The Mouth Microbiome: Why Overuse of Mouthwash May Undermine Your Health

For decades, we’ve been told that a clean mouth is a healthy mouth — that we should brush, floss, and rinse with an antiseptic mouthwash twice a day to kill bacteria and “banish bad breath.” But as research into the human microbiome has advanced, a surprising truth has emerged: the mouth is not meant to be sterile. In fact, killing off the bacteria in your mouth may do more harm than good.

The oral microbiome — a complex ecosystem of bacteria, fungi, viruses, and archaea — is essential to maintaining not only oral health but also systemic wellbeing. This community of microorganisms lines every surface of your mouth: gums, tongue, cheeks, and teeth. Far from being harmful, many of these microbes play vital roles in digestion, immune defence, and even cardiovascular regulation.

The Oral Microbiome: Your First Line of Defence

The mouth is the first gateway to your digestive system and one of the body’s most active microbial environments. Over 700 bacterial species have been identified in the oral cavity, each contributing to a delicate microbial balance known as homeostasis. When this balance is maintained, beneficial bacteria keep harmful species like Streptococcus mutans and Porphyromonas gingivalis under control. When disrupted — a condition known as oral dysbiosis — inflammation, gum disease, tooth decay, and even systemic illness can follow.

Key Functions of the Oral Microbiome

1. Maintains pH Balance: Beneficial bacteria help neutralise acids produced by food and other microbes, protecting enamel and tissues.

2. Supports the Immune System: Oral microbes train the immune system to recognise and respond appropriately to potential threats.

3. Promotes Nitric Oxide (NO) Production: Certain bacteria convert dietary nitrates from vegetables into nitrites, which are then transformed into nitric oxide — a compound vital for vascular health, blood pressure regulation, and cellular energy.

4. Connects to Gut Health: The mouth and gut are closely linked; imbalances in the oral microbiome can influence gut microbial diversity and vice versa.

How Mouthwash Disrupts the Microbiome

Most commercial mouthwashes are formulated to kill 99.9% of bacteria — a promise that sounds appealing but overlooks a crucial fact: not all bacteria are bad. Studies now show that regular use of antiseptic mouthwash, especially those containing alcohol, chlorhexidine (CHX), or cetylpyridinium chloride (CPC), can significantly disturb the balance of beneficial oral bacteria.

What the Research Shows

• A 7-day study found that using chlorhexidine mouthwash twice daily altered the composition of the salivary microbiome. Beneficial Bacteroidetes and Fusobacteria declined, while opportunistic Firmicutes increased. Participants also experienced lower salivary pH, higher glucose levels, and a drop in salivary and plasma nitrite — indicating reduced nitric oxide production.
  (Plymouth University, 2022)

• A 2024 Microbiology Society study reported that an alcohol-based mouthwash promoted the growth of opportunistic bacteria such as Fusobacterium nucleatum and Streptococcus anginosus — both associated with periodontal disease and even certain cancers.

• Systematic reviews have confirmed that daily antiseptic mouthwash use can decrease microbial diversity — a hallmark of dysbiosis — and impair the nitrate–nitrite–NO pathway essential for vascular health.

The Mechanisms of Harm

1. Reduced Nitric Oxide Production: By destroying nitrate-reducing bacteria, mouthwash can impair nitric oxide synthesis, potentially influencing blood pressure and cardiovascular function.

2. Microbial Dysbiosis: Killing beneficial microbes creates an opportunity for harmful bacteria to dominate.

3. Increased Acidity: Studies have shown that chlorhexidine can lower salivary pH, increasing the risk of cavities and enamel erosion.

4. Systemic Effects: Opportunistic microbes linked to oral dysbiosis have been associated with inflammatory and metabolic disorders throughout the body.

Rethinking Oral Hygiene: From Sterilisation to Symbiosis

The goal of oral hygiene shouldn’t be sterilisation but symbiosis — supporting a balanced microbial ecosystem that defends against pathogens while maintaining essential biological functions. This is where the principles of functional medicine align beautifully with modern microbiome science.

Healthier Oral Care Strategies

1. Use Mouthwash Sparingly: Reserve antiseptic rinses for short-term use after dental procedures or during active infection — not as a twice-daily routine.

2. Choose Gentle Formulas: Opt for alcohol-free, natural mouth rinses or those designed to support microbiome balance.

3. Focus on Mechanical Cleaning: Brushing, flossing, and tongue cleaning effectively remove plaque without harming beneficial bacteria.

4. Feed Your Oral Microbiome: Eat nitrate-rich vegetables (like beetroot, spinach, and rocket), avoid excess sugar, and stay well hydrated.

5. Consider Probiotic Support: Just as spore-based probiotics like FLORISH Spore Probiotic with Fulvic Acid rebuild gut flora, emerging research supports the use of oral probiotics to restore microbial balance in the mouth.

The Oral–Gut–Systemic Connection

A healthy mouth sets the stage for a healthy gut. The bacteria we swallow with saliva continually seed the gastrointestinal tract, meaning oral dysbiosis can cascade into gut imbalance and systemic inflammation. Conversely, supporting gut health through spore-based probiotics like FLORISH can positively influence the oral microbiome by reinforcing the immune system and improving nutrient absorption.

FULFIXER Fulvic Acid also plays a supportive role here: fulvic minerals enhance cellular nutrient transport and provide trace elements that beneficial microbes — both oral and gut-based — rely on for optimal function. By maintaining this microbial harmony, the mouth–gut axis remains strong, reducing inflammation and supporting overall vitality.

Practical Takeaways for a Healthy Mouth Microbiome

• Brush twice daily and floss or use interdental brushes regularly.

• Avoid excessive use of antiseptic mouthwashes.

• Choose products that support rather than sterilise the microbiome.

• Eat a nutrient-rich, whole-food diet with plenty of green vegetables.

• Supplement strategically with microbiome-supportive products like FLORISH and FULFIXER.

• Stay hydrated and maintain balanced saliva production.

The Bigger Picture: Functional Medicine Meets Oral Health

From a functional medicine standpoint, oral health is an extension of whole-body wellness. The microbial ecosystems of the mouth and gut work together, influencing everything from digestion to inflammation, blood pressure, and even mental health. By respecting and supporting these microbial communities rather than annihilating them, we can promote resilience, balance, and longevity.

In the end, the healthiest smile isn’t just the whitest — it’s the one supported by a thriving microbiome.

References

• Rosier BT, et al. Oral Microbiome Shifts After 7 Days of Chlorhexidine Mouthwash. Plymouth University, 2022.

• Microbiology Society. Alcohol-based Mouthwash Disrupts Oral Microbiome Balance, 2024.

• Calleja-Macias IE, et al. Systematic Review: Mouthwash Effects on the Oral Microbiome, PubMed 2023.

• Lundberg JO, et al. Nitrate–Nitrite–NO Pathway and Oral Bacteria’s Role in Cardiovascular Health, ResearchPortal.hw.ac.uk.