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New antibiotic targets IBD and AI predicted how it would work

healthsci.mcmaster.ca

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Re: New antibiotic targets IBD and AI predicted how it would work

#21

Post by Llamamoe »

smeej wrote: post #5
voxl wrote: post #4

Earlier quoted context omitted.

We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!" All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to fi…

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

Sounds like you first decimated the bacteria with antibiotics, and then made it heavily disadvantaged by eating something that preferentially feeds other gut bacteria. What was the food, out of curiosity?

Re: New antibiotic targets IBD and AI predicted how it would work

#22

Post by Llamamoe »

marginalia_nu wrote: post #19
jgord wrote: post #6

Earlier quoted context omitted.

Any hypothesis for why eating only one thing would solve IBD ? Would that select for a particular biota / micro-fauna environment ? or cause less mechanical / chemical inflammation ? glad it worked in your case.

Not the person you're replying to, but my own IBD went away completely after I did keto for an extended period. This was a decade ago and it hasn't come back even as my diet returned to normal. In my n=1 experience, it seems maybe significant dietary changes can perturb the gut ecosystem out of whatever state corresponds to IBD.

They sometimes can, but most properly gut-adapted microbes only have their relative prevalence reduced by diet changes, by and large people unfortunately tend to snap back once diet is discontinued.

Ideally, you'd combine that with doing a stool transplant first, since it's the main thing (other than just antibiotics) that causes permanent compositional changes.

Re: New antibiotic targets IBD and AI predicted how it would work

#23

Post by gut_throwaway »

smeej wrote: post #5
voxl wrote: post #4

Earlier quoted context omitted.

We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!" All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to fi…

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

[dead]

Re: New antibiotic targets IBD and AI predicted how it would work

#24

Post by noosphr »

KLK2019 wrote: post #2

Here is the original study published in nature microbiology. https://www.nature.com/articles/s41564-025-02142-0 Wanted to share what I thought the interesting parts. From the university press release. "To date, AI has been leveraged as a tool for predicting which molecules might have therapeutic potential, but this study used it to describe what researchers call “mechanism of action” (MOA) — or how drugs attack disea…

Does anyone have the pre-print? I'm not affiliated with a university any more and the usual suspects don't upload papers overnight any more.

Re: New antibiotic targets IBD and AI predicted how it would work

#25

Post by noosphr »

bongodongobob wrote: post #14
zaptheimpaler wrote: post #13

Earlier quoted context omitted.

> Indeed, after his lab’s discovery of the new antibiotic, Stokes connected with colleagues at MIT’s Computer Science and Artificial Intelligence Lab (CSAIL) to see if any of their emerging machine learning platforms could help fast-track his upcoming MOA studies. It must be so cool to work at a university. You can just walk across campus to meet with experts and learn about or apply the cutting edge of any given fie…

That's only if there are experts there. The average college is not really what you're thinking it is.

You can email them and they are usually quite happy to talk.

Of course not when they get a media storm like these people. But I regularly correspond with experts in adjacent fields who have interesting papers put out.

Re: New antibiotic targets IBD and AI predicted how it would work

#26

Post by touisteur »

noosphr wrote: post #25
bongodongobob wrote: post #14

Earlier quoted context omitted.

That's only if there are experts there. The average college is not really what you're thinking it is.

You can email them and they are usually quite happy to talk. Of course not when they get a media storm like these people. But I regularly correspond with experts in adjacent fields who have interesting papers put out.

Can confirm that most of the times when reproducing/implementing a paper or trying to extend it to another field, researchers are pretty OK (some very enthusiastic) to chat over email about it. As long as you've actually read the paper(s) or read the code (if any), and there's no expected free-work...

I sometimes get unpublished artefacts (matlab/python/fortran code, data samples) just by... asking nicely, showing interest. And I'm not even in academia or a lab.

Re: New antibiotic targets IBD and AI predicted how it would work

#27

Post by jinnko »

marginalia_nu wrote: post #19
jgord wrote: post #6

Earlier quoted context omitted.

Any hypothesis for why eating only one thing would solve IBD ? Would that select for a particular biota / micro-fauna environment ? or cause less mechanical / chemical inflammation ? glad it worked in your case.

Not the person you're replying to, but my own IBD went away completely after I did keto for an extended period. This was a decade ago and it hasn't come back even as my diet returned to normal. In my n=1 experience, it seems maybe significant dietary changes can perturb the gut ecosystem out of whatever state corresponds to IBD.

I had a similar experience, i.e. strict keto for 9 months and fully came off meds with no signs of UC or asthma. UC came back after around 2 years and I don't remember how long before I had to start asthma meds again. I can no longer do keto though, each time I try I get palpitations now after around a week.

Re: New antibiotic targets IBD and AI predicted how it would work

#28

Post by mywacaday »

noosphr wrote: post #24
KLK2019 wrote: post #2

Here is the original study published in nature microbiology. https://www.nature.com/articles/s41564-025-02142-0 Wanted to share what I thought the interesting parts. From the university press release. "To date, AI has been leveraged as a tool for predicting which molecules might have therapeutic potential, but this study used it to describe what researchers call “mechanism of action” (MOA) — or how drugs attack disea…

Does anyone have the pre-print? I'm not affiliated with a university any more and the usual suspects don't upload papers overnight any more.

Their inboxs might be overflowing but researchers usually happy to email a copy if you don't have access elsewhere

Re: New antibiotic targets IBD and AI predicted how it would work

#29

Post by make_it_sure »

smeej wrote: post #5
voxl wrote: post #4

Earlier quoted context omitted.

We don't know. It's probably a combo of genetic factors and bacteria. It's at the very least complicated and multifaceted, because you can't just take a culture or biopsy of inflamed skin and say "A ha! This is clearly different!" All the most effective treatments try to turn off parts of the immune system, and even though have minor success with some patients going through multiple different immunosuppressants to fi…

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

i do the same, eating same thing for 2 years. While i don't have big IBD symptoms, i cannot now introduce new food, every time i try to introduce even very very small doses, i get a strange disproportionate reaction of my gut.
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