Phages, Part I: the life and history of Felix D’Herelle

Remember when I was obsessed with the microbiome? I still am. I still think it holds the key to understanding our immune system and, by extension, human health and disease. I still think we’re being crowdsourced by microbes. Long after our idiocy, greed and hubris have destroyed any possibility of human survival on our planet, they’ll be happily bubbling away in a toxic pool somewhere.

The picture I painted of the microbiome was incomplete, I’m sorry to say. I’d like to introduce you to a little-known but critical player in the drama, a beastie that I only recently met, thanks to an interview with Monash biologist Jeremy Barr. 

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For the forests

Today an interesting thing came up in my Facebook feed: it’s the International Day of Forests. No kidding.

What a coincidence, I think to myself. Here I am, mulling over the idea of writing a blog post on something, anything, as long as it’s not depressing or political in nature, and my latest obsession comes and knocks at the door. Me! Write about Me! Continue reading

Eat sh*t and … thrive!

IMG_1040Everybody’s talking about the microbiome these days. If you’re not taking probiotics, you’re probably eating sauerkraut and swilling kombucha. I know I am.

What’s the Microbiome? I’m glad you asked. See, the human body is made up of about 10 trillion human cells. And that same body is also home to 100 trillion bacteria. Your mouth, nose, armpits, bellybutton, skin and especially your gut are teeming with thousands of different species of bacteria. Collectively, they’re called the microbiome. If you took them all out, they’d weigh about 2 kilos.

And then you’d die, because they play a crucial role in keeping you alive. Continue reading

The One-body Problem

Da Vinci Vitruve Luc Viatour2Hello, December. What happened to November? All of October I was busy with the Yoga Project, happily scribing away my impressions, downward-dogging my way into a new yoga comfort zone. And then it seemed that November just floated right on by.  And then yesterday, December 1, I opened the New York Times (oh joy) and I realized that I had been subconsciously working on a blog post for the entire month. It’s long, but I hope you still read it.

I’ll call it the One Body Problem. Which is this: We only get one body. This is it. You get the body you were born with, like it or not. And then you die. Continue reading

You want fries with that?

Gydle has been silent the entire month of November. No excuses, I just didn’t have anything to say. Then I woke up this morning and my brain was teeming with ideas. Was it something I ate?

First, I have a great gift idea.

I got an e-mail the other day from “American Gut.” Imagine my excitement! The Human Food Project is live on IndieGoGo. For only $99 and a stool sample, you can get a list of the microbes colonizing your gut. Upscaling is a bargain – it’s $180 for two samples, $260 for three and a mere $320 for a family of four! Continue reading

More microbe than mammal

I know I’m supposed to be in hibernation, but something came up that was so good I just had to share it with you.

You know by now that I am totally fascinated by the human microbiome, those trillions of microbes that make up most of the human organism. I’ve written here on Gydle about how microbes in our guts may implicated in a variety of ailments, from diabetes to Parkinson’s to obesity and irritable bowel disease.

I also wrote recently that the massive NIH-finded Human Microbiome Project has had a number of publications like this one in Nature Magazine that outline thier discoveries about the makeup and function of a “healthy” human microbiome.  I have a feeling that what we find out about the microbiome may well revolutionize our approach to health and medicine.

You might also remember from last year that I’m also fascinated by the concept of crowdsourcing, a kind of data gathering approach that takes information freely and painlessly from tons of people who are just going about their ordinary lives. They’re mined for data while driving, surfing the internet, ordering things online, logging into websites, reading wikipedia pages, looking at the stars, pooping… Continue reading

More microbiome madness

All kinds of exciting things have been happening, and I haven’t written about any of them. Some of them involve running, and they will appear in the next post. This one is about my other current favorite topic, the human microbiome.

Last week The New York Times had two very interesting articles, one about eating the weeds in your backyard, and another about the human microbiome. The first one speaks for itself. Apparently eradication can be dropped in favor of ingestion. Maybe I’ll give it a try. In any case it eases my weed aversion just that much more. The second article covers research being done in association with the Human Microbiome Project. Here’s my favorite quote:

Dr. Barnett Kramer, director of the division of cancer prevention at the National Cancer Institute, who was not involved with the research project, had another image. Humans, he said, in some sense are made mostly of microbes. From the standpoint of our microbiome, he added, “we may just serve as packaging.” Continue reading

Adventures in fermentation

I’m making friends with my microbiome.

Seems the prudent thing to do. I don’t want it to decide that this body is badly managed and thus a waste of time, and chuck it for a healthier version. No, not just yet. I have some stuff to write still. So I’m treating my gut flora to a microbial playdate. I want the symbiotic ecosystem that is my body to function optimally.

Not long ago in one of my internet ramblings I stumbled upon kefir, a fermented milk product originating long, long ago in the Caucasus. The word kefir (pronounced keh-fear) is related to the Turkish word keif, which means “feel good.” Kefir is a drinkable probiotic made with either water or milk using a gelatinous matrix of yeast and bacteria that are curiously called “grains.” (They have no relation whatsover to real grains like wheat or oats.)

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Weather bugs

I mentioned in an earlier post that I have a sneaking suspicion that we’re being crowdsourced by bacteria. Remember? The human body has 10 trillion cells in it. We also each harbor about 100 trillion microbes. There is more microbial DNA in the human body than human DNA. That post.

We know relatively little about this huge population, but one thing we do know is that it’s not random. I claimed, back in May 2011, that perhaps humans are not so much organisms as we are ecosystems.

We thought we were the top guns on this planet! We thought it was all about us! We thought our bodies were vehicles for our splendiferous brains! No, silly. We are being maintained. We exist simply as biomes for colonies of established bacteria. Our brains probably just evolved as the best way for our bacteria to ensure that they will continue to have thriving hosts, generation after generation.

You might have laughed that one off, and I can understand your reaction. It’s a little unsettling to think that humans aren’t the center of the universe. Galileo encountered a little resistance, too. I can be patient.

But why?  You might ask. Why would they want us to do their bidding? And what is their bidding?

Would it help you see my point of view if I told you that bacteria are controlling the weather, too?

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What’s the poop?

One of my favorite topics at the moment is the human microbiome. That’s the part of us that’s not human. Back in May, I wrote a post about it:

A human body has about 10 trillion cells in it. And that very same human body (yours, for example), is also home to 100 trillion bacteria. Your mouth, your nose, your armpits, your navel, your skin and especially your gut are teeming with thousands of different species of bacteria. If you could separate out all those bacteria from the rest of you, they’d weigh 2 kilos.”

I was suggesting (only partially in jest) that we’re actually being crowdsourced by a superior form of collective intelligence. Just last month, I wrote another post about how the gut microbiome plays an important role in mental health.

I was wrong on one count. I mentioned a study that had found that excessive use of antibiotics can permanently damage your gut flora. It turns out there’s hope after all. Here’s the story:

Antibiotic overuse can allow a particularly nasty (and appropriately named) microbe, Clostridium difficile, to set up shop in the gut. This critter makes you really miserable – recurrent bouts of  severe diarrhea, abdominal pain, nausea and vomiting. It stubbornly resists treatment – well, most treatments. There is one that works.

A fecal transplant.

It turns out that the gut flora from a healthy human donor can outcompete C. difficile, restoring gut health in no time flat. (Ce n’est pas si difficile…)

And where can this gut flora be found? Right. Someone else’s poop. Wait. Don’t go away. Bear with me for a minute, this is really interesting stuff (this is a picture of some E. coli, magnified 10,000 times, originally from the USDA).


gut bacteria

Dave brought it up this morning in our regular chat.

Dave: Apparently it works.

Me: works for what?

Dave: (sends a link) It cures gut infections caused by antibiotic therapy.  Gives new life to the phrase “eat shit”

Me: I see. repopulating the gut microbiome. I can write about that.

Dave: That’s why I instantly thought of you when I read about it. (That’s my story and I’m sticking to it)

Yes, indeed. The article he sent me describes the case of 75-year-old Pat Shoop, who had a nasty C. difficile  infection. Her husband valiantly offered to provide a batch of bacteria from his own, healthy gut.

… Bob was under pressure to produce a usable stool sample within 15 minutes of her scheduled appointment. […] He complied and the pair rushed to the clinic, where Dr. Rubin snaked a tube through Shoop’s nose and into her stomach. “It was 20 minutes,” she said. “He told me, ‘You’re not going to taste it, you’re not going to smell it.’”

Apart from the obvious question of what constitutes “usable” – consistency? size? – one wonders why Bob had to be under so much pressure. Couldn’t he just refrigerate his offering? Another thing not mentioned in the article was exactly how the sample was prepared. I had to go elsewhere to find that information:

An article in the Scientist describes how Australian gastroenterologist Thomas Borody did his first transplant (in the mid-1980s) :

…He collected stool from the woman’s brother, and after screening it for known pathogens, he stuck it in a blender, added some brine, and filtered it to get rid of any undigested material. The stool, now turned into slush, was administered to the patient — who had her gastrointestinal tract previously flushed — via two enemas over the course of two days.

In only days, the patient was cured. Her colitis never returned.

In fact, a recent study shows that fecal transplants (which often go under the more palatable monikers of fecal bacteriotherapy, intestinal microbiota transplantation or human probiotic infusion) successfully cure more than 90% of intractable C. difficile cases and many other cases of irritable bowel disease (IBD) and ulcerative colitis. The transplant is administered either via enema, or, as in Pat Shoop’s case, via a nasogastric tube.

Borody oversees 5-6 fecal transplants a week, mostly for patients with IBD. It’s catching on in the US, as well:

Currently, while most fecal transplants in the U.S. are performed exclusively to treat C. difficile, a growing list of doctors, […] are beginning to expand to other gut disorders such as inflammatory bowel diseases. Because stool is not yet a marketable biologic product, the procedure is not federally regulated.”

Note the use of the word “yet” in that last sentence. I sense an entrepreneurial opportunity here. If I weren’t so damn busy translating…

It’s considered a treatment of “last resort,” which is also a bit odd, seeing as it has been used in veterinary practice for ages to calm the bellies of ruminants. In fact, come to think of it, don’t animals regularly partake? Could it be they know something we don’t?

Lest you be tempted to get out the blender and take matters into your own hands, be aware that this is a job for professionals only. The wikipedia page on fecal bacteriotherapy says that “The best choice for donor is a close relative who has been tested for a wide array of bacterial and parasitic agents.The enemas are prepared and administered in a hospital environment to ensure all necessary precautions.” 

The page goes on to describe a new “safer, more effective, and easier to administer” form of fecal bacteriotherapy that’s being developed, which requires the patient to keep a refrigerated sample on hand. In the event that he/she develops a C difficile infection, the sample is extracted with saline, filtered, freeze dried and put into capsules. The patient can then repopulate her gut with her own microbiome just by popping a pill! Now that’s a win-win.

One obvious question arises, however: How many of us are paranoid enough to prepare ahead for a C. difficile infection?  

And another, given the current lack of federal regulation:  What’s the refrigerator shelf-life of a shit sample? 

You might be wondering what all this has to do with mental health.

In January 2011, an article appeared in NewScientist magazine, which you can’t read unless you have a subscription 🙁 , telling the story of an elderly Parkinson’s patient who came to her doctor with a horrible case of constipation and an infected colon. I think the doctor treated her with a fecal transplant from her son, but I don’t know for sure, since I’m not a subscriber. Anyhow, rumor has it her Parkinson’s symptoms miraculously disappeared along with her gut infection.

What I do know is that Borody is currently doing a clinical trial on 18 Parkinson’s patients using C. difficile antibiotics. It will be very interesting to see what happens. Could it really be as straightforward as swapping out our shit? Like I said in my earlier post, maybe it’s time we paid more attention to all those freeloaders in our bellies.