alt Hacker NewsOral microbiome sequencing after taking probiotics
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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.
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.
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.
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.
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.
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.
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.
Any opinions on using pure xylitol to stamp out streptococcus mutans and improve the oral microbiome.
A surprising amount of variation from day to day even.
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.
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
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).
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
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-a... the author concluded that they will use it again only because of the taste, not because it works.
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.
Eat 30 different types of fruits and vegetables every week. There is no 'hacking' your way to a good microbiome via these pills.
>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.