TL;DR
An N-of-1 experiment used Plasmidsaurus 16S nanopore sequencing to profile saliva before, during and after a 30-day course of BioGaia Prodentis. The product's Limosilactobacillus reuteri strains were not detected, but the oral community shifted—most notably a large post-course rise in Streptococcus salivarius.
What happened
A consumer experiment tested whether BioGaia Prodentis, an over-the-counter oral probiotic containing two Limosilactobacillus reuteri strains (DSM 17938 and ATCC PTA 5289), would colonize the mouth or alter the oral microbiome. Four saliva samples were collected: two pre-treatment baselines (days -4 and -1), the final day of a 30-day course, and one week after stopping. Samples were processed with Zymo DNA/RNA Shield and submitted to Plasmidsaurus for 16S sequencing (~5,000 reads per sample; $45 plus $15 extraction per sample). The nanopore reads had a median Q score of 23 and were ~1,500 nt long. No reads matched L. reuteri strains used in the product. The most notable change was a rise in S. salivarius to roughly 19–20% of the community one week after finishing the regimen; Streptococcus mitis declined while Veillonella tobetsuensis increased modestly. Classic gum-disease 'red complex' bacteria were not detected. The author notes considerable baseline variability and limited sampling as constraints on interpretation.
Why it matters
- Oral probiotics may not reliably colonize the mouth or may be transient and below common detection thresholds.
- Commercial nanopore 16S services make rapid personal microbiome profiling accessible at modest cost.
- Shifts between related species (e.g., S. mitis and S. salivarius) can occur over weeks, highlighting oral microbiome dynamism.
- Observed community changes could affect downstream metabolic interactions (for example, Streptococcus blooms feeding Veillonella), with possible implications for oral ecology.
Key facts
- BioGaia is a Swedish company founded more than 30 years ago that sells direct-to-consumer probiotic products and has a market cap reported at around $1 billion.
- BioGaia Prodentis contains two Limosilactobacillus reuteri strains: DSM 17938 and ATCC PTA 5289.
- The author used Plasmidsaurus' 16S nanopore service: approximately $45 for ~5,000 reads plus $15 for DNA extraction; the full four-sample experiment cost about $240 (plus supplies).
- Sample preparation: 100–250 µL saliva mixed with 500 µL Zymo DNA/RNA Shield and shipped in 2 mL screw-top tubes; the author bought Zymo Shield for about $70.
- Nanopore 16S reads returned had a median Q score of 23 (~99%+ single-read accuracy) and read lengths concentrated around ~1,500 nucleotides (typical 16S amplicon length).
- No L. reuteri reads were detected in any of the four samples; the closest matching read was ~91% identical to L. reuteri reference sequences.
- Streptococcus salivarius increased from near-absent in baseline samples to about 19–20% of the community one week after stopping the probiotic; S. mitis declined over the same interval.
- Veillonella tobetsuensis rose from ~2.1% to ~5.7% between baseline and the week-after sample, potentially linked to shifts in Streptococcus-produced metabolites.
- None of the periodontal 'red complex' bacteria (Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola) were detected in any sample.
What to watch next
- Whether L. reuteri is present transiently immediately after dosing and clears quickly—not confirmed in the source.
- If repeated or denser sampling across multiple individuals shows a consistent link between Prodentis use and S. salivarius blooms—not confirmed in the source.
- Longer-term follow-up to see whether the post-course S. salivarius increase persists or returns to baseline—not confirmed in the source.
- Direct clinical effects of Prodentis on measurable oral health outcomes (gum health, breath, caries risk) in routine consumers—not confirmed in the source.
Quick glossary
- 16S sequencing: A method that amplifies and sequences a portion of the ribosomal RNA gene present in bacteria to identify and estimate the relative abundance of taxa in a sample.
- Oxford Nanopore (ONT): A sequencing technology that produces long reads by detecting changes in electrical current as DNA strands pass through nanopores; it trades some per-read accuracy for long read length and rapid turnaround.
- Limosilactobacillus reuteri: A species of lactic acid bacteria used in various probiotic products marketed for gut and oral health.
- Q score: A measure of sequencing read quality; higher Q scores indicate lower probability of base-calling errors (e.g., Q23 corresponds to roughly 99% single-read accuracy).
- Red complex: A group of bacterial species (including P. gingivalis, T. forsythia, T. denticola) historically associated with periodontal disease.
Reader FAQ
Did the BioGaia Prodentis strains colonize the mouth in this test?
No L. reuteri reads matching the Prodentis strains were detected in any of the four samples.
Were gum-disease associated bacteria found?
No, the tested samples did not show detection of the classic 'red complex' periodontal bacteria.
Was the S. salivarius increase caused by taking the probiotic?
Not confirmed in the source; the S. salivarius rise occurred after stopping the course, and causal linkage was not established.
How reliable are these results for generalizing to other people?
This is an N-of-1 experiment with limited sampling and observable baseline variability; broader studies would be needed to generalize.
ORAL MICROBIOME SEQUENCING AFTER TAKING PROBIOTICS 2026-01-03 · health · quantifiedself, health, nanopore, sequencing Recently, a friend recommended BioGaia Prodentis to me. It is a DTC oral probiotic you can…
Sources
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