Oral microbiome sequencing after taking probiotics
blog.booleanbiotech.com
blog.booleanbiotech.com
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.
This happens a lot when people discover that you can order your own bloodwork. Reddit supplement and biohacking forums gets a lot of posts from people sharing bloodwork from two different dates and concluding that the changes are entirely due to their supplement regimen. When you’re only getting a couple tests it’s not easy to see that even day to day variations in these tests can be very large. Even timing of tests during the day, how you slept, or what you ate can have a lot of impact on many tests.
Doing some basic controlling without taking the supplement is important. Doing double-blind tests on yourself also isn’t that hard if you put some effort in. There have been some surprising results from people doing controlled tests on themselves and discovering that the supplements that looked promising on paper were either doing nothing or were trending toward being negative. Gwern’s experiments with magnesium supplementation which were generally flat with hints of trending toward being negative are a good example. That experiment was a good reality check during the era when the popular narrative that we were all severely magnesium deficient and the solution was high doses of magnesium for everyone.
You can get refrigerated probiotic supps at a place like Whole Foods.
Source: I used to work in the industry.
Maybe I misunderstood what my doctor said, maybe my doctor was just wrong, maybe it's actually extremely nuanced, maybe it's something I hadn't even considered. I guess all I'm saying is it's probably better to talk to your doctor(s) about it than follow self-sourced (in both the above and this comment) medical advice from HN.
None of their training really addresses that and while they might be more qualified to read research than random layman I would not in general ascribe authority to what a random practitioner has to say about probiotics. Frankly, the research on probiotics is still very much in its infancy and a LOT remains to be figured out.
Also right to highlight that just because there exist specialist in something does not mean we have the full or correct understanding yet, it's just your best place to find information regarding it unless you want to go join the field.
Great points!
Medical microbiologists would love to have a word with you. Medicine and medicine-adjacent disciplines each develop institutional knowledge that percolates from each specialized discipline.
> …the research on probiotics is still very much in its infancy and a LOT remains to be figured out.
I’m curious who you think does the research. It’s certainly not Bubba from down the creek.
If probiotics is what you’re after, why not eat or drink something fermented?
It's not "self-sourced" whatever that means (like that's a bad thing per se?). I saw the sausage being made and I spoke to the sausage makers. The source is the sausage makers, not me. Sorry I don't have a link. These facts may or may not be trade secrets.
This doesn't mean the comments should be assumed to be false any more than they should be assumed to be true. It also doesn't imply we necessarily have some way to provide an actual source either. Just that folks will have to go elsewhere if they want any certainty about this information, since we didn't provide any as random usernames on a message board saying we heard something before.
Yes, doctors are similar to mechanics or any other trade, in that some simply suck.
Some got Ds.
"even shelf-stable probiotics should not be kept above room temperature".
Hope that helps!
No way I could find a place this cold during Rio de Janeiro summer.
The best companies certify the viable count at expiration, I've seen many that do.
There is a difference between probiotics in live culture and shelf stable products but both can be viable methods of delivery.
https://seed.com/cultured/probiotics-refrigeration-storage-g...
On a few occasions when my dog has gotten sick, or needed antibiotics, shelf stabilized probiotics cleaned their digestion right up.
Are strains that only survive when refrigerated probably a higher count? Maybe. Are there stains that are better but can't be freeze dried? Probably. Are there shelf stable probiotics that are worth buying, especially if you don't have access to refrigerated stuff? Absolutely!
> PSA: If a probiotic is on the shelf, not in a cooler, it's probably not worth buying.
is exactly what I was responding to, along with your one word response "Yes" to that applying equally to all bacterial strains, which is also untrue.
If a probiotic is on the shelf, not in a cooler, it's probably not worth buying
Strains that only survive when refrigerated are maybe probably a higher count
There are probably strains that are better but can't be freeze dried
There are absolutely shelf stable probiotics that are worth buying, especially if you don't have access to refrigerated stuffIf you could just Google it up, not nearly as interesting to HN.
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.
I hope we see a lot more posts like this in the future.
I have just used them to dork around with my home lab to validate cloning results. Now I want to try something like this!
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.
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.
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
There is also a significant microbiome on your skin.
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
We evolved LPS detection so long ago that it's in our innate immune system instead of adaptive immunity. It's so ancient we share this immune function with fruit flies.
LPS detection is so good and immediate because it's tuned to pick up single instances of LPS molecules. Not a few nmol. Single molecules. Detection will trigger inflammation and immune scale up to deal with the problem.
If you go injecting LPS or E coli into your blood stream, of course your own body is going to kill you. It'll freak out and think WW III has started and begin firing the nukes in every direction to stop it.
This is septic shock.
Methanol is produced by a lot of bacteria, almost every human produces it within their body.
Chemically the problem with ethanol is that it's too close to methanol.
”Small amounts of methanol are present in normal, healthy human individuals. One study found a mean of 4.5 ppm in the exhaled breath of test subjects.[19] The mean endogenous methanol in humans of 0.45 g/d may be metabolized from pectin found in fruit; one kilogram of apple produces up to 1.4 g of pectin (0.6 g of methanol.)[20]”
”Ingestion of as little as 3.16 grams of methanol can cause irreversible optic nerve damage, and the oral LD50 for humans is estimated to be 56.2 grams.[66]”
19: https://iopscience.iop.org/article/10.1088/0967-3334/27/7/00...
20: https://onlinelibrary.wiley.com/doi/10.1111/j.1530-0277.1997...
66: https://aoemj.org/journal/view.php?doi=10.1186/s40557-017-01...