Category: Microcosm: The Book

Do you own your germs? My new piece for the New York Times on micro-bioethics

By Carl Zimmer | December 4, 2011 10:20 am

There are 100 trillion microbes that live in your body. Do you own them? Do they deserve the same protections as your own genes and cells? If someone genetically alters a microbe and claims that if you swallow it, it will let you lose weight, should that living germ be regulated as a drug?

These are a few of the questions I mull in a piece that appears in the Sunday Review section of today’s New York Times. I’ve been writing a lot about the microbial world for a few years now, but only recently did I encounter a group of bioethicists who are now pondering what sort of ground rules we should set up to govern science and medicine as we gain understanding and power over the microbiome. Check it out.

If you’re interested in reading more about all this, here are a few new papers (some free, some behind paywalls).

The Human Microbiome Project: lessons from human genomicsTrends in Microbiology (in press)

“Who owns your poop?”: insights regarding the intersection of human microbiome research and the ELSI aspects of biobanking and related studies, Kieran O’Doherty, BMC Medical Genomics 4 (1), (07 Oct 2011) info:doi/10.1186/1755-8794-4-72

Community Health Care: Therapeutic Opportunities in the Human Microbiome Justin Sonnenburg and Michael Fischbach, Science Translational Medicine 3 (78), April 13, 2011 info:doi/10.1126/scitranslmed.3001626

There will also be a book coming out next year edited by Rosamond Rhodes of Mount Sinai Medical School, but it’s not on the radar just yet. For now, here’s a powerpoint of a recent presentation from her research group (pdf)

[Image: Andrea Wan for the New York Times]

My kind of centerfold

By Carl Zimmer | September 30, 2011 12:23 pm

The folks at Wired recently asked me to put together a guide to the human ecosystem. You can get it in the October issue as a centerfold–the kind of centerfold that shows someone who took off the clothes, and then took off the skin. Bugs in your eyes, in your ears, in your gut, influencing your mind and health–they’re all there. Check it out.

Bellybutton biodiversity update: Wonderlands upon wonderlands

By Carl Zimmer | July 30, 2011 10:31 am

Last month I contemplated the staggering diversity of microbes in my bellybutton–an experience made possible by my participation in a survey of microbiome diversity carried out by scientists at North Carolina State University. At the time, I thought I was quite the host. I was informed there were 53 species living in my navel, some of which had never been seen on skin before and some of which were altogether new to science. I was even informed that I was a “wonderland.”

Well, the project is moving forward at quite a clip, and the scientists are starting to push more of their data online. Here you can see the species from the first 60 volunteers they’ve studied. The lists are coded by number–I’m B944. I appear to have lost a species so I’m down to 52. And 52 is, I’m seeing, nothing to blog home about. So far, the diversity champion is the anonymous owner of bellybutton B1288. 107 species! Now that’s a wonderland….

CATEGORIZED UNDER: Link Love, Microcosm: The Book

Goodbye, E. coli?

By Carl Zimmer | July 8, 2011 10:18 am

Lucas Brouwers, one of the new bloggers at Scientific American’s snazzy new blog network, takes a look at an intriguing paper (free pdf). The authors of the paper in examined many different strains of E. coli and come to a remarkable conclusion: they’ve been splitting apart so far that they may soon no longer be a single species. Check it out. (And, if you have a lot of time to spare, check out the rest of Scientific American’s fine line-up of bloggers.)

CATEGORIZED UNDER: Link Love, Microcosm: The Book

Last year: Arsenic life. This year: Chlorine life?

By Carl Zimmer | July 6, 2011 2:17 pm

[Note: Some folks don't like the phrase "chlorine-based life." I welcome suggestions in the comments for a better shorthand descriptor]

Last year, a team of NASA-funded scientists claimed to have found bacteria that could use arsenic to build their DNA, making them unlike any form of life known on Earth. That didn’t go over so well. (See my two pieces for Slate for a quick recap: #1, #2.)  One unfortunate side-effect of the hullabaloo over arsenic life was that people were distracted from all the other research that’s going on these days into weird biochemistry. Derek Lowe, a pharmaceutical chemist who writes the excellent blog In the Pipeline, draws our attention today to one such experiment, in which E. coli is evolving into a chlorine-based form of life.

As I wrote in Microcosm, scientists have been contorting E. coli in all sorts of ways for years now to figure out what the limits of life are. Some researchers have rewritten its genetic code, for example, so that its DNA can encode proteins that include amino acids that are not used by any known organism.

Others have been tinkering with the DNA itself. In all living things, DNA is naturally composed of four compounds, adenine, cytosine, guanine, and thymine. Thymine, shown in the upper left panel here, is a ring of carbon and nitrogen atoms, with oxygen and hydrogens atoms dangling off the sides. Since the 1970s, some scientists have tried to swap thymine for other molecules, such as the one show to the lower left here. This compound is called 5-chlorouracil, the “chloro-” referring to the chlorine marked here in red. No natural DNA contains chlorine.

A team of German scientists recently published the details of an experiment that has taken them a long way towards E. coli that live only on chlorouracil. They didn’t simply sit down and type out a new sequence for E. coli’s genome–we just aren’t smart enough to make such predictions. Instead, they harnessed evolution. The scientists fed a population of E. coli chlorouracil, supplementing their dieet with a little thymine to keep them from starving to death. Bacteria that picked up mutations that allowed them to use some chlorouracil instead of thymine were favored by natural selection. They lowered the thymine levels to increase the pressure on the bacteria to evolve more.

After five months of this evolution, the E. coli underwent a noticeable change. For one thing, they changed shape. They started out in the normal capsule shapes in the top photo, turned into the worm-like shapes below, and then later became capsule-shaped again. The scientists also found that the bacteria were slurping up chlorouracil. Ninety percent of the thymine in their DNA was replaced by chlorouracil. As Lowe writes, the scientists found that the bacteria were still incorporating some thymine into their DNA through a pathway no one had discovered before (which just shows how marvelously mysterious E. coli remains after a century of intensive study). The scientists shut down this new pathway, and found that the bacteria still grew happily. But now they only had 1.5% thymine in their DNA.

This E. coli is different from ordinary E. coli, with over a thousand mutations that enable it to take up chlorouracil. But it is not quite yet off the grid. If it is fed thymine and no chlorouracil, it can switch back to a conventional way of life. So now we’ll see if scientists can further evolve the bacteria so that they can only live on chlorouracil, and starve on thymine.

I checked in with Steven Benner, a chemist who has raised a lot of concerns about the arsenic-life research last year. What did he think of the new research?

“It looks true,” he said.

Benner also pointed out that using chlorine in DNA is a pretty modest changed compared to what would have been required to substitute arsenic for phosphorus in the backbone of DNA. Swapping in chlorine doesn’t change how the compound reacts with other compounds, doesn’t change its size much, doesn’t change its stability much, and so on.

On the other hand, it appears to have the advantage of being real.

[Update: Rosie Redfield, an outspoken critic of the arsenic-life research, just got back to me with nice things to say as well:

"This looks quite solid to me (I read it quickly). The technology is nice, very appropriate for the project. No red flags at all."]

Discovering my microbiome: "You, my friend, are a wonderland"

By Carl Zimmer | June 27, 2011 11:09 am

Some people get a thrill from getting their genome sequenced and poring through the details of their genes. I’m a bit off-kilter, I guess, because I’m more curious about the genomes of the things living in my belly button. And let me tell you: it’s a jungle in there.

I first became curious about my navel in January. I was in Durham, North Carolina, to attend a meeting, and as I walked out of a conference room I noticed a cluster of people in the lobby handing out swabs. They were asking volunteers to stick the swabs in their belly button for the sake of science. Our bodies are covered with microbes, and scientists are discovering weirdly complex patterns to their biodiversity. From fingers to elbows to chin to forehead, different regions of our skin are dominated by different combinations of species. But the bellybutton remained terra incognita.

I happily donated my microbiome to the study, which is being conducted by Jiri Hulcr and Andrea Lucky, two post-doctoral researchers in the laboratory of Rob Dunn at North Carolina State University. After a few weeks, Hulcr sent me a photo of a Petri dish in which some of the bacteria from my bellybutton were thriving. Then Hulcr and Lucky got down to the serious work of identifying the species in the navels of their volunteers (90 and counting).

Yesterday, Dunn sent me a spreadsheet detailing my own results. “You, my friend, are a wonderland,” he wrote.

To catalog the biodiversity of bellybuttons, Hulcr and Lucky are extracting the genetic material from their collection of swabs. They then compare these fragments of DNA to the millions of sequences that are stored in public databases. (They limited themselves to DNA from bacteria, so for now they’re not cataloging the fungi, viruses, and other creatures that may be lurking in our navels.)

Some fragments of navel DNA precisely match the DNA of a known species of bacteria. In other cases, they’re close enough to a species for Hulcr and Lucky to assign them to a genus, a family, a class, or  some higher unit of classification. In a few cases, the bacterial DNA is so exotic that all they can say for sure at this point is that it is bacteria.

Hulcr, Lucky, and Dunn had lots of questions about the things that dwell in the human omphalos. Are they different from the species that live in other parts of the skin? Do they differ from one person to the next? Is there a core set of species found in all navels? To address these kinds of questions, they tallied up the number of volunteers who carried each species, and investigated how each species makes a living.

All told, I now discover, my belly button harbors at least 53 species of bacteria. This, Dunn informs me, is a “whopping” number.

I’m not sure whether to feel good or bad about this revelation. On the good side, I know that diversity can make ecosystems work better. One of the most important services that our microbial ecosystem performs for us is protecting us from pathogens. They can outcompete invaders, kill them with poisons, and otherwise ward them off. Scientists have run experiments to test the effect of diversity on infections. They manipulated mice so that some had no resident bacteria, and others had low levels of diversity. The researchers found that pathogens did a better job of invading low-diversity mice than high-diversity ones.

So perhaps my belly button is especially well-defended. Still, I can’t help but wonder if I ought to scrub it with some steel wool. There are some very exotic things in there. Only a small fraction of my belly button bacteria were common among the other 89 volunteers. The microbes I share with most other volunteers tend to be ordinary skin dwellers that are typically harmless (although sometimes they can turn nasty and cause problems ranging from acne to staph infections).

But out of 53 species, 35 were present in only 10 or fewer other volunteers. And 17 species in my navel didn’t show up in anyone else. In the column for notes in Dunn’s spreadsheet, he’s annotated these species with scientific descriptions like “weird one” and “totally crazy.”

Several species I’ve got, such as Marimonas, have only been found in the ocean before. I am particular baffled that I carry a species called Georgenia. Before me, scientists had only found it living in the soil.

In Japan.

When I learned this, I emailed Dunn to let him know I’ve never been to Japan.

“It has apparently been to you,” he replied.

While I may be a bit of an outlier in the belly button department, I’m not a freak. Among all 90 belly buttons Dunn and his colleagues have studied so far, they have found 1400 species of bacteria, a number of which have never encountered on human bodies before. These species are probably not so out of place as they may seem, however. The diversity of the world’s microbes is vast–far bigger than the whole animal kingdom combined. For the most of the history of microbiology, scientists have focused most of their attention on bacteria that make humans sick–ignoring the huge number of species that don’t harm us, or that live elsewhere in the world. Many species are turning out to have a much wider range than scientists have previously appreciated. Bacteria have also evolved to leap from one niche to another to another. Take Pantoena–a lineage Hulcr and Lucky have only found in my belly button and that of one other subject. Most species of Pantoena infect plants. But a few lineages have shifted from plants to people. As scientists add more branches to the tree of life, they will probably find more such transitions.

In ancient Greek mythology, Zeus release a pair of eagles to find the center of the world–the “omphalos,” which means belly button in Greek. Several statues, like the one shown above, were built around the Mediterranean to mark the supposed place where the eagles landed. It’s wonderful to be part of an experiment that gives a new meaning to this ancient word. Each of us carries a biological omphalos: a small, lint-clogged center of the microbial world.

(For more information, check out Dunn’s new book, The Wildlife of Our Bodies, for which I happily provided a cover blurb.)

[Image: University of Kentucky]

The two faces of E. coli: my article in Newsweek and interview with the BBC

By Carl Zimmer | June 6, 2011 9:30 am

On Friday, as the E. coli outbreak gained horrific speed in Germany, Newsweek asked me to write about how this epidemic came to be. Scientists still have a lot to figure out about it, but some things are clear–in particular, that the bacteria have great scope for evolution into new deadly strains, thanks in part to the shuttling of viruses between them. (In my book Microcosm, I explain how this is true not just for E. coli, but for much of life.) My piece appears in the new issue of Newsweek, which you can read online here. (One late-breaking piece of news that didn’t make it in, by the way, is the finding yesterday that the new outbreak appears to have come from bean sprouts.)

While I was working on my Newsweek piece, a reporter for the BBC called me up for an article on the good side of E. coli. I explained how much of how we understand about life itself came out of research on this typically harmless bug, and that the biotechnology industry was build upon its biology. That piece came out over the weekend. Check it out.

[Image: glass microbe by Luke Jerram]

Another purge sale: autographed copies of the UK hardback edition of Microcosm

By Carl Zimmer | May 24, 2011 10:06 am

Last week I announced that I had 17 autographed copies of the US hardback edition of Microcosm, and in 85 minutes you folks cleared me out. There were a few cries of “Arg!” later on Facebook and Twitter, to which I responded that I still needed to deal with more books in advance of our house renovation. And so (voice turning crazy), here’s the next deal: we’ve got 8 autographed copies of the British hardback edition of Microcosm: E. coli and the New Science of Life. It’s out of print, but between now and next Tuesday, it’s available for ten dollars from my Amazon store.

Again, here’s a quick description of Microcosm: In the book, I tilt at one of my favorite windmills–the definition of life. But rather than try to take on all of life on Earth, I chose one species–the one that we know best of all. That would be our gastrointestinal lodger, Escherichia coli, the little bug that helped build modern biology and launch the entire biotechnology industry. In my biography of this scrutinized germ, I explore the origin of life, our inner ecology, and the search for life on other planets. You can find out more about the book on at, or check out this review from Anthony Doerr in the Boston Globe, in which he calls it “quietly revolutionary.”

If we run out of these books, remember that the paperback and Kindle editions are still in print, and I have plenty of other autographed books to buy. And we still have too many books in the house, so more sales will be in the offing. Thanks again!

CATEGORIZED UNDER: Book sale!, Microcosm: The Book

We purge, you save! Get an autographed hardcover copy of Microcosm

By Carl Zimmer | May 19, 2011 1:35 pm

As I wrote on Monday, we’re boxing up books in preparation for some house renovations. You were kind enough to take 21 autographed paperback copies of At the Water’s Edge off our hands–in about three hours.

Well, we have even more books that we’d rather sell than pack.

Here’s our new deal: we’ve got 17 autographed copies of the American hardback edition of Microcosm: E. coli and the New Science of Life. The hardback edition is out of print, but between now and next Thursday, you can buy them for the low, low price of  ten dollars from my Amazon store. (Cue Crazy Eddie again!)

In Microcosm, I tilt at one of my favorite windmills: the definition of life. But rather than try to take on all of life on Earth, I chose one species–the one that we know best of all. That would be our gastrointestinal lodger, Escherichia coli, the little bug that helped build modern biology and launch the entire biotechnology industry. In my biography of this scrutinized germ, I explore the origin of life, our inner ecology, and the search for life on other planets. You can find out more about the book on at, or check out this review from Anthony Doerr in the Boston Globe, in which he calls it “quietly revolutionary.”

Thanks for saving us from the purgatory of boxing books. If our stash runs out before you get a chance to buy a copy, bear in mind that the paperback and Kindle editions are still in print, and I have plenty of other autographed books for sale.

Update 3 pm: Wow! We sold them all in 85 minutes. Keep an eye out for more sales like this in days to come.

CATEGORIZED UNDER: Book sale!, Microcosm: The Book

Blood type, meet bug type: my new story for the New York Times

By Carl Zimmer | April 20, 2011 9:40 pm

For some time now I’ve been bewitched by the microbiome–those 100 trillion passengers that make our bodies their vessel (here’s a piece from the New York Times last year, and a long essay from last month). But I was especially intrigued by a paper that came out today in Nature. Scientists found they could sort people into just three distinct gut microbiomes, much like they can sort people into four blood types. Here’s my story in the Times, which will appear in tomorrow’s edition.

One thing that you won’t find in the article is some intriguing speculation I indulged in with the scientists I interviewed. Researchers have clearly demonstrated that microbes can influence their host’s behavior. They release molecules in the gut that travel into the blood and then into the brain. The bacteria that live in obese mice can make ordinary mice voracious. My fellow Discover blogger Ed Yong has written about how the microbiome can steer the development of mice to become more or less anxious as adults. In an upcoming review called “The Mind-Body-Microbial Continuum,” a team of microbiome experts ponder how our microbes might play a role in psychological disorders such as autism and attention deficit disorder. So it’s reasonable to wonder if our “bug type” influences our personality, much as the brain parasite Toxoplasma appears to.

I’ll be talking more about my story Thurdsay morning at 6:30 am and 8:30 am EST on the public radio show The Takeaway.

Update #1: Here’s the link to my appearance on the The Takeaway.

Update #2: Here’s a figure from the paper, representing the separation of the three types. It’s helpful when reading the skeptical comments from Joshua Shapiro of Princeton below.

Here’s the accompanying caption: “Phylogenetic differences between enterotypes. a–c, Between-class analysis, which visualizes results from PCA and clustering, of the genus compositions of 33 Sanger metagenomes estimated by mapping the metagenome reads to 1,511 reference genome sequences using an 85% similarity threshold (a), Danish subset containing 85 metagenomes from a published Illumina data set (b) and 154 pyrosequencing-based 16S sequences (c) reveal three robust clusters that we call enterotypes. IBD, inflammatory bowel disease. Two principal components are plotted using the ade4 package in R with each sample represented by a filled circle. The centre of gravity for each cluster is marked by a rectangle and the coloured ellipse covers 67% of the samples belonging to the cluster. IBD, inflammatory bowel disease. d, Abundances of the main contributors of each enterotype from the Sanger metagenomes. See Fig. 1 for definition of box plot. e, Co-occurrence networks of the three enterotypes from the Sanger metagenomes. Unclassified genera under a higher rank are marked by asterisks in b and e.”

CATEGORIZED UNDER: Microcosm: The Book

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

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