Planet You: The mysterious world of the microbiome

There are trillions of them on — and in — our bodies. Microbes have existed on earth for more than three and a half billion years. Makes you wonder who’s playing host to whom, and whether we humans are merely vessels for these tiny survivors. They influence everything from intestinal disorders to mental health conditions — and we're only just beginning to understand their power over us. Contributor Stephen Humphrey journeys into the mysterious world of the microbiome.
Microbe experts are now saying it’s a good idea to let children play outside and get dirty. Microbes they pick up in childhood could have health benefits throughout their lives. (Stephen Humphrey)
Listen to the full episode53:59

There are trillions of them on — and in — our bodies. Microbes have existed on earth for more than three and a half billion years. Makes you wonder who's playing host to whom, and whether we humans are merely vessels for these tiny survivors. They influence everything from intestinal disorders to mental health conditions — and we're only just beginning to understand their power over us. Contributor Stephen Humphrey journeys into the mysterious world of the microbiome.

Humans like to view themselves as the dominant life form on Earth but microbes have been here much longer than we have. There are many more of them than us. When we are all gone, they will still be here.- Erica Sonnenburg

Worms, Humans and Living Tubes

What could human beings ever have in common with worms?
 
For starters, humans and worms, along with a lot of other animals, can be described as "living tubes".
 
It's easy to see how that applies to worms. Their bodies look like mobile, muscular tubes. But not human bodies. We have feet, hands, skeletons and big heads with clever brains. But under the surface, we do share something in common: our digestive system. Worms were the first complex animals to evolve the setup of mouth, digestive tract and anus. Food comes in the mouth and waste comes out the other side. In-between, digestion happens. 

"And so a simplified way of thinking of the human body, with our digestive tract running from our mouth to our anus, is as a hollow tube," says biologist Justin Sonnenburg.

Food isn't all that moves through us. Tiny opportunists also tag along: bacteria, archaea and other microscopic life. Trillions of microbes become permanent residents of our insides, living off our food. These long-term occupants of our guts make up part of our "microbiome".

To microbes, the gut is prime real estate.

"I think from a microbial standpoint, we're a great little vessel that they can live in," says Erica Sonnenburg, who runs a microbiology lab with Justin, her husband, at Stanford University. "It's an added bonus that we have arms and legs that can move around and gather food to feed them."

But it's not just a one-way relationship. Gut microbes break down foods we can't digest, like complex starches, releasing nutrients such as riboflavin, folate, vitamin B12 and vitamin K.

Bone eaters on the ocean floor

This alien-looking creature is Osedax lehmani, a species of Osedax worm, which devours whale bones with the help microbes. In Latin, Osedax means “bone devourer". (Greg Rouse/Scripps Institution of Oceanography at the University of California)
Worms, those pioneers of the gut, also have microbes to help them digest — sometimes extraordinary things. For example, there's a genus of small aquatic worm which dines on whale bones.

Marine biologist Greg Rouse named it Osedax: Latin for "bone-devourer". This strange-looking worm — it resembles a feather duster — was found in 2002, noshing on a giant sunken whale skeleton.

"We were very surprised when we saw the bones of a whale off California that were covered in what looked like a shag pile carpet that was bright red," he recalls. "The part we could see on the outside, the red part, was feathery plumes full of blood. But the worm's bodies were actually down inside the bone. And they were digesting away the bone."

Osedax, scientists found, get these digestive super-powers from microbes living inside cells in their stomachs, which these contrarian worms keep on their outsides. 

"We now know via secreting acid to dissolve the bone they're actually uptaking the nutrients," Rouse says. Not eating as we know it, but fundamentally, humans aren't so different.  "Well, we share a deep similarity in that we are consumers of other organisms," says Rouse. "We are also heterotrophs, in that we consume food."

So how would bacteria see us differently than worms? Erica Sonnenburg suggests they might find us disappointing. As modern diets tilt toward processed foods less rich in things like fibre, diversity of microbes in our bodies declines. The health consequences of this are still being studied. What's clear is not as many microbes live in our guts anymore.
 
"Probably, based on the Western diet," she says, "they'd be happier in a worm."

Justin Sonnenburg is Principal Investigator at the Sonnenburg Lab in the Department of Microbiology and Immunology at Stanford University. 0:45

Guests in this episode:

  • Erica Sonnenburg is Senior Research Scientist at the Sonnenburg Lab in the Department of Microbiology and Immunology at Stanford University.
  • Justin Sonnenburg is Principal Investigator at the Sonnenburg Lab in the Department of Microbiology and Immunology at Stanford University.
  • Greg Rouse is a Professor in the Marine Biology Research Division, Scripps Institution of Oceanography at the University of California, San Diego.
  • Andrew Moeller is an Evolutionary Biologist at the Department of Ecology and Evolutionary Biology at Cornell University.
  • Dana Philpott is a Professor, Dept. of Immunology, Faculty of Medicine, University of Toronto.
  • Stephen Collins is Director of the Farncombe Family Digestive Health Research Institute, GlaxoSmithKline Chair in Gastroenterology and a Professor in the Department of Medicine at McMaster University.
  • Susan Poutanen is a Microbiologist at the University Health Network, Mount Sinai Hospital, Department of Microbiology, and a trained infectious disease physician.

**Special thanks to Christina and Sam Winger for sharing the recording of the birth of their son, Johnny.


Further reading:

Related websites:



**This episode was produced by Stephen Humphrey, Nicola Luksic and Sara Wolch.

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