Humans don’t rule the planet. Humans don’t even rule their own bodies. During the past 20 years or so, it’s become apparent that the guys in charge of everything are a nanometer across and run in packs, or perhaps more accurately, hang out in mobs. These gangs of microorganisms are together referred to as the microbiome, and we’re just beginning to understand what these worlds within our world do to us and for us.
First, a little data, according to “Dirt Is Good,” a recent book by Jack Gilbert, director of the University of Chicago Microbiome Center, and Rob Knight, director of the University of California Center for Microbiome Innovation, with science writer Sandra Blakeslee:
We’re outnumbered. Microbes outweigh all visible plants and animals on earth by a factor of 100 million. The total number of bacteria alone is a 1 with 30 zeroes after it: a nonillion. For the total number of viruses, add two zeroes to those 30.
We’re inexperienced. Microbes ran everything without an assist from humans, fish, ferns or even trilobites for about 3 billion of the last 4.5 billion years.
You’re a minority even in your own skin. For every one of your cells, there are 1.3 microbial cells in your body. About 30 trillion cells are yours; another 40 trillion cells in your body are microbes. Together, those microbes weigh as much as your brain — 3 pounds — and have an astonishing influence on that organ, to say nothing of the sway they hold on your digestive tract, your urogenital system and your immune system.
At this point, it’s an old joke but true: When the American poet Walt Whitman wrote, “I contain multitudes,” he wasn’t kidding. (“I Contain Multitudes” is also a 2016 book about the microbial world by science writer Ed Yong. )
While the existence of this microbial universe has never been a secret, until fairly recently, scientists had little access to its mysteries. Scientific scrutiny was limited to microbes that would grow in a laboratory, a remarkably teeny sample. What changed everything was the development of a technique to sequence microbial DNA directly from the environment. Pair that newfound ability with the rapid drop in the cost of genetic sequencing, and the field took off. “So what would have cost you $100 million 15 years ago costs you 100 bucks now, so there’s a whole lot that we can do,” Knight said in a phone interview.
For instance, science can now answer this riddle: Your baby hurls his pacifier onto the kitchen floor. To protect your infant’s health, which is the best way to clean it?
A. Run the pacifier under hot water.
B. Pop the pacifier in your mouth, swish it around, then give it back to your pitcher-in-training.
If you answered A, who can blame you?
But “Dirt Is Good” authors Knight and Gilbert would disagree. Their book examines how to raise healthy kids by leveraging what we know about our microbial overlords.
“Your mouth is full of antimicrobial peptides, full of good bacteria producing all these things to fight off the bad bacteria,” Knight said. Mom swishes the pacifier in her mouth, coats it with these germ-fighting peptides, and provides her kid a gift of beneficial bacteria. Whereas the bacteria in tap water? They’re not on your team. They’re unlikely to hurt you, but they’re not designed to fight human diseases that the mom’s immune system is.
Research shows we’re not only filled with these microbes; every hour, we shed clouds of them, a million particles of bacteria, fungi, viruses and the single-cell, nucleus-lacking members of the kingdom Archaea. Researchers at the University of Oregon found that our microbial shedding creates a near fingerprint, leading researchers in the forensic sciences to explore whether the bacteria left at a crime scene might someday be used to identify bad guys.
It should be clear by now that we’re not talking about bacteria as invaders; we’re talking about a polyamorous exchange with single-cell life partners that interact intimately with our immune system, affect our moods and mental health, and contribute to the regulation of our metabolisms, playing roles in obesity and Type 2 diabetes, and even driving our food cravings.
There’s no prescription, no exact formula to cultivate a microbiome that will, for example, prevent sugar cravings and diabetes, but several behaviors will enhance the survival of the best bugs, Knight said. For instance, exercise may foster beneficial gut bacteria populations. In mice, exercise reduces bacterial species that cause inflammation while increasing anti-inflammatory species. High fiber foods starve less-supportive bacteria and boost healthy types. Bacteria that ferment dietary fiber produce short-chain fatty acids. These fatty acids can reduce insulin resistance, a precursor of Type 2 diabetes.
“If you’re eating a diverse diet, especially with lots of different kinds of fruits and vegetables, and with fermented foods, that’s been shown to have a restorative effect” on the health of your gut microbiome, Knight said. Fermented foods include yogurt, pickles and kimchi — all have species of the helpful bacteria Lactobacillus.
Microbial health appears to play a role in brain health, a growing number of studies suggest. In one small study, children with autism who received fecal microbiota transplants showed reduced digestive complaints and improved communication and socialization skills. Although the study was too limited to provide definitive evidence, it’s promising, Knight said.
Microbes in the gut talk to the brain in several ways: They produce neurotransmitters — including 90 percent of the body’s serotonin, Knight said. They manufacture small molecules that float through the blood stream controlling which genes are turned on and which are turned off. They activate the immune system, which affects the brain. Finally, they can direct-dial through the gut’s vagus nerve — a line straight to the brain.
So, it’s good to help children grow a protective microbiome. For that, Knight and Gilbert have an easy answer: dirt. Kids with dogs, for instance, have a 13 percent reduced risk of asthma. Children on farms do even better, with a 50 percent reduced risk, they report.
“What we’re starting to find out is exposure to natural healthy bacteria in the environment is really important for training our immune system and making sure it doesn’t go really haywire and attack us,” Knight said.
As Knight and Gilbert write, “Get (kids) outside, let them interact with animals, allow them to play in the dirt, rivers, streams, ocean. Don’t sterilize everything they are going to touch or put in their mouth.”
A dirty kid, it seems, is a healthy one.