Did you know, your mouth is home to more than 700 species of microbes?

This delicate ecosystem is your first line of defence against pathogens, a key step in digestion. But here’s the twist: the habits you use to “freshen” your mouth can either nurture or disrupt this microbial community¹.

Brushing and flossing are important, but so is considering when you clean, what you use, and how natural approaches like oil pulling or tongue scraping can support balance. A growing body of research links oral microbes not just to gum health, but to conditions ranging from inflammation to brain and heart health ^2,3. This doesn’t mean oral care “causes” or “cures” these issues, but it highlights how small, daily rituals influence much more than just your smile.

Let’s look at oil pulling, mouth rinses, whitening approaches, flossing, and a few less-talked-about habits that can help you create a microbiome-friendly evening routine.

1) Coconut oil pulling; an ancient practice with modern microbiome relevance

What it is: Swishing edible oils (traditionally sesame or coconut) for 10–20 minutes, then spitting them out.

What studies show: Clinical trials suggest coconut oil pulling can reduce levels of Streptococcus mutans (a cavity-associated bacterium), lower plaque scores, and reduce gum inflammation when added to daily brushing. Lauric acid in coconut oil is naturally antimicrobial and may help balance bacterial populations ^4,5.

How to try it: Use a spoonful of edible coconut oil, swish gently before breakfast, and spit it into the bin (not the sink). Think of this as an addition to brushing and flossing, not a replacement.

2) Mouth rinses; protect, but don’t over-sanitise!

The issue: Many antiseptic mouthwashes wipe out “good” as well as “bad” bacteria. Research shows they can reduce populations of beneficial nitrate-reducing microbes, the key players in a pathway that helps regulate blood pressure and vascular function^6,7.

Natural alternatives:

• Warm saltwater rinses (used for centuries to ease inflammation and maintain balance), or natural mouthwash with no harsh chemicals.
• Herbal rinses (e.g., aloe vera, chamomile, or green tea extracts studied for their antimicrobial and soothing effects)⁸. These support oral freshness and comfort without over-disrupting microbial communities.

Bottom line: Rinses should complement, not dominate, your routine. If you use them, choose natural, alcohol-free, and microbiome-friendly options.

3) Whitening; a gentle approach

Many commercial whitening agents rely on peroxides that can strip enamel and alter oral flora if overused. Natural approaches may not achieve the same level of whitening, but they can support a cleaner, brighter appearance:

• Oil pulling can help reduce surface stains ⁴.
• Avoiding staining foods/drinks at night (coffee, red wine) helps protect enamel tone.
• Using gentle abrasives like baking soda occasionally (in moderation, and not as a replacement for brushing) may assist stain removal. Focus on a routine that protects enamel and keeps the oral microbiome balanced ⁹.
• Hydroxyapatite can gently whiten teeth by filling microdefects, forming a lightly opaque remineralised surface, and binding to plaque bacteria. All while reinforcing enamel rather than stripping it ¹⁰.

4) Flossing; timing matters

Interdental cleaning is a simple way to prevent microbial build-up between teeth; places that brushes can’t reach. While consistency is key, many practitioners suggest doing it at night: saliva flow drops during sleep, which means bacteria have an easier time colonising. Clearing food debris and biofilm before bed gives the oral microbiome a healthier baseline overnight ^11,12.

If floss feels fiddly, natural interdental brushes or water flossers can also help.

5) Beyond the basics; often overlooked, but powerful

• Tongue scraping: Removes odour-causing compounds and bacterial films that influence taste and breath¹³.
• Dietary link: A diet rich in polyphenols (berries, green tea, herbs) feeds beneficial oral bacteria, while excessive refined sugar feeds harmful ones¹⁴.
• Hydration: A dry mouth reduces the protective flow of saliva. Staying hydrated supports both oral microbes and remineralisation of enamel¹⁵.

3 microbiome-friendly takeaways

1. Oil pulling with coconut oil can support balance, use it as an addition, not a replacement.
2. Choose natural rinses (like salt water or herbal options) instead of harsh antiseptics for everyday freshness. For an off the shelf alternative use Gutology Liquid Biome+ Mouth Rinse. 
3. Floss (or clean between teeth) daily, ideally before bed, to give oral microbes the best overnight environment.

Here is Dr Seb Lomas, biological dentist explaining his own daily habits to a better oral routine...