Disagree. You can not make that claim without sequencing your mouth's microbiome in the absence of probiotics for a month as well (and, really, many more than one persom's). Was your diet controlled all month? Oral hygiene habits? Any of a million other variables?

Also, it's worth pointing out that the study was designed to test one hypothesis, and you need to be very careful about looking at further claims. This test only really provided evidence that these probiotics don't introduce L. reuterii.

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

Source: I used to work in the industry.

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 seems to be able to affect results quite a lot in some cases.

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

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

I hope we see a lot more posts like this in the future.

Doctors don’t really care to look at these kinds of issues. It took years of suffering and autoimmune issues (particularly muscle spasms and joint pain) alongside gut problems before I demanded a gastroenterologist test me for H pylori and SIBO: I was positive for both.

H pylori was a painful treatment process, but I cleared it after one round of quad therapy. SIBO on the other hand, a condition I think we hardly understand, has been hard to deal with. Many rounds of rifaximin with very minimal relief and no real answer as to how to deal with it.

Doctors are hesitant to help, so I’ve resulted to a lot of personal experimentation to deal with it. The only thing that ever worked (and it’s just anecdata so unsure) was sulbultiamine supplementation, but I can’t actually get that anymore and normal thiamine doesn’t help.

This is all to say: I think microbiome is supremely important to health, very few things seem to really impact it, and doctors are hesitant to deal with these systems at all. I’m sure FMTs will become much more popular for a variety of conditions, but it seems like it’s a real risk where not only might someone else’s microbiome not be a fit for your physiology, but you could be inheriting a variety of risks the donor is susceptible to but you are not.

I am not a doctor and much of what I’m saying may be wrong. Don’t quote me please.

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

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).

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

Japan seems to love creating fat soluble forms of thiamine. I've been experimenting with a form of thiamine called TTFD. TTFD is synthetic, there's a natural form called allithiamine, derived from garlic. There's also another form called benfotiamine. All of these are fat soluble and highly highly available forms of thiamine. TTFD in particular is associated with paradoxical effects where a person can have a temporary worsening of thiamine deficiency symptoms when first consuming TTFD. Thiamine is generally considered very safe, but these supplements are pretty hefty doses, so I would suggest treading lightly.

There's also some thinking amongst some doctors that sub-clinical thiamine deficiencies being more common than most doctors realize [0] [1]

[0] Thiamine Deficiency Disease, Dysautonomia, and High Calorie Malnutrition

[1] https://www.sciencedirect.com/science/chapter/monograph/pii/...

Perhaps for good reasons?

The science is messy, there are few proven interventions and every woowoo worrywart will be pestering their doctor. Your doctor is in an unenviable position.

With doctors in New Zealand, my one trick is to find good specialists and pay them privately.

I believe that a GP only helps point you in the right direction. Our public health system is mostly too overloaded to help (unless you have a critical problem and your GP helps you get in a queue).

Not sure what helps in other countries.

But I 100% agree that you need to take responsibility for healing yourself. Only you have the motivation, and the context and experience to judge your own problems -- however one needs to take care not to get caught in irrelevant or misleading deadends (especially when mislead by corporations or alternative woowoo freaks).

I went through a similar post-antibiotics gut nightmare. There are good doctors and there are bad doctors and like everything, there are fewer good ones than bad+average ones.

Seems like you got testing and treatment eventually, I'm sorry it didn't work better; I'm replying less for you and more for anyone who encounters similar. Shop around for your docs!

I got tested very quickly for both H Pylori and SIBO in 2019 on doctor suggestions, I'd never heard of either. Sounds like this was probably around the same time as you went through this based no the antibiotic course that messed up your gut being in 2017).

I went to three doctors in six months, the one that did the testing was the second one. The one who was confident in their knowledge but didn't do anything, including the testing -> immediate no-return-visit from me. The one who said "we don't really know how this works" but also didn't do anything -> no return visit, but appreciate the candor. The one I went back to is the one who said "we don't really know how this works, but let's test for these other things we've learned more about recently, and let's also try some experimental/off-label things." I was actually negative for both of those things, so there was even more random stuff beyond that, but the only one the doctor I liked was really resistant to was a poop transplant, though personally... seems like the only known way to repopulate some of the shit, pun intended.