The Microbiome Never Ceases to Amaze

By Carl Zimmer | July 20, 2010 2:08 pm

While I was away last week on vacation, the New York Times published my feature on the hidden jungle that each of us carries, known as the microbiome. I was very happy to come home to a lot of kind notes, tweets, and various communications about it. Yet I would never claim that my article delivered the Big Scoop on the subject. After all, we’ve known about the microbiome ever since Antonie Philips van Leeuwenhoek scraped his teeth over 300 years ago and discovered wee animacules in the scum. And as I wrote in my book Microcosm, Theodor Escherich discovered his eponymous Escherichia coli over a century ago in a quest to catalog the good microbes in babies’s guts, hoping to thereby identify the ones that were killing the children in droves. Even in the age of molecular biology, the microbiome has been well-chronicled. Jessica Snyder Sachs wrote a book back in 2007 called Good Germs, Bad Germs: Health and Survival in a Bacterial World that I heartily endorsed (and still do).

So why write a story now? That’s a question that science writers have to ponder a lot. Much of the most interesting science does not explode with a single experiment or the unearthing of a single fossil. It’s a stately unfolding, a long-running collaboration/competition. For me, the time seemed ripe thanks to a couple recent papers that catalogued vast amounts of DNA in the collective genome of our microbial lodgers. Scientists have long known that the genes in the microbiome outnumber human genes by perhaps 10 or 100 to 1. But now we’re finally getting a database of that genomic richness.

And then, at a recent conference, I heard about a fecal transplant that saved a woman’s life. I knew I had my lede. But I called my editor to make sure that I could kick off the article that way, given that so many readers peruse the Times over breakfast. You never know. To anyone who experienced a fascinated nausea, my apologies.

In the days since my article came out, a series of new papers on the microbiome have been published. Today the Times published an editorial about one of them, a study of the incredible diversity of bacteria-infecting viruses we carry. Even identical twins harbor different sets of viruses. And yesterday, Caltech researchers described how multiple sclerosis may be the result of the way bacteria manage our immune systems.

Still, I’m glad I didn’t wait for all the good science to emerge. I would still be waiting 20 years from now.

PS–Here is a list of links for my Times article:

The fecal transplant paper

Genomes of the microbiomes

A catalog of 3.3 million genes

Bacteria teaching the immune system

The paper on how microbes infect us at birth

The microbes of the lungs

[Image: A beautiful bacterial colony]

Comments (8)

  1. Never feel you have to explain “why now”? If anything, science journalism is biased toward sensational new claims. Any thoughtful and well written description of a scientific issue is worthy of column inches.

    Also, the fecal matter story is a news hook. The lede starts “Scientists are regularly blown away by the…”

  2. NewEnglandBob

    Thanks for the extra education in microbiomes and in the English Language. From Wikipedia:

    The most important structural element of a story is the lead (or “intro” in the UK) — the story’s first, or leading, sentence. (Some American English writers use the spelling lede (pronounced /ˈliːd/), from the archaic English, to avoid confusion with the printing press type formerly made from lead or the related typographical term leading.[3])


    [CZ: I love all the old journalism lingo. Orphans, widows, and all the rest…]

  3. CZ, me too. Are there names for the different types/lengths of stories – traditional news that lead with the lede vs. magazine-like story that introduces a character or event first (the hook).

  4. Simon

    Coincidentally I was listening to an old (May 2007) Mark Crislip “Quackcast” this morning (#16 Probiotics http://www.quackcast.com/spodcasts/files/podcast_15.mp3) where he was talking about a study of 15 people with C. Difficile diarrhea who weren’t responding to antibiotics – they were all given fecal transplants from their partners and 14 recovered immediately.

    The conclusion was something along the lines of “the closer your probiotic is to fecal matter, the better it’ll be for you gut”!

  5. Thank you for your nice article on the human microbiome! We’re the MetaHIT consortium you refer to in your article that published the 3.3 million genes catalogue using metagenomic sequencing last March. We simply wanted to add that a lot of the actors you cite in your paper as well as representatives from other microbiome initiatives from around the globe are gathered inside the International Human Microbiome Consortium (IHMC – http://www.human-microbiome.org ).

    You can also follow us on https://twitter.com/MetaHIT

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The Loom

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

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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