THE MOUTH MICROBIOME

The human mouth is a microbial rainforest: 700+ interdependent microbial species call it home, and most of them are working in your favor. While we've learned to feed our gut bacteria, we've mostly ignored the bustling ecosystem in our mouths. If anything, bacteria in the mouth are still considered “the enemy.” Yet if we are to learn anything from our experience with gut ecology (or planetary ecology), it’s that we succeed primarily by nurturing favorable conditions. Now that we understand the critical importance of the mouth microbiome, we can apply the lessons we learned in the gut.

This review explores the science available on the use of probiotic supplements and other practices aimed at cultivating a healthier mouth microbiome.

QUICK TAKES

• Exercise is the best single well-studied intervention to improve the oral biome.

• Oral hygiene can be optimized: the Deep Dive reviews issues with toothbrushes, toothpaste, tongue scraping, and more

• Eating sugar and processed carbohydrates, and taking antibiotics harm the oral biome.

• We can reduce gingivitis, bad breath, strep throat, upper respiratory infections, dental cavities, and improve the immune system and resistance to infections in the mouth with Strep salivarius (strains BLIS K12 and M18), and also L. reuteri.

• The oral microbiome can likely be improved with a combination of Strep oralis, uberis, and rattus, and also with L. reuteri.

• Bad breath can be reduced with Weissella cibaria and Pediococcus acidilactici (these are both very new to me!!)

• For systemic (whole body) inflammation, we only have data on mice, but it’s promising with S. thermophilus (strain 19). In a video, researcher Erika Sonnenburg mentioned that a probiotic mixture had anti-inflammatory effects in research subjects who adhered to a healthy diet.

FAVORITE FINDS

I recommend buying most supplements from the original company website (not Amazon), unless you have access to an online dispensary like Fullscript, or they are available on iHerb.

Streptococcus salivarius K12 (BLIS K12)

• BLIS Probiotics - BLIS Probiotics are the world's first oral probiotics, developed in New Zealand and backed by more than 30 years of research. See multiple clinical effects in the Deep Dive.

• Fullscript offers S. salivarius K12 (BLIS K12) as well as M18 (Florassist), or a combination product (Hyperbiotics) aimed at reducing upper respiratory infections and dental caries (Fullscript is an affiliate link).

• Great Oral Health - BLIS K12 and BLIS M18, Lactobacillus acidophilus, reuteri, salivarius, paracasei, thermophilus, and Streptococcus salivarius

• NOW Foods - OralBiotic lozenges

ProBiora3 (S. oralis, S. uberis, S. rattus) Products

A patented blend of three strains of beneficial bacteria that improve the oral microbiome. Contains Strep oralis KJ3, S. uberis KJ2, and S. rattus JH145.

Lactobacillus reuteri Products

• Kirkman Group - Lactobacillus Reuteri Plus contains seven billion CFUs of Lactobacillus reuteri (L. Reuteri), and one billion each of three other Lactobacillus strains (plantarum, acidophilus and rhamnosus)

• BioGaia - Baby probiotic drops with L. reuteri

• Bulk Probiotics - L. reuteri powder 500 billion CFUs/gram for making yogurt

Weissella cibaria CMU Products

• OraTicx - Weissella cibaria CMU and W. cibaria CMS1 target bad breath (halitosis).

Hydroxyapatite Toothpaste

As a chocolate lover, I get a kick out of FYGG’s chocolate flavored toothpaste! They also have mint and vanilla flavors.

Toothbrush UV light disinfectant

This sounds far fetched, but I’ll be trying the VIOlife Zapi UV cleaner, just because it’s cute, and then storing my toothbrush in a drawer.

DEEP DIVE

The Oral Microbiome: A Complex Ecosystem in Your Mouth

The mouth harbors one of the most diverse and dynamic microbial ecosystems in the body, housing over 700 different bacterial species along with fungi, viruses, and other microorganisms. This complex community plays a crucial role in maintaining oral health and has far-reaching implications for overall whole body health, including brain health (Adil, 2025).

The oral microbiome begins developing at birth and continues to evolve throughout life. In the first few days of life, pioneer species such as Streptococcus, Veillonella, and Fusobacterium serve as early colonizers. As teeth emerge and the oral environment matures, additional genera establish themselves, creating the foundation of the adult oral microbiome.

Health vs. Disease States

In a healthy oral cavity, beneficial microorganisms maintain a delicate balance, preventing the overgrowth of pathogenic species through competitive exclusion, production of antimicrobial compounds, and modulation of local immune responses.

Various factors including poor oral hygiene, dietary choices high in sugars and processed foods, lack of exercise, and antibiotic use can disrupt this balance, leading to dysbiosis. Harmful bacteria include Streptococcus mutans (associated with dental caries), Porphyromonas gingivalis, and Tannerella forsythia (linked to periodontal disease).

The Oral-Systemic Health Connection

Research increasingly demonstrates that oral health extends far beyond the mouth. Oral bacteria apparently travel throughout the body, and imbalances have been linked to cardiovascular disease, diabetes, respiratory infections, adverse pregnancy outcomes, and even neurological conditions like Alzheimer's disease. This connection highlights the importance of maintaining a healthy oral microbiome not just for dental health, but for overall wellness.

Therapeutic Opportunities

Understanding the oral microbiome has opened new avenues for preventive and therapeutic interventions. Rather than simply eliminating bacteria through antimicrobial treatments, researchers are now exploring how to restore and maintain beneficial microbial communities through targeted probiotics, prebiotics, and other microbiome-modulating approaches. This represents a paradigm shift from a purely antimicrobial approach.

FIRST THE FOUNDATION

1. Eating less sugar, fewer processed carbohydrates, and more fiber improves mouth microbiome diversity (Angarita-Diaz, 2022; Olsen 2023; Zhou, 2024). The Mediterranean diet has been associated with a better oral biome, though these are observations, not experimental findings (Augimeri, 2024). Fruits, vegetables, nuts, and seeds have antimicrobial activity against oral pathogens (Augimeri, 2024). Juicing, however, may negatively affect the oral ecology (Sardaro, 2025) — smoothies are probably preferable, but no direct evidence is available. Fermented foods modify the oral microbiome temporarily. Not much information is available on the long term effects of consuming fermented foods on the oral biome (Ibarlucea-Jerez, 2024).

2.Pesticides and food preservatives predictably disrupts the oral microbiome (Ponce-Rosas, 2022; Irwin, 2022). Direct clinical trials of organic food consumption are not available. BPA (and likely the substitutes as well) reduces abundance of Strep bacteria critical to oral microbial balance.

3. Exercise: both HIIT and steady-state cardio improve the oral biome, thus improving overall health (D’Ercole, 2025; Matsumoto, 2021; Pugliese, 2019). In patients with fatty liver disease (now called MASLD), exercise triggered the appearance of bacteria that reduced mouth inflammation (Matsumoto, 2021), which would benefit the overall health of those patients.

4.Tongue scraping reduces bad breath, and probably improves the microbiome (Mosaico, 2024). Flossing improves dental outcomes, but impact on the oral biome is not known (Sambunjak, 2011). Waterpiks work at least as well as flossing for reducing plaque and gingivitis and may be superior for improving periodontal health. Little evidence is available however (Goyal, 2013). Mouthwash tends to reduce bacteria indiscriminately, resulting in dysbiosis and preventing some of the beneficial impacts of the mouth biome (Brookes, 2023).

5. Toothpaste can decimate the microbiota: definitely avoid antibacterial toothpaste and consider avoiding fluoride toothpaste (Shang, 2020). Hydroxyapatite toothpaste helps remineralize enamel and reduce caries risk (Amaechi 2019), and was found “not inferior” to fluoride toothpaste for tooth decay. Impact on the biome is not clear. Toothbrushes unfortunately become contaminated with bathroom aerosols and harmful mouth bacteria and re-seed the mouth at every use (Shang, 2020). A UV toothbrush cleaner (this one is $39) kills off toothbrush germs without leaving a residue.

6. Oil pulling reduces the overall bacterial load temporarily but it’s not clear if it improves the biome. It most likely does not improve plaque or gingival indices (Zhao, 2022; Shah, 2020, Tothova, 2023; Peekikayil 2015; Kaushik, 2012; Zurcher, 2025).

PROBIOTICS FOR THE MOUTH

Streptococcus salivarius BLIS K12 and other Strep

Upper Respiratory Tract Infections: A randomized, double-blind, placebo-controlled trial involving 112 healthy adults demonstrated that daily S. salivarius K12 supplementation for 4 months significantly reduced the incidence of upper respiratory tract infections compared to placebo, with efficacy correlating with protocol adherence (Liu et al., 2024). Several other studies also demonstrate this, especially for children, with Lactobacillus acidophilus, and with Bacillus coagulans (ConsumerLab section on probiotics).

Immune Modulation: Clinical research revealed that S. salivarius BLIS K12 triggers acute systemic immune responses, including increased IL-8 levels at 24 hours, elevated regulatory T cell frequency at 7 days, and higher IL-10 and IL-12 concentrations at 7 days post-ingestion (Laws, 2021). Taking 2 billion cells of S. salivarius K12 once daily for 14 days (along with standard of care) reduced the percentage of patients with severe COVID (Di Pierro, 2022).

Pediatric Applications: In children with recurrent pharyngeal streptococcal disease, 90 days of BLIS K12 supplementation resulted in a 90% reduction in strep throat and significant decreases in various other infections, including tracheitis, viral pharyngitis, rhinitis, flu, laryngitis, acute otitis media, and enteritis (Di Pierro, 2016).

Oral Health Benefits: A three-month trial in 42 high caries risk subjects found that S. salivarius K12 lozenges significantly improved cavity prevention compared to controls (Poorni, 2022). Additionally, the probiotic demonstrated efficacy in safely reducing the incidence, onset, and duration of severe oral mucositis in cancer patients (Peng, 2024).

Mucosal Immunity: Short-term S. salivarius K12 supplementation increased salivary secretory IgA levels and secretion in healthy subjects, supporting enhanced mucosal immune function (Bertuccioli, 2023).

Other strep probiotics: Participants who used a combination of 3 Strep (oralis, uberis, rattus) as an adjunct to scaling and root planing in periodontitis had lower harmful salivary bacterial counts at 12 weeks (Teughels, 2015).

Lactobacillus reuteri / Limosilactobacillus reuteri

Reduction of Periodontal Pathogens: In a randomized clinical trial, daily administration of L. reuteri tablets for 8 weeks in gingivitis patients significantly reduced counts of harmful bacteria in subgingival samples compared to placebo, without significant changes in clinical variables (Slomka, 2024).

Microbiome Modulation: Twelve-week supplementation with L. reuteri DSM 17938 and PTA 5289 induced a shift in oral microbiota composition, as shown by 16S rDNA sequencing, but did not affect species richness.

Antimicrobial Activity: L. reuteri produces reuterin, a broad-spectrum antimicrobial agent. Clinical studies confirm its antibacterial effect against Streptococcus mutans in healthy individuals and against Porphyromonas gingivalis in periodontitis patients, though effectiveness varies.

Lactobacillus plantarum and paracasei, Bifidobacterium lactis

A study in Sweden showed that subjects taking these two probiotics had slightly fewer colds than subjects taking placebo (Ahren, 2020).

A study in Brazil showed benefits for users of a lozenge containing Bifidobacterium lactis HN019 for one month after a deep cleaning (Invernici, 2018).

Weissella cibaria, Pediococcus acidilactici

Halitosis Reduction: Weissella cibaria CMU tablets reduce halitosis (bad breath) compared to placebo. Further reviews confirm its commercial use and effectiveness in oral care for halitosis (Lee, 2018).

Elevated levels of Pediococcus acidilactici in tongue coatings have been moderately associated with the reduction of oral malodor, but robust clinical trials are lacking. Most evidence is indirect or from mixed probiotic formulations. I can only find this probiotic as an additive for making sausage.

Reducing Inflammation

Streptococcus thermophilus (strain 19) reduced pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) in organs and attenuated LPS-induced sepsis in mice. If this is also true in humans, it would be one of the ways that probiotics can reduce whole body inflammation.

S. salivarius M18 improved gingival inflammation locally but was not assessed for systemic effects.

Antibiotics are Harmful

I found no clinical studies demonstrating that antibiotics improve the oral microbiome to positively impact health conditions. Instead, antibiotics consistently disrupt both oral and gut microbiomes, leading to negative health outcomes. They cause oral and gut dysbiosis, worsen periodontitis (and even oral bone loss!) (Langdon, 2016; Zhang, 2023). They cause long-term microbiome alterations and increase antibiotic resistance genes in the individual who took the antibiotic (Wu, 2022). They have negative impacts on oral immune function and metabolic pathways (Zhang, 2023). Clearly, antibiotics can be necessary, but they are absolutely overused.

IN SUMMARY

The practices that promote general health, especially exercise and good nutrition also support a balanced oral microbiome. This creates the foundation for beneficial bacteria to thrive naturally.

For specific oral health concerns, targeted probiotic interventions offer additional therapeutic options. Strains like Streptococcus salivarius BLIS K12, Lactobacillus reuteri for periodontal support, or Weissella cibaria CMU for bad breath provide a supportive approach to common challenges.

This represents a shift from traditional antimicrobial approaches to one that cultivates a diverse, resilient oral ecosystem. Rather than clumsily eliminating bacteria, the goal is nurturing beneficial microorganisms that naturally maintain health, resist disease, and promote thriving.

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