microbiome – Seattle Science Writer

Zoo inside you

This book lights a rare sort of fire. Prepare for ideas that catch and flame and race. You will focus and refocus on the surprises that Ed Yong keeps bringing on page after page of “I contain multitudes.” He’s playing with your sense of scale and identity.

You’ve heard of the microbiome, the one in your gut is most often discussed in the grocery aisles where well-meaning people claim to be buying special yogurt to help their digestion. The human gut microbiome is millions of microscopic creatures that live in a symbiosis with us – their hosts – and digest our food and communicate with our brain. But Yong is taking you on a bigger journey, a better setting of context, a longer long view.

“All the visible organisms that we’re familiar with, everything that springs to mind when we think of “nature,” are latecomers to life’s story. They are part of the coda. For most of the tale, microbes were the only living things on Earth.” [pg.7]

Gently, and with exquisite detail, Yong shows readers the characters and colonies and “social” lives of microbes inside a pangolin, a squid, a cicada, a rat and a mosquito. Knowing that his readers may hang by their fingernails, he offers metaphor and analogy to give us hand holds on a journey more like Alice’s in Wonderland than a simple march from step to step.

“Think of it this way: an animal’s genes are like set designers in a theater – they create the stage upon which specific microbes can perform. Our environment – friends and footsteps, dirt and diet – then affects the actors that take the stage. And random chance lords over the whole production, which is why even genetically identical mice that live in the same lab end up with slightly different microbiomes.”

Yong wisely takes time, in the chapter “The Long Waltz” to take us inside the very identity and labeling arguments between scientists. How do we frame and label new understanding. Should we say “symbiosis” or should we accept new frames like “holobiont?” New ways of seeing require new words. This book makes you question the very definition of “me” or “mine.” Are you driving or being driven?

One key power that microbes have is exchanging genes with one another, an ability known as horizontal gene transfer. In Yong’s imagination, we see it as a giant boozy party scene.

“They can exchange DNA as easily as we might exchange phone numbers, money or ideas. Sometimes, they sidle up to one another, create a physical link, and shuttle bits of DNA across: their equivalent of sex. They can also scrounge up discarded bits of DNA in their environment, left by their dead and decaying neighbors.” [pg 191]

Our journey includes some potential fixes that researchers propose. One leverages a bacterium to vanquish mosquito-borne diseases. Another engineers a microbe that could peer into our bodies and repair problems. Yong wisely includes many caveats with those rosy future pictures. But mostly he leaves us gaping, awestruck, at a new way of seeing ourselves in a new mirror.

Scientists shovel dirt in book for parents

Should you wash the pacifier, if it falls on the ground, or should you lick it off and give it back to your child?

Two scientists tackle this – and hundreds of other questions about dirty and clean in the new book, “Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System.” Hint – They fall on the side of licking and returning the pacifier, with qualifications.

Both Jack Gilbert and Rob Knight are parents. They’ve been sleepless in the nursery, and worried about vaginal versus c-section births. They’ve framed the science as a series of parent questions from pregnancy and childbirth itself all the way up the playground years. Science nitpickers will find plenty of details about what is called the microbiome – the ecology of all the microscopic creatures who share our skin and our guts. (And our hair, and our armpits, and …)

Gilbert is a PhD and professor of surgery and director of the Microbiome Center at the University of Chicago. Knight is a PhD and professor of pediatrics and computer science at the University of California, San Diego. Gilbert and Knight are not medical doctors, and don’t give medical advice. Their co-writer, Sandra Blakeslee, wrote for the New York Times for many years.

These three bring academic heft to their answers, often quoting specific research projects that have established certain science principles. There are more than 180 references in the book’s appendix.

But scattered in the pages, there is room for humor.

“Should I wash dishes in the dishwasher or by hand? What’s best for microbial health?”

“Is it okay for my child to touch poop?”

Before we look at the answers to these questions, let’s just explain that the last few years have seen an explosion of discoveries about the benefit of healthy microbes in the human gut. People who are infected with one microbe, C. difficile, are sometimes cured by a transplant of feces from a healthy person. Conditions such as depression and autism have been studied by comparing the microbes living in the intestines of patients with and without those issues. But the explosion of research has led to a corresponding explosion of hype.

Parents may feel especially confused. Perhaps you have heard that exposing children to a certain amount of dirt may help protect them from developing allergies. There is truth to that, and this book goes into pages of details.

On the dish question, the scientists explain that the extra-hot drying cycle of some dishwashers is probably too much cleanliness. They recommend hand washing dishes. As they write, “You want your kid to be exposed to more, not fewer, bacteria in daily life.” On the poop question – they are generally saying it is OK but there are important limits.

Should I take my child to a farm? Should we get a dog?

With careful but clever explanations, the scientists say “yes” to both the farm visits and the dog. But they may surprise you with some other answers. They don’t routinely advise eating yogurt, for example, even though it has the reputation of carrying “good” microbes, often called probiotics. Probiotics is the opposite of antibiotics, which kill bacteria. Probiotics often contain what are called “good” bacteria.

But the book explains that there is no evidence that probiotics always make people’s guts healthier. The whole field of what is known as probiotics is filled with claims that promise one outcome, but frequently don’t deliver it.

Should I give my child probiotics if he has diarrhea?

In this example, the scientists say “Yes.” Studies do show the value of giving an infant with diarrhea a probiotic. The precise answer to the question gives an education in how the relatively young science of microbial health defines “good” bacteria, and how there is evidence for infants that shows certain probiotics help in that situation. But they also explain exceptions and nuance.

Reading the whole book may leave you with an awestruck appreciation for what is not known. The true dimension or “population” of microbes that constitutes the healthiest possible gut is not established yet for most people. There are layers and layers of complexity surrounding what we eat, because some of what we eat is “food” for the bacteria themselves and other things we eat are broken down into elements that we actually absorb to power our own cells.

In the 14 chapters and hundreds of questions, the authors slowly educate us to a awesome admiration for the colonies that share our body. Each person is a planet. Each part of the body carries its own colony of microbes, which thrives in a dynamic communal way, competing with each other for certain resources, but also driving off invaders in some cases that might make the person-planet sick.

For a deeper dive into what is called the “hygiene hypothesis” and how exposure to more diversity in childhood may keep children from allergies and asthma, see this New England Journal of Medicine article.

The more we know about the complicated interplay of these creatures, the more questions we may have. It isn’t an easy time to wash the dishes.

Resources:

Review of book by pediatrician Perri Klass of The New York Times.

Centrifuge – smashing science into theater

What happens when an actor has to keep putting on a skull-cap, in order to look bald, over and over? Audiences howled, as his errant hairs poked out, and he began his lines imitating Jeff Bezos of Amazon fame. The fake-Jeff was just one character in a set of five science plays. Each play only 10 minutes long and all of them part of a festival known as Centrifuge.

In other plays, reluctant astronauts hunted down life on Saturn’s moon, Enceladus. Newlyweds obeyed the beeped warnings of Fitbits on their wrists predicting “argument” approaching, the way the silly robot of “Lost in space” kept saying “Aliens approaching.” A family hid in a bunker from the frightening reality of ordinary crowds of other people.

Besides a hilarious ribbing of both Bezos and space-exploration rival Elon Musk, a different dystopian play focused on overuse of the mood-enhancer ecstasy or MDMA. Writer Wayt Gibbs holds a model of that molecule above.

Centrifuge is a week-long improvisation between volunteers of two tribes – theater and science. David Mills and his wife, Catherine Kettrick, lead this project. Full disclosure – I was one of the science writers in May 2017.

You can’t predict what will happen as the week unfolds. With close to 30 people involved, who have full-time other jobs, plenty of obstacles show up. Pets get sick, relatives call, jobs demand. Randomness drives the schedule, just as in a lab where randomness divides mice into controls or experimental subjects.

Monday: Five science writers and five playwrights are randomly assigned to each other, leave the room in minutes and spend time talking in dyads about some research the science writer has brought in.

Wednesday: Five playwrights turn in roughly six-page scripts of new plays inspired by that talk. Actors, who wait for their names to be pulled from hats, are assigned to the five plays. They begin reading the scripts out loud with a randomly assigned director. As I watched, four actors began turning names into people – adding back stories and motivation to small gestures.

Just to shorten this a bit, by Friday the five plays, including 5-minute introductions about science by each writer, debut to the public. A lot of logistics – sets, costumes, lighting, sound and pacing get expertly handled by the theater tribe.

My playwright was Jim Jewell, whose full-time day job is teaching college students composition. The play he created in 48 hours was amazingly complex with four characters from a family. It was less about the gut microbiome research I described to him Monday, and more deeply about how people resist ideas. How might people react to knowing their bodies are more microbial colonizers than “self?” See my earlier post for more about microbiome.

Unlike science, no measurements are taken after this week of mixing. We didn’t examine the audience to rate their hilarity. We didn’t measure the science writers or playwrights to give them a 2 or an 8 in “inspiration.” But what might have changed in us?

I’m hoping Wayt, as well as Alan Boyle, Greg Scheiderer, and Elle O’Brien will tell me some of their musings on that question for a future post.