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Our Microbiomes Are Making Scientists Question What it Means to Be Human

Are we people or a "megaorganism?"
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When you’re young, everyone tells you that you are a unique individual. The idea of individuality stretches back centuries, but as we learn more about our bodies, some biologists have suggested that the microorganisms within us mean we’re more like a collection of trillions of organisms than an individual person.

An article published in early February in the open access journal PLOS posits that microorganisms that live in your mouth, your stomach, and your skin “challenges our concept of self.”


It wasn’t until 1695 that when walking through the gardens with a German princess, the philosopher Gottfried Wilhelm Leibniz conceived of the individual. As the story goes, Princess Sophie said she didn’t think he could find two leaves that were the same. “So they were beginning to pick leaves, and each leaf was different, of course,” Tobias Rees, director at the Berggruen Institute in Los Angeles and co-author of the PLOS paper, told me via Skype. Leibniz suggested that every leaf was individual.

Before that, “humans were part of a natural, god-given cosmos and they were not really separate from nature,” Rees said. “Even the artificial or the technical was said to only complete what nature left incomplete.”

As the natural sciences developed, though, we began to think more like Leibniz thought of leaves: the brain, the immune system, and the genome all seemed to make us individual.

The physician Franz Gall once told Immanuel Kant that the shape of his brain and therefore his skull was what made him a philosopher, Rees said, which most philosophers cite as the transition point to when people began thinking of the brain as individual. Thousands of brain studies later, it’s hard to think of yourself as an individual without one.

In 1960, an Australian immunologist named Sir Frank MacFarlan Burnet won the Nobel Prize for his work demonstrating that the immune system differentiated the self from the nonself. The immune system separates us from the pathogens, viruses, and bacteria that make us sick.


Studies in genetics and Watson and Crick’s discovery of DNA gave more credence to the idea of individuality.

But as scientists learn more about the microbiome, the idea of humans as a singular organism is being reconsidered: “There is now overwhelming evidence that normal development as well as the maintenance of the organism depend on the microorganisms…that we harbor,” they state (others have taken this position, too.)

Microbes, which comprise about half the cells in our bodies, exert an influence over the human brain, immune system, and gene expression, among other body processes (previous claims that microbial cells outnumber human cells 10-to-1 have been debunked.)

"Certainly microbiomes impact all sorts of aspects of behavior in mammals and likely in humans, but so do drugs. So does TV. So does schooling. Does this mean now our concept of self should include what drugs we take?"

Microbes can produce neurotransmitters like dopamine, which is involved in feelings of euphoria and aggression, Thomas Bosch, a professor of Zoology at Kiel University in Germany and one of the paper’s co-authors, told me via email. An imbalance in gut microbes has been linked to certain behaviors and diseases, including autism, depression, Parkinson’s Disease, Alzheimer’s, allergic reactions, and certain autoimmune diseases, though much of this research is still in its infancy.

This doesn’t mean humans aren’t unique—we are obviously different from one another—but that our uniqueness doesn’t just stem from genetics or our brains but also from the other organisms living in and on our bodies.


“What was traditionally considered as part of the humans self is largely of bacterial origin, i.e. nonself,” Bosch said.

New discoveries in microbial research are “a philosophical and artistic invitation to learn to think differently about ourselves,” Rees said.

Microbial genes also contribute enough to human traits that the authors argue that gene-editing technology like CRISPR-Cas9 needs to be reassessed with microbes in mind.

“[Human] genomes are intertwining genomes,” Bosch said.

When we consider the fact that microbes have such influence on our brains, immune systems, and genomes, it suddenly becomes difficult to define a human “individual.” Rees said that when he first reached out to his co-authors, they were troubled by their findings.

“They have been thinking about themselves as human, as individuals, as discrete and bounded, and now they’re not?,” Rees said.

So Rees and his fellow authors argue that the definition of a human individual is much more fluid than we originally thought. We are a vibrant community, or, as the authors put it, a “megaorganism.”

"The human is more than the human"

Not all microbiologists or philosophers are convinced, however. Ellen Clarke, a lecturer in philosophy at the University of Leeds in the UK who specializes in the philosophy of biology, says the microbial contribution to a human organism doesn’t fundamentally change who we are.

“We have plenty of traits that depend on genes outside of us—I can’t reproduce without a mate, for example,” she wrote me in an email. So why should the influence of microbes matter so much in comparison? She does believe, however, that the microbiome as a whole provides “a good antidote to individualism.”


Similarly, Jonathan Eisen, a microbiologist and professor at UC Davis, feels that the authors overstate the influence of microbes on our behavior.

“Certainly microbiomes impact all sorts of aspects of behavior in mammals and likely in humans,” he wrote me in an email statement. “But so do drugs. So does TV. So does schooling. Does this mean now our concept of self should include what drugs we take?”

Eisen also points out that these ideas are not entirely new. Previous research has already looked into an expanded idea of humanity, like the hologenome concept developed in the 1990s, in which a genome is defined as the sum of all the genes of all cells (human or otherwise) in the body. He wouldn’t go as far as saying that this needs to change our definition of self.

Eisen said the microbiome presents a good opportunity for scientists, philosophers, and artists to discuss intersections between their work work, while Clarke remains more skeptical. “It sounds a bit overblown,” she said.

But perhaps this is why we need more of these discussions between researchers of all disciplines: to determine exactly how we should think about ourselves. And, even if the minutia of the arguments are disputed, it’s difficult to reject the microbiome’s influence.

As the authors write in the paper, “the human is more than the human.”