8 ms·

Oral microbiome sequencing after taking probiotics

• ravedave5 8mo ago
  A surprising amount of variation from day to day even.
• temp0826 8mo ago
  I have been wondering about these oral probiotics for a while. I have used BLIS K12 lozenges before and had a strange experience- it seemed like they changed my baseline for what I could detect as fresh/clean breath and I began noticing everyone else's breath (which isn't exactly pleasant, even if it's not bad per se). I never asked anyone or received feedback about my own breath personally but it made me very curious what anyone who's breath I noticed would have sensed.
• net01 8mo ago
  i remember reading about "lumina probiotic" Has anyone done research on it since, reviewing thier claims ? 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
  • TheJoeMan 8mo ago
    I recall they were offering a few people mail-in swabs to test if the colonization had taken hold, but haven’t read any follow-up.
• SirensOfTitan 8mo ago
  Only tangentially relevant, but I’ve dealt with mouth and gut microbiome issues my whole life, the latter exacerbated by a strong antibiotic I had to go on in mid 2017 for a super resistant staph infection. L Reuteri supplementation and “L Reuteri yogurt” was one of those alternative methods I read about (though I’m skeptical that reuteri is the dominant strain in this “yogurt”) 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.
  • robocat 8mo ago
    > Doctors don’t really care to look at these kinds of issues 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).
  • majormajor 8mo ago
    > 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. 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.
• biotinker 8mo ago
  I love that this is something that is feasible for someone to just do right now as a hobbyist or blogger. The prices involved here are very reasonable and well within reach of someone wanting to do some project, though not yet at "sequence your microbiome every day" levels. I hope we see a lot more posts like this in the future.
  • the__alchemist 8mo ago
    Yea; Plasmidsaurus slaps. Especially if you live near one of the drop boxes. (e.g. a research university) $15/sample, and they email the results the next morning. This sort of service is enabled in part by nanopore sequencing. I have just used them to dork around with my home lab to validate cloning results. Now I want to try something like this!
• samuell 8mo ago
  Nice experiment and writeup! 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 https://github.com/treangenlab/emu [2] https://github.com/genomic-medicine-sweden/TRANA https://github.com/genomic-medicine-sweden/TRANA
• compass_copium 8mo ago
  >However, there is some light evidence that the variation I see is not just intra-day variation. Specifically, there are several species that stay consistent in frequency across all samples: e.g., Neisseria subflava, Streptococcus viridans, Streptococcus oralis. 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.
  • rossdavidh 8mo ago
    Well, they did say "light evidence" rather than "proof".
  • Aurornis 8mo ago
    Unfortunately self-testing something like this isn’t trivially cheap, so the self experimenters tend to skip the very important control step. 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.
• throwoutway 8mo ago
  I would love to see this same analysis with a gut probiotic! I am never convinced if I'm wasting my money, which strains are best, should I do refrigerated or shelf-stable, etc.
  • staticassertion 8mo ago
    As far as I am aware, fiber has infinitely superior research behind it with far more drastic effects. Just take fiber if you're worried about gut health imo.
    • monkpit 8mo ago
      Yes, feeding good bacteria is the best bet. Probiotics are transient, they don’t colonize.
      • ungreased0675 8mo ago
        How do they get there initially?
        • ac29 8mo ago
          The environment we live in and the foods we eat are hardly sterile. There is also a significant microbiome on your skin.
    • throwoutway 8mo ago
      I agree, but if one has ever taken an antibiotic then they should replace the bacteria that they lost? Strong antibiotics completely destroy the gut biome
      • staticassertion 8mo ago
        The research doesn't strongly support probiotics even in that case one way or the other.
  • 8mo ago
• CGMthrowaway 8mo ago
  PSA: If a probiotic is on the shelf, not in a cooler, it's probably not worth buying. The best companies certify the count of organisms at time of manufacture, but no counts are guaranteed at the shelf. Probiotics are living organisms and ought to be refrigerated for max lifespan. You can get refrigerated probiotic supps at a place like Whole Foods. Source: I used to work in the industry.
  • Aeglaecia 8mo ago
    does this apply universally to bacterial strains ?
    • CGMthrowaway 8mo ago
      Yes
      • zdragnar 8mo ago
        The Internet almost universally disagrees, based on a quick search: https://seed.com/cultured/probiotics-refrigeration-storage-guide/ https://seed.com/cultured/probiotics-refrigeration-storage-g...
        • CGMthrowaway 8mo ago
          Lyophilization is a fancy word for freeze-drying. "If a probiotic is refrigerated, it doesn’t mean it’s a better quality" is of course true. But nothing that I said is false. If I am getting probiotics from a quality source, I am going to prefer the refrigerated product over the "shelf-stable" one every time.
          • zdragnar 8mo ago
            There's a difference between "choosing one over the other" and the original claim of shelf stabilized probiotics being not worth buying. 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!
• knowitnone3 8mo ago
  interesting and well written article. I would imagine what you eat, amount of saliva, dental hygiene, and a lot of other variables would affect your oral microbiome. what would be a better test is for people with "red complex" bacteria to take this and see the results. the fact that it didn't colonize tells me this is pretty much useless like most probiotics https://medicine.tufts.edu/news-events/news/are-probiotics-all-theyre-cracked-be https://medicine.tufts.edu/news-events/news/are-probiotics-a... the author concluded that they will use it again only because of the taste, not because it works.
• OutOfHere 8mo ago
  Wasn't there recently a discussion of a risk of methanol formation from an ethanol producing strain? I sure hope that none of your strains produce ethanol.
  • cluckindan 8mo ago
    Why not? Ethanol kills competing bacteria and is only produced in microscopic quantities. Methanol is produced by a lot of bacteria, almost every human produces it within their body.
    • OutOfHere 8mo ago
      Isn't methanol a strong poison? I do not believe that any probiotic or native strains produce it. Chemically the problem with ethanol is that it's too close to methanol.
      • cluckindan 8mo ago
        From Wikipedia: ”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/10.1088/0967-3334/27/7/007 https://iopscience.iop.org/article/10.1088/0967-3334/27/7/00... 20: https://onlinelibrary.wiley.com/doi/10.1111/j.1530-0277.1997.tb03862.x https://onlinelibrary.wiley.com/doi/10.1111/j.1530-0277.1997... 66: https://aoemj.org/journal/view.php?doi=10.1186/s40557-017-0197-5 https://aoemj.org/journal/view.php?doi=10.1186/s40557-017-01...
        • OutOfHere 8mo ago
          It doesn't mean it's safe to risk adding to the burden. The danger is that low-grade non-acute toxicity over the natural level could still be harmful over time. All it could take is one mutation.
• dekhn 8mo ago
  This article is basically cargo cult biotech.
  • ch4s3 8mo ago
    Tech bro woo at its finest. Can’t wait until they discover crystals.
• bzmrgonz 8mo ago
  I want this for nasal microbiome. I think modern living is wreaking havoc on our upper respiratory track. We need to find a way to regenerate or improve nasal cavity microbiome.
  • cluckindan 8mo ago
    Just don’t get caught insufflating your probiotics during lunch hour :)
  • ahstilde 8mo ago
    I think your best bet is first curing your allergies. That's what I've been working on for 5 years: www.wyndly.com
    • chasebank 8mo ago
      how do you test for allergens? i did 5 years of immunotherapy shots, twice weekly at a doctors office and i had to stay 30 minutes after each shot for the anaphylaxis risk. it worked quite well but it was really inconvenient.
      • bzmrgonz 8mo ago
        my allergy is triggered by dust mites and pollen. Not sure what the anit-mites component is in a healthy sinus cavity, but i'm sure I'm missing it. I think essentially the equivalent of wax in our ear canal. As for pollen, go figure on that one, boost my testosterone levels? I don't know.
  • inglor_cz 8mo ago
    Nasal rinsing may help. In my case, it reduced my number of colds per year from 6 to approx. 1, and they also tend to be milder. This was likely accompanied by some change in nasal microbiome as well.
    • bzmrgonz 8mo ago
      I'll look into this, maybe a salty flush. Logic is... people who live at sea or beach will 100 percent have a very saline/salty sinus cavity. So either salt sauna, or salt nasal rinse.
• ck2 8mo ago
  the supplement industry is ridiculously sketchy and virtually unregulated wild-west 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
• bhouston 8mo ago
  Hmmm makes me want to sequence by own oral biome just for kicks or my gut flora - two sides of the same system. That would be neat and I would definitely pay $100 for either if it included an analysis.
• mcc1ane 8mo ago
  https://arstechnica.com/science/2018/09/probiotics-if-you-dont-just-just-poop-them-out-they-may-muck-up-your-guts/ https://arstechnica.com/science/2018/09/probiotics-if-you-do...
• dsego 8mo ago
  Any opinions on using pure xylitol to stamp out streptococcus mutans and improve the oral microbiome.
• port3000 8mo ago
  Eat 30 different types of fruits and vegetables every week. There is no 'hacking' your way to a good microbiome via these pills.
• daveguy 8mo ago
  Fun fact: kombucha is an excellent source of probiotics and is refrigerated. 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).
• deleted 8mo ago
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