Oral Microbiome Sequencing After Taking Probiotics

their claims on their website:

replaces S. mutans, alters oral microbiome, reduces acid via ethanol metabolism, produces antibiotic, freshens breath, brightens teeth, lasts decades. etc

i am very skeptical of it

You can get refrigerated probiotic supps at a place like Whole Foods.

Source: I used to work in the industry.

I used to turn my nose up at it, but I got some branching out at a beer bar that tasted pretty good (0.5% ABV so you'd puke from too much liquid before getting drunk). It seemed more of a breakfast drink so I had a few ounces every morning. Most regular I've been in my life. That said, the "evidence" presented in the article should not be considered due to the lack of controls (just look at the variance between day -4 and day -1). Both this comment and the article are anecdotal.

But kombucha is a lot cheaper than manufactured probiotics, refrigerated, and the drink is acidic so the bacteria in the drink should already be well suited to the stomach pH (1-3 vs 2.5-3.5 kombucha).

On a tangent, nice to see Plasmidsaurus using Emu [1], which has been shown to work great for 16S ribosomal RNA analysis on ONT by basically everyone I've heard who tried it. It has a nice algorithm for predicting if variants are due to ONT sequencing errors or are true variants, based on an expectation maximization algorithm, and thus working around the somewhat limited accuracy in ONT reads. Pretty clever stuff.

And if you want to run your own analysis on the raw data using Emu, you might want to try out our Trana pipeline built around Emu in Nextflow [2]. Apart from running Emu, it does some of the preprocessing like filtering, as well as exporting as Krona diagrams etc.

We're just putting it through validation at the clinical microbiology lab at Karolinska here in Stockholm right now.

The main caveat worth mentioning is that the choice of database will affect your results a lot. Might be worth comparing Plasmidsaurus' choice of databasese with the one shipped by default with Emu.

[1] https://github.com/treangenlab/emu

[2] https://github.com/genomic-medicine-sweden/TRANA

and probiotics are the absolute worst of the industry with endless lies in claims and products that often test with nothing of the claim in them

if you want to try probiotics

1. start with a single strain probiotic, multi-strain are often lies

2. try an extremely well known/proven probiotic

want to know something is happening? try lp299v Lactobacillus Plantarum

it's cheap, it's been studied for 30+ years so lots of trials and proven claims

it won't colonize, no oral probiotic will colonize, so you have to keep taking it or it's gone in a few days from your GI