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DAVIS, Calif. — Microbiologist Jonathan Eisen has a knack for really annoying his fellow scientists.

He calls them out for overhyping their findings, or for inviting too few women to speak on panels, or for choosing to publish research in prestigious journals available only to subscribers instead of open-access publications. His crusading spirit knows no boundaries: Eisen once bestowed a “Genomic Jerk” award on himself for getting his facts wrong in a blog post.

All this, plus a playful social media presence, has earned Eisen a reputation as one of the most influential life science researchers on Twitter.


But what he really wants is to use that megaphone to help people understand bugs.

From an office crammed with lemur skulls, tubeworm shells, and dusty boxes of dead butterflies, Eisen aims to promote public understanding of the microbiome, the vast assortment of microbes that live in and all around us. Bacteria, he points out, are ubiquitous — in people’s guts, on their skin, and in every environment. They can cause infections and disease, but they are also essential to health and life.


Eisen, a professor at the University of California, Davis, wants to change what he calls a “bipolar” attitude toward bacteria.

On one side is widespread germophobia — the fear that “there are germs everywhere, microbes on McDonald’s play structures, and we’re all going to die,” he said. “On the other hand,” he said, “we have the other end of the spectrum, which I call microbiomania — [the belief] that all microbes are good and will magically cure all your ailments.”

Eisen points out a favorite quote he has taped to his bookshelf in his office at the UC Davis Genome Center. Andria Hautamaki for STAT

Swinging at ‘charlatans’

Eisen tries to puncture such hype by regularly giving out an “Overselling the Microbiome” award to “charlatans” who propose simplistic solutions to complex problems. He also does a lot of everyday myth-busting via Twitter, which doesn’t always endear him to his colleagues.

Last month, for instance, a news story in Science described an experiment in which researchers staged a fake burglary and collected hundreds of swabs from the mock crime scene to see what they could learn about the bad guys.

Jack Gilbert, a University of Chicago biologist, isolated microbial material from the samples and correctly concluded that one of the “burglars” consumed about 10 alcoholic drinks a week and that another took migraine medication. He predicted that scientists may one day be able to use unique microbial signatures to place a person at a crime scene.

Eisen was horrified. He worried that such a process could wrongfully implicate innocent people — and he took his concerns to Twitter.

Gilbert — who considers himself a friend of Eisen — was taken aback. He felt Eisen had overreacted to what was meant as an initial exploration of where the science may ultimately go.

“When Jonathan shouts, tens of thousands of people listen,” Gilbert said. “I wonder how many of those took what he said and basically now think I am a complete hack.”

He called Eisen an “immense power for good” in the world of science but noted that “when you are on the wrong end of his fire hose it can feel like a witch hunt.”

Eisen also tangled with colleagues last fall after working with them on a manifesto calling for more collaborative research into bacteria. Eisen wanted to publish in an open-access journal so the public could have a look. The team insisted on offering it to the more prestigious subscription journal Science.

In protest, Eisen withdrew his name from the manifesto. In typical fashion, he then bluntly chastised his colleagues.

“I think publishing such an article in a closed-access manner is a mistake,” he wrote on Facebook. “So I removed my name. Sad day for me. And I think a sad day for the field.”

Dr. David Relman, a microbiologist at Stanford University, said Eisen’s determination to speak up makes him unique: “He’s willing to say what needs to be said, even if it might jeopardize his standing with funding agencies and publishing.”

A puckish personality

When Eisen gave a TedMed talk a few years ago — “Meet Your Microbes” — he wore a necklace made of plush toys shaped like bacteria on stage. He tossed some of the models into the audience. And then he tweeted about it.

The tweet captured both his deadpan sense of humor and his drive to get the public interested in his beloved bugs. It also helps explain why Eisen has more than 35,000 followers on Twitter, despite his rather cryptic handle, @phylogenomics, which refers to the intersection of the fields of evolution and genomics.

(His brother, Michael Eisen, a geneticist at University of California, Berkeley, is also a prolific tweeter and cofounder of the open access journal PLoS.)

When he’s not talking bugs, or taking down hucksters, Eisen uses his social media megaphone to press for more gender equity in science.

Cold Springs Harbor Laboratories organized a conference last year on the history of genome sequencing; Eisen tallied the gender of each speaker on his blog. “47 speakers. 4 of which are female. For a whopping 7.8% female speakers,” he wrote. “This truly makes me sick to my stomach.”

Elisabeth Bik, a microbiome scientist at Stanford, said Eisen’s advocacy on behalf of women makes a difference. “Because he’s in such a position of influence, when he writes about it people notice,” she said.

Eisen gave Bik a regular column in a widely read blog he manages, “He makes a conscious effort to offer women a chance to shine,” she said.

Jonathan Eisen
A Petri dish shows colorful microbe growth at the UC Davis Genome Center. The fungi appear fuzzy, while the bacteria are smooth and shiny. This sample came from an undergraduate student who was comparing the effectiveness of different disinfectants. Andria Hautamaki for STAT

A deep personal interest in gut bugs

Eisen’s interest in microbes has deep personal roots.

He’s had type 1 diabetes since he was a teenager, which means his body destroyed his own insulin-producing cells, and he must regularly monitor his blood sugar and inject himself with insulin.

One theory about autoimmune diseases like diabetes is that they stem from some kind of “dysbiosis” — an extreme imbalance among the trillions of microbes in the gut. The idea is that such an imbalance could trigger an inflammatory reaction and cause the immune system to attack the body’s own organs, such as the pancreas, where insulin is produced.

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Few things infuriate Eisen more than alternative health promoters who hype this theory as fact and promote quickie “cures” for dysbiosis, such as reseeding the gut microbiome with a new colony of bacteria by transplanting fecal matter from a healthy donor into the patient’s colon. (While fecal transplants have been shown to be effective for a deadly bacterial infection called Clostridium difficile, they’re unproven for other conditions.)

“I saw one clinic advertising fecal transplants for everything including type 1 diabetes, and I was like, ‘Wait a second,’” Eisen said. “People with type 1 diabetes don’t have beta cells that make insulin anymore. I have no beta cells in my body, so what the hell is fixing the goddamn dysbiosis going to do for me?”

Eisen has twice “honored” neurologist and alternative health evangelist Dr. David Perlmutter, author of the bestsellers “Grain Brain” and “Brain Maker” for promoting fecal transplants as a treatment for serious neurological conditions, including autism and Alzheimer’s. In one of many critical tweets, he called Perlmutter a “snake oil salesman.”

Not surprisingly, Perlmutter sees it differently. “Snake oil is harsh criticism,” he said in an interview.

“I don’t believe people should be going out and getting fecal transplants for themselves and their children willy-nilly,” he said. “What I am suggesting is that our current level of science suggests that reprogramming the gut microbiome may offer us a brand new therapeutic option.” He added that the field needs more solid scientific studies.

Eisen wears his “Cats for Science” T-shirt promoting his lab’s citizen science study of the cat microbiome, the “Kitty Biome Project.” A feline enthusiast himself, Eisen keeps a picture of his former cat on the door. Andria Hautamaki for STAT

On the prowl for kitty poop

Eisen, who came to work on a recent day in a “Cats for Science” T-shirt and shorts, is canny in finding ways to stoke public interest in microbes.

He teamed up with Science Cheerleaders, an organization of current and former cheerleaders involved in science, to collect bacterial samples from sporting events and public places — like half-court at a basketball game and the surface of the Liberty Bell — and sent them to the International Space Station to see how they’d grow.

And he’s working with Holly Ganz, a fellow cat lover and staff scientist in his lab, on the Kitty Biome Project, which aims to collect and sequence the DNA of bacteria found in feline poop — from rescue cats at the Berkeley animal shelter to cheetahs in Africa. The goal: To see what can be learned about the links between microbes and the health of cats.

Ganz’s team sends out collection kits to cat owners, asking them to collect a bit of kitty poop and mail it in to the lab. Last year, the lab ran a Kickstarter campaign to raise money for genome sequencing and collected $24,000.

“We thought this could be a great way to do outreach about the microbiome and interest the public,” Ganz said.

For his part, Eisen rejects any suggestion that he ought to focus his research more narrowly.

“Specialize? Who says I have to specialize?” he said. “Talk to anybody in my lab and you’ll learn that focus and I do not get along.”

Correction: A previous version of this story misspelled the name of Stanford scientist Elisabeth Bik.