TED: Astrophysicist/computer programmer analyzes own gut, diagnoses his IBD

[WillowJ]

So this scientist analyzes his own microbiome and diagnoses IBD in himself. He does use supercomputers and whatnot, but at the end he explains that he thinks this avenue will soon be open to everyone:

ETA: the first bit has music (volume was loud to me) and is flashy, but after the TED introduction it was easier to watch

on youtube:

on TED:
http://blog.tedmed.com/?p=3580

another thing that stood out to me was his lab values. they were not consistently significantly abnormal. so maybe all those slight abnormals mean something. especially when we avoid doing labs on crash days.

 

[Bob]

Thanks Willow. Fascinating!

 

[Waverunner]

This is the best talk I have seen for many years. Thank you, WillowJ.

 

[perchance dreamer]

I read the article in The Atlantic about Larry called The Measured Man, July/August 2012, but hadn't seen the Ted talk. Larry's my first cousin, but I haven't seen him since '73.

 

[Sasha]

Fascinating! Watched it twice.

Thanks for posting it.

 

[leela]

really great talk.; thank you Willow. i do wish we could tell him about replacing the missing good bacteria, though.
let's hope he knows that.

 

[Sasha]

really great talk.; thank you Willow. i do wish we could tell him about replacing the missing good bacteria, though.
let's hope he knows that.

I was surprised he didn't mention faecal transplant.

 

[WillowJ]

or at least probiotics

 

[Waverunner]

I'm 100% sure that he knows about microbiome transplants but I guess he wanted to test methods with less *yuck* factor. I mean, what he did was a valid approach. Try to reduce the overgrowth of certain bacteria with ABs and see what happens. The problem he encountered was, that they came right back. So this method didn't work very well.

The next approach could be probiotics but here we have the problem, that most probiotics contain the same few strains of bacteria while the gut microbiome consists of 500 - 1000 different strains. Unfortunately, there are no new probiotics on the horizon, at least to my knowledge.

After that, he could try a microbiome transplant and here we encounter the last, big problem. The gut has lots of defense systems. What do we do, if the imbalance of bacteria is not caused by the environment (ABs, wrong foods, illness etc.) but because the body and the immune system suddenly attack the wrong bacteria? In this case, rebalancing the gut wouldn't help because the body always would return to the same state of dysbiosis. We would need to desensitize the gut for the right bacteria but this is probably very hard.

 

[Sasha]

I'm 100% sure that he knows about microbiome transplants but I guess he wanted to test methods with less *yuck* factor. I mean, what he did was a valid approach. Try to reduce the overgrowth of certain bacteria with ABs and see what happens. The problem he encountered was, that they came right back. So this method didn't work very well.

The next approach could be probiotics but here we have the problem, that most probiotics contain the same few strains of bacteria while the gut microbiome consists of 500 - 1000 different strains. Unfortunately, there are no new probiotics on the horizon, at least to my knowledge.

After that, he could try a microbiome transplant and here we encounter the last, big problem. The gut has lots of defense systems. What do we do, if the imbalance of bacteria is not caused by the environment (ABs, wrong foods, illness etc.) but because the body and the immune system suddenly attack the wrong bacteria? In this case, rebalancing the gut wouldn't help because the body always would return to the same state of dysbiosis. We would need to desensitize the gut for the right bacteria but this is probably very hard.

And yet people who get such transplants for IBS are reporting complete and lasting remission (I think). Which seems weird, because you wouldn't think a relatively small amount of transplant matter could recolonise the gut in the face of such a lot of well-established competing bugs, let alone all the immune issues that you raise.

I wonder if the faecal transplant people have done the sort of microbiome analysis pre- and post- like he has. He said only five people had had that much analysis but I'd have thought researchers would have done it for the patients in their trials.

 

[Waverunner]

And yet people who get such transplants for IBS are reporting complete and lasting remission (I think). Which seems weird, because you wouldn't think a relatively small amount of transplant matter could recolonise the gut in the face of such a lot of well-established competing bugs, let alone all the immune issues that you raise.

I wonder if the faecal transplant people have done the sort of microbiome analysis pre- and post- like he has. He said only five people had had that much analysis but I'd have thought researchers would have done it for the patients in their trials.

That would have been needed but I don't think, that it has been done. In the end you have to scratch your head, why they don't approach IBD from this more objective standpoint and try to figure out, what role the microbiome plays. It's not very expensive to sequence parts of the microbiome (under 90 dollars) but yet it is seldomly done in studies.

Microbiome transplants work perfectly well for c. difficile infections and there was a new study abou UC as well. About 70% of patients with UC went into remission but it only consisted of 10 patients and remission doesn't mean cure. The good news is, that there is a bigger study on the way [130 patients with UC, double blind]:

http://www.ccfc.ca/site/c.ajIRK4NLLhJ0E/b.8343767/

 

[Mark]

Really interesting and exciting talk. But when he talks about being 'a long way from home' and describes the 'normal' gut bacteria profile, I wonder whether he's taken into account the finding that in humans there are 3 distinct 'enterotypes' (or types of ecosystems), which have been compared to blood groups:
http://healthland.time.com/2011/04/21/you-know-your-blood-type-but-whats-your-gut-bug-type/

The German research claims 3 enterotypes, based on whether Bacteroides, Prevotella, or Ruminococcus are dominant. Bacteroides and Prevotella are both of phylum bacteriodetes, but Ruminococcus is a Firmicute.

Whereas he describes his profile as 'far from home' because it is dominated by red (firmicutes) rather than blue (bacteroidetes), and seems to assume that a bacteriodetes-dominated profile would be normal, in contrast the German research suggests that a firmucute-dominated profile (which his profile is) is actually one of 3 valid enterotypes. Since he shows a pie chart for the average Crohn's patient indicating a fimicute-dominated profile, it may well be that a firmicute-dominated profile is the type most prone to various forms of inflammatory bowel diseases, but it's far from clear that a bacteroides-dominated profile is the 'right' or 'healthy' or 'normal' one, as he appears to assume.

I think he's very probably right that we are now beginning to transition to a new age of medicine which will be based on individual data, particularly on the microbiome and genome, with personalised treatments and detailed tracking of data being the new paradigm...that change is incredibly disruptive because it runs contrary to the entire traditional model of evidence-based generic treatments using large trials to prove efficacy, but that revolution does appear to be under way and Andreas Kogelnik talked about this at the Invest in ME conference yesterday.

But the double-edged sword of this new paradigm is that while we now have the capacity to gather this vast amount of data, we actually know next to nothing yet about what that data really means - we're only just beginning to analyze it - and the 'individualised medicine' paradigm is also going to have to challenge our instinctive assumptions that we are all basically the same - human - and that the 'correct' biology can be defined by averaging the biology of healthy adults.

On the face of it, the contrast between how he's interpreting those red and blue slices in the pie chart, and what the German research says about enterotypes, appears to be a case of making a false assumption about the 'average' distribution automatically being the 'right' or 'good' or 'healthy' distribution. Then again, maybe he's right and perhaps the firmicute-dominated type is indeed a damaged ('mass extinction') state rather than being one of three 'valid' types. This is certainly a very exciting area of research to watch.

 

[Bob]

Larry Smarr has a twitter account, in case anyone is interested in following:
https://twitter.com/lsmarr

And here are some articles, for further reading:
http://www.theatlantic.com/magazine/archive/2012/07/the-measured-man/309018/
http://www.technologyreview.com/featuredstory/426968/the-patient-of-the-future/

Here's a long conference video, in case anyone is interested (I haven't watched it all yet) (it's not all about the gut):
www.youtube.com/watch?v=37u0SPZGK6Q

There's loads of stuff about him on the internet, if you do a google search for Larry Smarr.