>This is one of the most polarizing choices one can make as a biomedical research scientist. The alternative to the hockey stick is to use glass beads that you autoclave then sprinkle on the plate and roll around. People are very passionate about their chosen method and will attempt to convert you.
It turns out vim vs emacs is a universal phenomenon.
> While unhappy microbiomes can be unhappy in their own way, we do not have a consensus on what a “healthy” gut microbiome looks like, either. In collaboration with a continent-wide consortium in Africa, our lab helped catalogue the species found in healthy adult women across the continent. We found over 1,000 new species relative to what had been previously described in studies focused on Western countries.
>Companies trying to introduce targeted combinations of microbes into the gut are thus forever shooting at a moving target.
IIRC, the only semi-reliable way to "adjust" one's microbiome is to find someone who is healthy (and preferably your target body composition/energy levels/psychological profile; and, even more preferably - and possibly paradoxically - who is as close to "you", genetically and physiologically, as possible), harvest and freeze their feces, and take a daily, months-long course of the resulting poop pills, hoping that their gut microbes colonize your own digestive system.
Very, very well written and enjoyable to read!
I loved this! The article was written in such an approachable way for someone less familiar with microbiology
Learning that MIT has an ancient bottle of rotting milk reminded me of my 9th grade science teacher. He had been teaching for decades and had a tremendously messy little office attached to his classroom. The pièce de résistance of his menagerie of scientific oddities was a large fish tank filled with many strata of mottled goos. I asked what it was and he said it used to be an ordinary aquarium, filled with fish and water, and he just left it alone for 20 years.
I bet one of them tastes fantastic
Playing the long-game version of oil production
That was a fun read. The author has a really good storytelling style.
I dont understand why the cold brew test had fewer bacteria than the steeped teas. If the bacteria are shielded in spores, shouldnt it be expected that they have the same amount of bacteria?
I think it’s just that the bacteria in the hotter container woke up to a warmer, nicer environment. Warm temperatures are much better for bacterial growth. While it was too hot they didn’t seem to care at all since their spores protect them completely from damage.
They could have some coating that make them stick to the content of the tea bag, basically affecting their solubility.
Perhaps just random variation? They only did one plate, after all.
Agreed - I really enjoyed the writing. I'd have normally skimmed for the conclusion but ended up reading it all. Shame that that's so rare these days.
This is kinda disgusting but I think applies to this discussion.
Blue cheese. Its living mold. I think it tastes good.
BUT.. when I eat it, I notice a few days later that my excrement smells more like blue cheese as well. My guess is that I'm inoculating my own digestive tract with blue cheese molds.
Another mishap happened with my cat too. I gave her some beef from our supper. Some of the gorgonzola blue cheese sauce got on it, but I thought I cut and kept the blue cheese off. Nope, I didnt, not enough. She had diarrhea for the next 2 days cause it wrecked with her digestive tract.
Maybe this will help a microbiologist.
thanks now I'm imagining you farting spore clouds
Kopi Luwak is coffee that’s been digested by a cat, and it’s very valuable.
You might be onto something, have you considered trying the cat blue cheese?
So under most brewing conditions a nonzero amount of this microbe survive, but that count is 3 orders of magnitude lower what might be termed a “therapeutic dose?”
What even is a good experimental design for probiotic tea? Brew -> agitate in hydrochloric acid & digestive enzymes for X minutes -> mix with billions of existing gut microbes (that may kill this microbe or out-compete it for resources) and incubate at body temperature -> count the number of new colonies of this particular microbe?
The author does mention that a synthetic digestive system was used in another experiment, so you may be correct!
Hockey stick? Glass beads? What happened to the good old inoculating loop?
Loops are good for streaking. It's hard to get even coverage with a loop, so loops would make it hard to get accurate CFU/ml counts. Loops are more likely to get you single colonies even if you're inoculating from a high density culture, so loops are usually used when picking single colonies is the goal. Sterilized cheap flat toothpicks work pretty well for streaking too.
People interested in this: if you are ever in Amsterdam, I recommend to visit the Micropia museum: https://www.artis.nl/en/artis-micropia
Among many stunning things, they have a shelf full of foods and drinks (behind glasses) with age labels, ranging from days to years. It is fascinating to see how they evolve over time.
thanks for this
Love this museum! It's child and adult friendly. They also have the best souvenir: a collab with a local brewery for wild ales (sour beer)!
Cool story with an interesting ending (to me at least).
Just a tiny nit... Should "Brewed as directed for 4 minutes in boiling water." be "Brewed as directed for 4 minutes in boiled water." Was the tea sitting in water that was boiling or placed in water that just boiled? The later is how I brew my teas.
Left in previously boiled water for 4 min. We can deduce this from the second sample, which simulates forgetting your tea bag in the mug for 15 min.
I think GP meant in the tea instructions
Isn't boiled water what goes up into the air?
The boiled water (assuming even heating throughout) is what reaches boiling temperature, 100°C, which is the entire pot. Additional energy applied to the pot/water after that point turns at some rate the already-at-100°C-boiled-water into water vapor/gas/steam. If you stop heating before all the already-at-100°C-boiled-water disappear, you have left what is or will have been "boiled water".
spores are the reasons that labs use autoclaves instead of boiling to sterilize things. autoclaves are pressurized so can reach much higher temperatures
I didn't know pressure is used in sterilisation. Trying to look up why that helps, the Wikipedia article on autoclaves does not explain why but says it uses 1 bar, which would be equivalent to ambient pressure (atmosphere at sea level is ~1.01 bar). Does it maybe mean an additional bar, so twice atmospheric pressure?
Wikipedia also says it uses steam, not just hot air, and again doesn't say anything as to why
Do you know why pressure and steam help?
Edit: I may have found it while looking at what I thought was an unrelated part of the rabbit hole. Gravity displacement sounds like antigravity technology but it's apparently the cheapest autoclave type and means "displace using gravity" (by letting gravity do its thing; not adding in a vacuum pump). What it's displacing is air. This matters because
> Steam at 134 °C can achieve a desired level of sterility in three minutes, while achieving the same level of sterility in hot air requires two hours at 160 °C. (—Wikipedia)
I'm now assuming that pressure must help push the air out, and steam is used for having better heat conductivity. Neither is quite spelled out but that's my best guess currently
I'm pretty sure it is because when there is high pressure the boiling point of water is higher.
In case anyone else is curious about the current status:
> The Milk was declared missing on August 20th, 2022.
> The dorm’s extended mailing list of over 300 current students, alumni, and other assorted Random-adjacent humans was contacted, twice.
> In the end, no Milk.
https://mitadmissions.org/blogs/entry/guest-post-the-random-...
Just imagine a "Missing Milk" [1] on the side of a milk carton campaign. I'd be so confused haha.
[1] https://en.wikipedia.org/wiki/Missing-children_milk_carton
Did they ever put its photo on the side of a milk carton?
Humans should wear shirts with a missing milk photo on it.
Fascinating post. Why did the author steep the tea at home?
"It was at this point I realized I needed a sterile-ish way to transport the steeped tea and tea bags from my house to the lab."
Was steeping the tea at home somehow relevant to the experiment?
Probably frowned on to bring in food stuff and make it in a bio lab.
If I had to guess, it would be because that's exactly the environment and process that consumers will use, so it would capture variables such as "what if the probiotic was out-competed by a bacteria living on your mug?"
And then I would assume the sterile transfer was to preserve this state of the tea as-made without changing it on the way to the lab.
So bring mugs to the lab? Make the tea in a kitchen at the lab?
A great read from the author. It reminded me of my previous life as a bioprocess engineer, where I led investigations into biologically contaminated batches in biotech. It was fun stuff and I still remember some of the best advice I received from an Executive Vice President to never underestimate a microbe.
On this subject, I once led an investigation in which Bacillus cereus somehow survived in situ media sterilisation for 30 minutes and >121.1°C, despite there being no cold spots. At the end we realised it was the bioburden load of a media component and water temperature used during compounding.
> it was the bioburden load of a media component and water temperature used during compounding.
In English, please ;-)
I put it in AI and even that couldn't fix the sentence sufficiently for me to understand it completely.
"So, in ordinary language:"
"One dirty raw ingredient introduced far more spores than expected, and the way it was mixed into the water made the sterilization cycle less effective against them. The autoclave itself was probably not broken."
"The exact relationship to water temperature remains somewhat ambiguous because the HN commenter did not provide the detailed investigation findings."
It actually took me a minute to decide whether or not to upvote the AI-content post. But it was informative, you were forthcoming on the origin, and the GP has yet to elaborate. Thank you for posting that.
To be fair I omitted some key information. The 'dirty raw ingredient' mixed in room-temperature purified water wasn't sterilisable. The same process but mixed in 60°C purified water was sterilisable.
> about 7 out of 10 people in the U.S. were prescribed antibiotics in 2024 according to <CDC data>.
This blew my mind so I double checked the source. It links to https://www.cdc.gov/antibiotic-use/hcp/data-research/antibio... which contains some numbers but not the claim. It links to various reports, the latest one (2024 at the time of writing) https://www.cdc.gov/antibiotic-use/media/pdfs/2024-Annual-Re... says at the top of page 2 that the prescription rate is 679 and 775 doses per 1000 people in 2024, depending on the gender. That matches the 7-in-10 number so I'm guessing this is where the statistic comes from
Doesn't that reflect how many prescriptions there were rather than what number of people got it prescribed? See also page 3 where Mississippi has 1167 doses per 1000 persons. Either the number of people is wrong (if the prescription given to a tourist and counted towards this statistic, the tourist should also be counted as person, but the CDC says they take the population count from a census) or it's about doses and not about what part of the population got an antibiotic in the last year. In both of these cases, you can't conclude 116.7% of people got antibiotics prescribed. The claim in the article based on that CDC data sounds to me like saying 520% of the people drink alcohol when, in reality, 10% drinks a bottle a week and the rest nil
I'm probably misunderstanding the CDC report but I'm not sure how I should be able to tell that
Yes I stopped reading there after checking the source myself and seeing the same discrepancy. I had also noticed earlier in the article she wrote, "This finding was great news for Napoleon. The French were losing money, and perhaps more alarmingly, their reputation, exporting wine to the British – the wine would “spontaneously” go bad during shipping."
Pasteur was born after Napoleon was exiled. Maybe she is referring to Napoleon III, but then it's misleading to just write "Napoleon." Two factual mistakes in the first couple pages and I can't trust the rest. Especially on a topic I know little about so I can't be discerning regarding.
Wait is that individual doses? Like one prescription would commonly be for 20-30 doses.
I had 2 or 3 rounds of antibiotics and steroids in 2025 for a stubborn ear infection.
There's no way 7 in 10 people were prescribed antibiotics in 2024. This looks like a simple and egregious misinterpretation of the data, which seem to be all too common. I could believe there were 700 prescriptions given in the US per 1000 people in the US population. But many of those would be repeats to the same smaller number of people. I still would say there's way too much antiobiotic use - every time doctors have wanted to give me antiobiotics it wasn't necessary.
This would be my read.
Hell - my children just this year would have counted for 10+ doses (my daughter 6 all by herself for a series of severe ear infections).
Yes, it's "number of prescriptions" (but not "number of people prescribed" or "number of doses"). One person could be prescribed an antibiotic (or multiple) several times a year.
I'm amazed that there are 1216 antibiotic prescriptions per 1000 people per year in West Virginia though (2.5x the rate of California or Colorado, which itself frankly seems pretty high). Are large parts of the South just awash with bacterial infections, are people being prescribed antibiotics for viral illnesses, or are they just taking antibiotics prophylactically?
> antibiotics prophylactically
Ticks are pretty bad nearby in WPA, I've taken antibiotics prophylactically for them.
What about ivermectin? I've taken ivermectin prophylactically when traveling because I'm afraid of bed bugs. Pretty sure you can do the same with ticks. Just stop by your local farm supply store and pick up some of that nasty apple flavored horse paste. Just make sure you dose it right. Easy to do. Absolutely disgusting.
I boiled water today and survived.
Interesting… did you boil the water with you inside of it?
Cooked.
Non-native speaker here. I hadn't noticed there are two words for what seems like the same thing. Is there a difference between a water boiler and a water cooker?
oh, no that wasn't a correction - it was a pun because "cooked" in American slang means "broken / destroyed / over". In parent's context, "boiling" is correct.
"Boiling" does have a few meanings in English. As a verb, it can either mean "cook in boiling liquid", or it can mean "heat a liquid to its boiling-point". As an adjective, it means "heated to boiling-point". Also "boiling angry" means very, very angry.
Another organism that survives pasteurization is paratuberculosis, in milk. It is commonly found in commercial dairy herds. In my opinion, this is alarming.
Many consider it to be a candidate for the cause of Crohn’s disease. Johne’s disease, which occurs in a subset of cattle infected by paratuberculosis, bears many similarities to Crohn’s disease.
When Crohn’s disease was first described, it was believed to be an intestinal tuberculosis, though tests seemed to counter this idea; to this day, it remains difficult to test humans for paratuberculosis infections.
[0] https://www.sciencedirect.com/science/article/abs/pii/S07400...
[1] https://www.journalofdairyscience.org/article/S0022-0302(19)...
More good reasons to avoid the expensive poison water called milk
can you explain why you feel this way, instead of making radical claims without saying why?
As if millions of mammals suddenly cried out in terror, and were suddenly silenced.
To be fair, this was a comment about commercially produced cows milk.
Then the statement can be corrected:
As if billions of mammals suddenly cried out in terror, and were suddenly silenced.
Spore forming bacterium are notoriously resistant to most ways of killing them. There's even a species that can resist radiation amounts that are 1000x the dose needed to kill a human.
I want this mutation. You have little nano-crawlers going up and down your DNA strands fixing problems. It’s like ECC RAM for the essence of YOU. And you’re basically immune to cancer.
> It’s like ECC RAM for the essence of YOU
Buddha would like a word with you
So if, say, you were completely irradiated - every atom of your being - and fully repaired, would you still be 'you'?
/Is that a transporter energizing I hear?
That is not how spores work.
Let the man dream (and possibly write interesting scifi about it).
It is in fact how Deinococcus radiodurans works:
Deinococcus radiodurans has a unique quality in which it can repair both single- and double-stranded DNA. When damage is apparent to the cell, it brings the damaged DNA into a compartmental ring-like structure where the DNA is repaired, and then is able to fuse the nucleoids from the outside of the compartment with the damaged DNA.However, to bring it full circle, Deinococcus radiodurans does not form spores!
> Clues for future search of extremophile microbial life on Mars
That paragraph is pretty extraordinary with what is being claimed.
Crazy to think that anything could survive 25 kGy.
25 kgy, not great, not terrible.
WAOW I understood that reference! Hahaha that is a REFERENCE that I UNDERSTAND funny lmao
What would you consider as great?
They’re referencing the 3.6 roentgen meme, originally from the HBO series Chernobyl.
Well played k1ko :D
This almost throwaway line from the article struck me as an example of what we can do with technology, if we choose to put our billions of dollars towards it: "I downloaded the BC30 genome".
What’s even more shocking to me: one can “3D-print” downloaded genome, too! What a time to be alive.
You might enjoy: "Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine" (2020)
Being much smaller than a whole organism genome, the base-pairs are literally published in a WHO Word-document. :p
https://berthub.eu/articles/posts/reverse-engineering-source...
It's a shame it became such a weird political football, because the story of the mRNA COVID vaccine is absolutely in the "we are as gods" pantheon - the virus was sequenced, and 3 days later two separate labs had sequences for the vaccine. Phase 1 trials began within 3 months. To go from "weird novel pathogen" to "enough engineered vaccine candidate to start Phase 1 trials" is some legitimate sci-fi shit.
What felt Sci-Fi to me was when I saw this Stack Exchange question about what the A's at the end of the COVID virus sequence meant: https://biology.stackexchange.com/questions/90607/does-the-g...
Edit: I found the wrong one; I think the one I remember was https://bioinformatics.stackexchange.com/questions/11227/why...
Thankfully the political football is simmering down - I think we have mRNA flu vaccines in progress now, and attempts to stop that failed.
I was a conscious adult when all that was going down, so I can remind you, that on top of standard lunacy, there were legitimate concerns about safety of injecting something novel and untested to large parts of the population, genuine collusion to get as many people as possible injected, harassment that went both ways, and last but not least, there were many people who took one of the many vaccines and had life crushing, incurable side effects, not even mentioning the ones who died.
So the "political football" characterization is itself very political.
> So the "political football" characterization is itself very political.
According to your description it sounds completely accurate.
I've heard a lot of arguments that sounded, at first glance, like legitimate concerns. But I haven't seen any that weren't rooted in "People are telling me to be scared so my concern must be legitimate," or "I don't know how this works and it sounds new so I'm worried."
I think people with followings online got a ton of economic benefit from scaring people, the same as the rest of the news industry. Remember Upton Sinclair: "It is difficult to get a man to understand something, when his salary depends on his not understanding it."
The ONE thing I know of that survived study was the higher incidence of myocarditis in young men with Moderna, and provider guidance lists it as a potential side effect. However, the Novavax vaccine had the same myocarditis outcome without being mRNA, and the Pfizer mRNA didn't have that outcome.
It's very unlikely clinical trials would have exposed that issue, so even in hindsight, none of the concerns seem to have been legitimate.
> I think people with followings online got a ton of economic benefit from scaring people
Yes, it was very upsetting at the time and unfortunately remains a constant. I guess one has to go through that at least once to recognize a grifter.
> so even in hindsight, none of the concerns seem to have been legitimate.
The point was not only that the vaccines were rushed, it was also that there was a tremendous amount of coercion to force people into taking them. There are a few countries that didn't do that (Sweden comes to mind) and they ended up not having a much worse outcome than anyone else. I think it was a very telling moment in modern history, because it exposed a lot of myths, e.g. the American myth of gun ownership to stand up to a tyrannical government was totally shredded. The government turned tyrannical re: vaccines and mandates, did the guns help?
> There are a few countries that didn't do that (Sweden comes to mind) and they ended up not having a much worse outcome than anyone else.
I have no doubt Sweden did better than say sub-saharan africa. But it seems to me that only their neighbors are good comparison and they did worse than all of them.
Norway 1,050 deaths / million
Denmark 1,696 deaths / million
Finland 2,058 deaths / million
Sweden 2,812 deaths / million
> The government turned tyrannical re: vaccines and mandates, did the guns help?
I mean, the federal government had no mandate. So like were Floridians going to shoot up DeSantis because he didn't make a mandate? Or shoot up the other guy they elected, Trump (Biden not president until Jan 2021).
And then you don't really expect New Yorkers who elected Coumo to then shoot him up either?
[1]: https://en.wikipedia.org/wiki/COVID-19_pandemic_death_rates_...