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> 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

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.

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-...

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.

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.

https://en.wikipedia.org/wiki/Deinococcus_radiodurans

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?

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".

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?

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.

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)...

spores are the reasons that labs use autoclaves instead of boiling to sterilize things. autoclaves are pressurized so can reach much higher temperatures

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?

I loved this! The article was written in such an approachable way for someone less familiar with microbiology

>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.

Hockey stick? Glass beads? What happened to the good old inoculating loop?

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.

Very, very well written and enjoyable to read!

I boiled water today and survived.

> 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.

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.