Eisen Lab in the News

Broadcast, Print and Digital Media Coverage (Selected Examples)



To describe the overselling of the microbiome, University of California microbiologist Professor Jonathan Eisen coined the term “microbiomania”.He runs a blog called The Tree of Life that hands out awards to those who oversell it and he has had no shortage of candidates, including the uncritical reporting on Lauren Petersen’s research on cyclists.

And that filter is sometimes worse than not having a filter,” says Jonathan Eisen, a microbiologist at UC Davis and open-science advocate. (He’s on the board of BioRxiv.) “There’s reasonable evidence that trying to get something published in the snooty, high-impact-factor journals may correlate with making something more wrong than if you hadn’t.”

“If people got credit for this, they’d all do it,” Eisen says. “It’s not that complicated. Most people want to share info sooner rather than later.” The story of scientific publishing is a long one, but it isn’t over.

 “A great resource for following the hype (or, “microbiomania” as he calls it) is this blog by Jonathan Eisen, PhD, a biologist at UC-Davis who researches the evolution and function of the microbiome.”


“One aspect of hand sanitizers that is usually overlooked is that they can affect bodies’ microbiomes in a few ways, and some of these ways could be bad,” says Jonathan Eisen, a microbiologist at the University of California at Davis. While they are killing potentially dangerous microbes, they are also altering the communities of beneficial bacteria on the skin.

Critiques of researchers’ posts come from within the scientific community as well as from outside it, and scientists need to respond carefully to foster intelligent, polite discourse. But that doesn’t always work. Jonathan Eisen, an evolutionary biologist at the University of California, Davis, freely tweets about science topics, his own work and interesting papers or presentations. He has got into arguments on Twitter in connection with some posts.

He once found himself embroiled in a nasty spat with supporters of a journal when he had retweeted a post that disagreed with one of its editorials. A Twitter user began to attack the critics, including Eisen, who blocked the user as the battle escalated. He received support from colleagues on the thread and in e-mails, but stayed off Twitter for a few weeks afterwards. Now, when things heat up online, he gets up and walks away.


Jonathan Eisen, professor at UC Davis said that in case of outbreak of an infection, the reason behind the virulence of the bacteria could be detected with the help of whole genomic sequencing study. The analysis would help in identifying the gene involved in causing the virulence such as presence of antibiotic resistance and toxin genes.

It’s time to push back. One way is to hold scientists, philanthropists, and the press accountable. In 2014, Jonathan Eisen, professor at the Genome Center at the University of California, Davis, compiled a lengthy list of articles on the hype surrounding the genome project—many of them either complaining of promise fatigue or pricking the bubble of inflated expectations. We can and should continue writing, collecting, and sharing such pieces. Fund science liberally, but reward knowledge more than market value. Encourage science literacy, not just cheerleading. And teach skepticism of technology, medicine, and the media.

“The science here has enormous potential and I do not want that potential to be damaged by the BS and the hype,” said Dr. Jonathan Eisen, an evolutionary biologist at the University of California, Davis. He uses his science blog, “The Tree of Life,” to pick apart what he sees as microbiome lies or misconceptions. “The microbiome is ripe for snake oil because it is so complex and thus easy to lie about and oversell,” Eisen said.

The scientific community should “be very careful about how we present and interpret such work,” says Jonathan Eisen, professor of medical microbiology and immunology at the University of California, Davis. Eisen has been openly critical of the study’s media coverage.

  • June 12, 2016. Interview with Kirsten Dirksen. “Quantified “selves”: a smartphone tool to meet your microbes (& microbiologist Jonathan Eisen)”. Article. Youtube
  • June 4, 2016. Interview with Tools of Science.
  • May 17, 2016. Sally Addee article at New Scientist. Microbiomania: The truth behind the hype about our bodily bugs
  • May 17, 2016. STAT article on microbiomes. “Is Gut Science Biased?
  • May 17, 2016. Bioworld articleabout White House Microbiome initiative by Michael Fitzhugh .

Critics of other administration-led science endeavors, such as the Human Genome Project and BRAIN initiatives, have expressed concern about the top-down nature and structure of those projects. In the MBI, however, University of California professor and microbiome expert Jonathan Eisen sees something different and more nuanced: a collection of distributed projects under a big umbrella rather than a run of the mill Big Science project dictated by central administrators. In a recent blog post, he called the project a good thing that’s “more likely to support small science and creative science.”

Last week evolutionary biologist Jonathan Eisen, PhD, UC-Davis, used a series of tweets to pounce on a University of Manchester promotional tweet relating to Alzheimer’s disease that he found “really disturbing.”

“There’s a feeling in the community that open access comes with no review, but that’s not true,” Jonathan Eisen, chair of PLOS Biology’s advisory board and an advocate for open-access publications, tells Wired. “I don’t think this will mean anything for open access journals, and it shouldn’t, because it happens at top journals too.” But because formal journals rarely address social-media criticisms, they are able to avoid the same negative spotlight, explains Dr. Eisen.“PLOS ONE should be handling this better to break the myth,” adds Eisen. “They’re one of the bigger open-access journals, so they need to be more careful.”

On the other hand, the old big-dog journals have their problems, too—plagiarism, errors, and so on. “I don’t think this will mean anything for open access journals, and it shouldn’t, because it happens at top journals, too,” says Jonathan Eisen, chair of PLoS Biology‘s advisory board and a big-time advocate for open-access (though unaffiliated with PLoS ONE). “Science took ages to address blog and social media criticisms of incorrect information because they only respond to formal criticisms. PLoS ONE is responding to social media, which most journals pretend doesn’t even exist.”

Eisen says that open-access journals have gotten so big, statistically it makes sense that on rare occasions they’ll have missteps. “There’s a feeling in the community that open access comes with no review, but that’s not true,” he says. “PLoS ONE should be handling this better to break the myth. They’re one of the bigger open-access journals, so they need to be more careful.”

Finally there was Jonathan Eisen, a microbiologist at the University of California, Davis who has become an outspoken critic on social media of the lack of diversity at scientific conferences. He said his awareness about barriers to women’s participation started when he saw a nanny watching a baby outside a scientific conference; she’d been hired so the infant’s mother could attend the conference.

“It was literally one of those light bulb epiphany moments where my privilege in my life came front and center to me, because it had never occurred to me to that this would be an issue for anybody,” Eisen said. “I changed on that day from being an oblivious, privileged person to being a little less oblivious, privileged person,” he said.

“These results come with some caveats. For instance, the researchers aren’t sure the DNA fragments are actually from bed bugs — they may may be detecting an entirely different, but related, species. It’s also possible that the DNA found in the subway stations isn’t from an insect at all, cautions Jonathan Eisen, an evolutionary biologist at the University of California–Davis, who wasn’t part of either research team. “I think it’s interesting if they really found bed bug sequences in their subway data. But I’m not even remotely convinced from what they report here that is the case.”

Policing the microbiome is central to Eisen’s identity”. Lovely Wired profile of Jonathan Eisen.


If and when they do, however, it would be wise – in this era of media microbiome hype – to keep the find- ings in perspective. The microbiome is only one facet of biology, says Eisen, who periodically doles out an “Overselling the Microbiome” anti- prize on his web site; so, too, are genes, environment, and frankly, luck. “We are an organism that is the sum total of all of these things,” he says. “The microbiome is just one layer.”

“If we can get a handle on rare biosphere, we might be able to say if there is or is there not any extinction,” says Jonathan Eisen, a microbiologist at University of California, Davis. But one challenge is that sequencing tools can’t determine whether the detected DNA came from a living or dead organism. And because microbes can multiply rapidly, their populations can change with the season or the weather. Just because something is rare now doesn’t mean it is rare at some other time, Eisen notes.

Inspiring scientists to launch studies to better understand such dynamics is just one of the goals of World Soil Day, which is helping cap a year-long research and outreach initiative known as the International Year of Soils. Eisen, for one, laments not being able to jump into a soil submarine to explore underground, the way marine biologists examine the deep sea. But he and other researchers say that, until someone invents such a craft, there are plenty of other ways we can better understand what’s going on beneath our feet, if we just take the time to look.”

“Still, Eisen and others caution against making too much of the results of the study, citing arguments often made in applying results from mouse studies to conditions in people. “The absolute key to me is the overselling of the relevance to autism,” he says. “This is not autism; it is some behaviors that resemble behaviors seen in human autism.”

“Vous n’invitez pas assez de femmes, ce sera sans moi. Des hommes qui boycottent les estrades 100% masculines, comme le microbiologiste Jonathan Eisen… cette position fait des émules. Dernier exemple en date : ce samedi 10 octobre, à Rouen.”

Jonathan Eisen, a professor at the Genome Center at the University of California-Davis, says he doesn’t think the science is quite there yet. “Yes, people may shed various pathogens that go into the sewer system,” he says, “but we still don’t know what to look for and how to detect these organisms at low levels.”

I think right now it is a research project,” says UC-Davis’ Jonathan Eisen. “A cool, fun project on microbial diversity and the human environment… without any obvious use yet.”

Though the data showed promise, Eisen says, there are still many unknowns and far too much complexity involved in trying to drill down into this kind of information to have a functioning surveillance system. And there are a series of other obstacles that still have to be considered.

“There are issues of privacy that they didn’t address at all or issues of false-positive correlations that you might detect,” he explains. “It is really cool to get data from global populations, and I think it is going to be really useful for some purposes. But I don’t see screening sewage systems in airport facilities as a proven avenue for doing that.”

Unfortunately for now, Eisen says, successful poop surveillance is just an exciting hypothetical.

“It is interesting—really interesting, actually,” he says. “But I think right now it is a research project. A cool, fun project on microbial diversity and the human environment that is unquestionably worth doing, but without any obvious use yet.”

As part of his TED talk, microbiologist Dr. Jonathan Eisen talks about how microbes play a role in our defense, boost our immune system, protect our auto-immune system, fight off stress, and more.”

“For instance, Jonathan Eisen, a professor of microbiology at the University of California at Davis, has tracked diversity in STEM fields for several years. His commentary on the issue includes a running list of conferences with poor gender ratios among speakers.”

Even some of the claims made by “germ experts” are bogus, says Jonathan Eisen, a professor of microbiology at the University of California, Davis. Scientists, he adds, often “oversell” their results by making misleading or unsupported claims.

Take a case-control studyfrom University of Cork in Ireland that found professional rugby players had a greater diversity in microbes compared to healthy controls. The study’s authors wrongly interpreted their results as evidence that exercise boosts diversity of gut bacteria. It was a mistake of mixing up correlation and causation, and the media followed suit, as Eisen wrote on his blog “The Tree of Life.”


Not surprisingly, many in the scientific community don’t agree with the authors’ conclusions. One criticism, voiced by the University of California, Davis’s Jonathan Eisen on his The Tree of Life blog, is that “career progression” topics—like salary and promotion—are lumped in with workplace topics—such as hostility and physical aggression against women—and yet, the authors only discuss data relevant to the career progression-related issues. Evidence suggesting relative equality in this area, then, seems to have led to the assumption that “other workplace issues must not be a problem,” Eisen wrote. “[That’s] a dangerous and unsupported connection.”

For more of this, see UC Davis Biologist Jonathan Eisen’s ongoing “Overselling the Microbiome” award series.

And so many in the world are worried about another virus. However, along with much of the medical literature on Ebola, as Jonathan Eisen recently wrote, so too is much of the literature on HIV, TB, and malaria still locked behind paywalls.

“In July, Jonathan Eisen—one of science’s most famous Twitter personalities and the author of the popular blog The Tree of Life—was lauded for turning down a paid honorarium at a conference because there were too few women invited to speak there. According to Eisen, there is no basis for an uneven ratio of male to female speakers in biology because there are enough women doing great work to be included equally alongside their male peers—in his letter to the conference host, he wrote, “As someone who is working actively on multiple issues relating to gender bias in science, I find this [gender ratio skew] very disappointing. … I simply cannot personally contribute to a series which has such an imbalance and I would suggest that you consider whether anything in your process is biased in some way.”

“The irrepressible microbiologist Jonathan Eisen says at his Tree of Life blog that he meant to write about this specious datum in 2007 but got distracted. He confesses that he even found himself quoting it in a TED talk, although he had sworn he wouldn’t.”

Jonathan Eisen, an American evolutionary biologist at the University of California, called the Royal Society “a club of mostly older white men that every year picks more similar members to join their club”.

“CHEERS to Jonathan Eisen, a professor of microbiology at UC Davis, who recently turned down an opportunity to be part of a lecture series at another university on principle — too few women were invited. “In my field, there just isn’t that big of a difference in the percentage of males and females at various academic levels,” Eisen said. “And so when there’s a skewed ratio, there’s a sign that something is amiss.” Eisen said the response to his decision, which also included turning down a $2,000 honorarium, has been “amazingly positive.” Add our voice to the chorus: Thanks, Professor, for not just talking the talk, but for walking the walk.”

“Given the virus’s abundance and how widespread it is, it is probably going to be very important for understanding the ecology of the human gut,” University of California, Davis, microbiologist Jonathan Eisen, who was not involved in the study, told NPR. “And it likely infects a group of organisms [the Bacteroides] thought to be really important for health.”

As microbiologist Jonathan Eisen wrote in his blog, “Vaginal birth and breastfeeding can be viewed largely as delivery mechanisms for microbes (and the food for the microbes).” Thanks, mom!”






2008 and before

Press Coverage for Project MERCCURI Space Microbes Project

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