentially pressing pause on the nitrate–nitrite–NO system that your cardiovascular system depends on. If you truly need a rinse, go targeted and temporary—things like oil pulling or dentist-guided products that support your specific oral microbiome instead of carpet-bombing it.

ditch antiseptic mouthwash one of the best changes you can make for BETTER oral health

Electric vs Manual, Why Flossing Still Wins, and the Great Water Flosser Debate

Technique always wins over gear, but some tools do make the job easier. Electric toothbrushes help remove the guesswork. Timers keep you honest and pressure sensors prevent that over-zealous scrubbing that can slowly erode enamel. Manual brushes can work beautifully, but most people don’t hit the angles or pressure consistently.

Flossing remains non-negotiable. Brushing covers about sixty percent of the tooth surface. The rest of the action happens between the teeth, where anaerobic bacteria hang out in tight spaces that toothbrush bristles can’t reach. These are the bacteria that drive gum inflammation, bleeding, and shifts in metabolic markers.

Water flossers are fantastic for flushing under the gumline and around orthodontics, implants, or deeper pockets. They help with bleeding and reach areas string floss can’t easily navigate. But they don’t fully scrape the sticky plaque off tight contacts. The best combo is old-fashioned string floss plus the water flosser… the Batman and Robin of oral mechanics.

If you want to really evaluate your technique, use a disclosing tablet. It temporarily stains plaque and makes it obvious which zones you consistently miss. Yes, it’s humbling. Yes, it works.

Purity Coffee Beans tested for mycotoxins and antioxidants and best roasting temperatures

The Tongue: A Microbial Billboard You Can Clean

The tongue is a surprisingly large contributor to bad breath, taste changes, and ongoing inflammation. Its porous surface collects a thick biofilm that reseeds the entire mouth all day. Tongue scraping physically removes that layer more effectively than brushing the tongue, and studies show it reduces volatile sulfur compounds—the real culprits behind morning breath—and improves taste.

Scraping is mechanical, not microbial warfare. Used gently, it removes the junk without wiping out beneficial species. If someone has a thick white coating, recurrent thrush, or stubborn halitosis, scraping often pairs well with oil pulling or short courses of targeted antimicrobials… while also addressing the upstream factors like gut dysbiosis and low saliva flow.

Any persistent white patches, asymmetry, or lesions that don’t improve are a reason to see a dentist. The goal is to support tissue health, not ignore warning signs.

Tongue Scraping is an underrated tool for better oral health and oral microbiome balance

Food, Probiotics, and Timing: Simple Add-Ons That Actually Work

Diet plays a quiet but powerful role in shaping the oral ecosystem. Xylitol gum or mints after meals help starve cavity-forming bacteria by interrupting their sugar metabolism. It’s a practical tool for those moments when brushing isn’t possible.

Oral probiotics are another area with real potential. Streptococcus salivarius strains K12 and M18 help support upper airway resilience, tonsil health, and breath. Lactobacillus reuteri DSM 17938 produces reuterin, a compound that helps inhibit candida and support healthier gums. These can be especially helpful after dental cleanings or when saliva testing shows a gap in key species.

Speaking of saliva—timing matters. Meals shift the mouth into a more acidic environment for about thirty to sixty minutes. Brushing right after acidic exposure can damage enamel, so it’s better to brush before breakfast or focus on rinsing and chewing xylitol afterward.

When It’s Time for a Dentist Who Sees the Whole Picture

Some scenarios call for a deeper look: persistent bleeding gums, chronic halitosis, mouth breathing, recurrent thrush, a history of metal fillings, or root canals that never quite feel settled. This is where biological dentistry shines. They use tools like saliva testing, 3D imaging, and ozone-assisted cleanings to identify infection pockets, support microbiome balance, and preserve the nitrate-nitrite-NO pathway that keeps blood vessels relaxed.

The biggest message we hope patients take away is simple: your mouth is not a separate department of your body. It’s the front porch of your metabolic and immune health. The routines you build—daily brushing, real flossing, the right toothpaste, an intelligent attitude toward mouthwash, and a clean tongue—are upstream of everything from cardiovascular function to energy production.

Care for the ecosystem, and the whole house runs better.

THE FACILITY ORAL HYGIENE PRACTICES CHEAT SHEET

TOOTHPASTE

✅ Best Choice: Hydroxyapatite. Biomimetic mineral. Supports enamel repair. Gentle on the oral microbiome. Great for dry mouth or sensitive enamel. [Shop Toothpaste]
Avoid:
❌ SLS (strips mucosa, triggers canker sores)
❌ Triclosan (broad-spectrum antimicrobial that wipes out the good guys too)

BRUSHING

Electric Toothbrush: Timer + pressure sensor = fewer missed spots and less enamel abrasion. Consistent, predictable, fool-proof.
Manual Brush: Totally fine if technique is excellent… but most people need the assist.

Why does pressure matter? Scrubbing is not a personality trait. Light pressure protects enamel.

When is the best time to brush? Before breakfast! (Seriously! Just AskTheDentist) Post-meal acidity lasts 30–60 minutes, and brushing during that window can wear enamel. After meals, rinse with water or chew xylitol gum and wait to brush.

manual versus electric toothbrush for best oral hygiene support

FLOSSING & WATER FLOSSERS

String Floss: Non-negotiable. Reaches tight contacts. Scrapes biofilm where anaerobic, sulfur-producing bacteria hide.

Water Flosser: Great add-on. Reaches under the gumline, around appliances, and reduces bleeding. Not a replacement for string floss—think rinse + scrape.

“If you hate flossing, a water flosser is still a win. It’s not a substitute for string floss, but it’s absolutely better than doing nothing.”

TONGUE CARE

Tongue Scraper: Removes biofilm from a porous surface that constantly reseeds the mouth. Lowers sulfur compounds (the “why does my breath exist like this?” smell). Improves taste. Quick, mechanical, effective. [Tongue Scraping 101]
Brush ≠ Scrape: Brushing spreads bacteria around. Scraping lifts them off.

MOUTHWASH

❌ Skip Antiseptic Rinses: Even alcohol-free versions disrupt nitrate-reducing bacteria for 12–24 hours. This tanks your nitrate→nitrite→NO pathway and nudges blood pressure up.
✅ Better Options: Oil pulling or Dentist-guided rinses used for a specific purpose.

GUMS, MINTS & PROBIOTICS

Xylitol Gum or Mints: Starves cavity-forming bacteria. Perfect after meals when you can’t brush.

Oral Probiotics:Streptococcus salivarius K12/M18 → breath, tonsils, airway support or Lactobacillus reuteri DSM 17938 → periodontal support, candida control. **Take as lozenges or liposomal rinses, not swallowed capsules.

WHEN TO LOOP IN A DENTIST

Persistent bleeding gums
Chronic halitosis (bad breath)
Mouth breathing
White tongue coating that doesn’t improve
History of metal fillings or root canals and/or second opinion on root canals
Recurrent thrush or gum infections

A biological dentist can use saliva testing, 3D imaging, ozone, and targeted tools to protect the oral microbiome and cardiovascular health. [Local to Denver? Visit Dr. Popp at Colorado BioDental!]

Research Highlights from Episode 34: Oral Health

Oral microbiome balance supports cardiovascular, metabolic, and immune function through the nitrate → nitrite → nitric oxide pathway. [Bryan, et al]
Antiseptic mouthwashes can suppress nitrate-reducing bacteria for 12 to 24 hours, reducing nitric oxide availability and nudging blood pressure upward.
Hydroxyapatite toothpaste remineralizes enamel without altering the oral microbiome the way stronger antimicrobials can.
Sodium lauryl sulfate (SLS) increases mucosal irritation and is associated with more frequent canker sores.
Triclosan disrupts beneficial oral bacteria and contributes to microbial resistance.
Brushing reaches about 60 percent of tooth surfaces; flossing targets anaerobic, sulfur-producing bacteria living between teeth.
Electric toothbrushes improve plaque removal and reduce enamel abrasion by controlling pressure and timing.
Water flossers reduce bleeding and reach under the gumline but do not replace traditional floss for tight contacts.
Tongue scraping reduces volatile sulfur compounds, improves taste, and limits biofilm reseeding across the mouth.
Xylitol interrupts cavity-causing bacteria’s metabolism, reducing plaque formation when brushing isn’t possible.
Oral probiotics such as Streptococcus salivarius (K12, M18) and Lactobacillus reuteri DSM 17938 improve airway support, breath odor, gum health, and candida balance.
Saliva acidity spikes for 30–60 minutes after meals; brushing during this window increases enamel erosion.

Meet The Functional Medicine Team behind Facilitated:

Mitchell Rasmussen, DC, CFMP: Mitchell is a certified functional medicine practitioner with a doctorate of chiropractic at The Facility Functional Medicine Clinic in Denver, Colorado.

Lots of letters behind this name. I went into the field of chiropractic knowing I wanted to practice Functional Medicine. My biggest passion is the immune system. I've focused a lot of post-doctoral education on immunology and clinical applications for chronic diseases like Lyme and other tick-borne pathogens, viral burden, and mold exposure.

The Long Version

Kate Daugherty Functional Nutritionist at The Facility Denver

About Kate Daugherty, MS, CNS: Kate is a certified nutrition specialist and functional nutritionist at The Facility Functional Medicine Clinic in Denver, Colorado.

I embarked on my career journey in neuroscience, which seamlessly transitioned into further education in human nutrition. Utilizing food as medicine to treat the mind-body connection is truly remarkable. I believe our eating habits nourish our soul just as profoundly as they do our body.