Why Medicine Dabbling In The Microbiome Scares Me

One side effect of my dive into microbiome research is the startling realization that experts in medicine and health know much, much less than we think they do. Heck, even within microbiome research, it’s amazing how researchers seem to not keep up very well — I see so many studies premised on not very solid, and often outdated, assumptions. And often premises that completely conflict with one another. Ie, “Because Firmicutes are associated with obesity, we wanted to…” and “Because Bacteroidetes are the result of an unhealthy Western diet, we wanted to see if…” It’s as if they don’t talk to each other. But that’s a discussion for another time.

I bring all of this up because I came across this report: Cancer scientists seek to stop radiotherapy’s side-effects on ‘friendly’ gut bacteria.

When I first read that headline, I expected a report about how doctors are becoming more sensitive to the effect their treatments and procedures have on the microbiome. Which is a very positive thing to see. But if you actually read the article, that doesn’t seem to be the case at all:

“One possibility is that different populations of bacteria in a person’s guts are making them more or less susceptible to radiotherapy.”


“The aim is to build up a profile of gut bacteria which will allow us to predict who will suffer side-effects that might limit the effectiveness of the radiotherapy. Then we can think of finding ways to treat people in advance of radiotherapy in future.”

Mmhmm. Please, go oooooooon……

One technique would involve administering medicines that would alter the makeup of a patient’s population of gut bacteria. Alternatively their entire population of gut bacteria could be removed and replaced with another from a donor, a technique called a faecal transplant.



Call me crazy, but this sounds to me like the opposite of what the title suggested. What these doctors seem interested in is modifying gut bacteria — perhaps drastically — in order to make radiotherapy more effective.

And that’s scary. The idea that these people will figure out the “right bacteria” any time soon, and then try to proactively alter or demolish someone’s gut based on that, is very scary. Why? Because this is the same person who, in this article, said:

“Men and women have a startling amount of bacteria in their stomachs…”

Yeah. I bet he can also see Russia from your colon. The stomach is notable for being a place in your GI that is extremely hostile to bacteria. Too acidic. It has a startlingly low amount of bacteria.

It’s truly astounding to me just how strong of a proclivity these people have toward not only intervention, but extreme intervention. You can sense how titillating it is for them. A real chance to “geek out.” Even if they do identify an enterotype that is more amenable to radiotherapy, how do they know that enterotype won’t produce other side effects in an individual? How do they know that enterotype will be compatible with that person’s genotype?

If anything, emerging microbiome research teaches the opposite lesson: We don’t know as much as we think we do, so tread lightly. But some people just aren’t built to understand that lesson, I guess. No, they’re built to get really “science-y” and bring us things from the future. Hammer, meet nail:

“The crucial point is that we are now becoming aware of how important the bacteria in our guts are to our general health – and that should help direct us to a range of new drugs and treatments for all sorts of different conditions in future,” said Dearnaley.

Thank you, doctor from the future! See? Where we’re going, we won’t need common sense and a basic understanding of human anatomy…

— Heisenbug


11 thoughts on “Why Medicine Dabbling In The Microbiome Scares Me

  1. Sometimes I think I am too naive for this world. I was thinking the worst that could happen is when medical practitioners start giving nutritional advice. Singing all the while “What a friend we have in Ancel, what a friend in Keys we have”.
    I am beginning to think that Dr Thomas O’Bryan was right after all : Translational research takes an average of 15 years or more, for it to reach the ‘lower’ echelons.

  2. I distrust research. I went into academia thinking it’s a bunch of people learning from each other and building up knowledge. My experience was far from that.

    The sheer proliferation of journals and research means a lot of stuff is getting published. Unfortunately, it doesn’t mean more good stuff. The quality of research varies just like the quality of everything else, and as an outsider to the field it is difficult to identify the good quality. In my field, standards for publication were intentionally relaxed. For one, the editors needed to fill the journals. For another, they needed to attract the powerful people’s work. That’s often where the powerful people would dump their lesser quality stuff. I was asked many times to just make sure a submission just wouldn’t embarrass anybody. I refused those. Research is very often published with known flaws and shortcomings, with the stated conclusions often different from what the research really shows.

    Worse, everyone is protecting their turf and reputations. It’s no good to be wrong, even if the field advances. And it’s the powerful guys who have the most incentive to protect their turf and the best means to do so. I’ve seen some nasty stuff. The most egregious was a very senior person’s open backlash toward someone who had proven one of his ideas mathematically incorrect (that means there was no ambiguity). That person suffered for a long time. So the young researchers become indoctrinated to the older’s point of view, and so it continues.

    There are some good apples. But in my experience, good quality research in which the stated conclusions and the data (and statistical methods!) match are very rare.

    • Wilbur, I agree with you. I used to work for a major scientific publisher and learned that the Editors-in-Chief had absulute power in keeping dissident publications out of the journal. It wouldn’t get past the peer review process. What was left for the unfortunate scientist? Try and find another journal that would accept the paper. That is how the fat hypothesis that Ancel Keys launched in the 50’s was perpetuated until today.

  3. Coincidentally, I was sitting in a bar in a Houston airport yesterday, and ran into a nice couple whose son worked at a famous cancer center in the city. When I asked what his son was doing, they said he was working on almost exactly this issue–the effect of chemotherapy on gut bacteria. (I can’t seem to get away from that subject!) I have no idea if this effort was taking the same “hammer-nail” approach, but certainly would not be surprised if it was…actually I’d be shocked if it wasn’t.

    Ultimately I think it’s a matter of needed a sense of control, and that’s what this approach gives them. Our uncertainty is probably easier to maintain given that we’re not surrounded by dying, suffering children. And I’m not saying that sarcastically.

    • That’s a big, complicated topic, but suffice it to say, beneficial gram-positive bacteria (like lactic acid bacteria in fermented foods) are adapted to survive passage through the harsh acidic environment of the stomach. That’s a large part of how they are adapted to be commensals with humans. If you are interested in the nitty gritty: http://mmbr.asm.org/content/67/3/429.full

      I did catch Norm’s post, thanks.

  4. Dr. Bonnie Basler’s Tedx talk on how bacteria ‘talk’ through quorum sensing. Towards the end she discusses how this can be used to help overcome antibiotic resistant infections. But what I found most interesting was when she mentioned ‘pro-quorum sensing’ (unfortunately she didn’t mentioned details). Wouldn’t that be huge? http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate
    This a pretty basic talk if you know a lot about microbiology but very well done.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s