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".
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.
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.
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?
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.
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?
15 minutes is just not very long at all when cold brewing even at room temperature. And this was refrigerated (4C) so I'm sure the flavor would be minimal. You would normally cold brew for at least 8 hours at that temperature. So much less of the tea is ending up in the tested water.
If you look at the pictures of the plates the one with cold brew and where the full tea bag is added to the plate seems to have a good bit more growth than the others (there is a larger image of this one). So it doesn't seem like the spores are necessarily unaffected by the boiling just that some survive (or maybe they all survive but only some decide to start growing?). The thing I find strange is that the tea bag that was directly added without any brewing doesn't seem to have much growth at all. Actually, also that in the one with the tea bag added after cold brewing that has extra robust growth much of that growth seems to happen away from the visible pieces of tea.
I agree that the author has great style and I find it interesting to think about where and how bacteria (and fungi) like to grow.
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.
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.
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.
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.
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.
>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.
spores are the reasons that labs use autoclaves instead of boiling to sterilize things. autoclaves are pressurized so can reach much higher temperatures
> 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
Author of the article here, thank you for pointing this out out! I added the following correction to my article: "Killing bacteria thus became a major preoccupation of modern life. Its most visible manifestation today might be taking antibiotics (first available in the 1940s): there were ~700 antibiotic prescriptions per 1000 people<4> in 2024 according to CDC data. A close second might be the dizzying array of disinfectant products found in U.S. grocery stores." I added this footnote as well: "<4> Author correction 7/28/26: I reported this initially as “7 in 10 people were prescribed antibiotics,” but a commenter on another site pointed out that the original report data likely reflects a smaller number of people getting repeat prescriptions, so I have reported the raw data from the CDC report instead."
> 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.
31 comments
[ 2.5 ms ] story [ 18.8 ms ] threadBeing 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...
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.
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?
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)...
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?
If you look at the pictures of the plates the one with cold brew and where the full tea bag is added to the plate seems to have a good bit more growth than the others (there is a larger image of this one). So it doesn't seem like the spores are necessarily unaffected by the boiling just that some survive (or maybe they all survive but only some decide to start growing?). The thing I find strange is that the tea bag that was directly added without any brewing doesn't seem to have much growth at all. Actually, also that in the one with the tea bag added after cold brewing that has extra robust growth much of that growth seems to happen away from the visible pieces of tea.
I agree that the author has great style and I find it interesting to think about where and how bacteria (and fungi) like to grow.
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.
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.
> 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-...
https://en.wikipedia.org/wiki/Deinococcus_radiodurans
"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?
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.
It turns out vim vs emacs is a universal phenomenon.
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
>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.