Koalas, Chlamydia, Microbiomania, Katie Dahlhausen, John Oliver, Russell Crowe, and me.

I love Chlamydia.  Really I do.  It was in a paper analyzing two Chlamydial genomes that I first noticed a very strange pattern of genome evolution.



This in turn led to our discovery that large genome inversions in bacteria and archaea are most common when they are symmetric around the origin of replication.



This may be my favorite paper from my entire career and I owe it all to Chlamydia.

Plus, there are all sorts of jokes one can make with the Giant Microbe Chlamydias like

Ironic I know but putting Chlamydia near my special place makes it awkward to go #ucdmicroboome pic.twitter.com/DR8eEJdDOA

— Jonathan Eisen (@phylogenomics) October 27, 2017

and

It reminds me of when we all kept giving each other chlamydia with @phylogenomics 's 'Gut Check' game at #scifoo :D who doesn't love a free set of crabs lol! https://t.co/ltuxAbKFFC

— Carin Anne Bondar (@carinbondar) February 14, 2018

But that is not what I want to talk about here.  I want to talk about this fascinating project that Katie Dahlhausen in my lab has been working on for a few years. You see, she went to Australia and came up with a great idea for a thesis project after hearing a bit about Chlamdyia infections in koalas.  What she became interested in was trying to answer the following question: Does the antibiotic treatment used on koalas infected with Chlamydia have any negative consequences.  And in particular does it affect koalas ability to live on eucalyptus leaves since the general consensus was that microbes in the koala gut degraded toxic compounds from the leaves. So if these microbes were essential then treating with antibiotics might have some major negative side effects.

We did not have funds to work on this project, but she really wanted to work on it so she started an Indiegogo campaign to raise funds for some initial work. And she developed a collaboration with Adam Polkinghorne from Centre for Animal Health Innovation as well as some other folks and traveled to Australia to collect samples for some microbiome work.  And then she came back to UC Davis and spent some time getting microbiome data (in the form of 16S rRNA gene sequences) from koala poop and built environment samples and then she analyzed with some help from a few others and we wrote up a paper that was published last week.

Dahlhausen KE, Doroud L, Firl AJ, Polkinghorne A, Eisen JA. (2018) Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJ 6:e4452 https://doi.org/10.7717/peerj.4452

I think her paper is really nice.  And one part I liked is that she (and the rest of us on it) tried to be really cautious with our conclusions.  First, that was simply an observational study where she collected samples from koalas that were undergoing treatment regimes determined by others (e.g., veterinarians) and they were not conducting a study to test any specific hypotheses.  But Katie and others did make some interesting findings that are in the paper and as far as I thought, we very cautious in making any conclusions about what the fundings meant.  We just did not have enough samples or enough control to make any major conclusions about exactly what, if any, connection there was between chlamydia, antibiotics, microbiomes and koala health.

Here is the abstract

Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydiainfections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala’s health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities.

Basically the major conclusions reported in the abstract were

• No statistically significant differences between treated and untreated koalas were observed in alpha diversity of microbial communities 
• No statistically significant differences between different antibiotic treatments were observed in alpha diversity of microbial communities 
• Thee alpha diversity was statistically significantly higher for microbial communities from koalas that lived through antibiotic treatment versus those who did not 
• Community composition was different for koalas on antibiotics that died versus those that survived or never received antibiotics
• OTUs that are very closely related to Lonepinella koalarum correlated with a koala’s health status
• This last finding is of interest since this Lonepinella koalarum can degrade eucalyptus toxins in the lab and it has been proposed that it may be important for koala survival when eating eucalyptus

Basically that was it for the main findings.  Pretty simple and certainly worth pursuing in larger, better controlled experiments, but not solid proof of, well, anything about the connection between antibiotics, the microbiome, and health effects on koalas. 

Alas, despite our attempts to be careful, that was not how the world found out about our work.  I found out when Katie sent me a message on slack.

Can you check to see if you can read this link? I'm not sure if I can't read it because I'm out of the US or it truly is behind a paywall.   https://www.newscientist.com/article/2164459-medicine-for-sick-koalas-turns-out-to-actually-kill-them/ Either way, I'm a little ticked off. The tittle and opening sentences (all I could see of article) are extremely misleading. This is someone who wanted to write about my koala paper - didn't interview me, just contacted. I don't want my name behind bad science communication. Is it disrespectful to the reporter to vent about not being able to read an article I'm (potentially) mentioned in?

Eventually we got the text:

By Bob Roehr 

Curing chlamydia in koalas can be just as deadly as the disease itself, and now we know why. 

In humans, chlamydia is a common infection and can cause reproductive health issues. But for koalas it is more serious: the strain that infects them is often lethal. Koala chlamydia is transmitted during sex and, more commonly, through pap: a faecal product that females use to wean their joeys. A vaccine is in the works but it’s not ready yet. 

So for now the best option seems to be antibiotics to kill the infection. But koalas often suffer serious side effects from antibiotics, so Katherine Dahlhausen at the University of California Davis and her colleagues tried to find out why. 

They gathered faecal samples from sick koalas and scanned them to see what microorganisms were living in them. Like humans many other animals, koalas have “friendly bacteria” living in their guts that help them digest food. 

The team found that antibiotics had little effect on most of the friendly bacteria, but one species was often completely wiped out: Lonepinella koalarum. This species is crucial because it breaks down harmful chemicals called tannins, allowing the koalas to digest the tough eucalyptus leaves that make up almost all of their diet. 

Without L. koalarum to detox the tannin, the koalas seem to literally starve to death.
The research is preliminary, says Dahlhausen, so other gut bacteria may also be involved.
So far, no one has found an antibiotic that will both kill chlamydia and leave the friendly gut bacteria alone. It might be possible to feed koalas a probiotic diet to restore L. koalarum, but research on this is in its infancy 

For now, “faecal transplants may be the best method for offsetting the detrimental effects of antibiotics,” says Dahlhausen. 

The rise in chlamydia infections among koalas is partly down to stress caused by habitat loss, says Deborah Tabart, chief executive officer of the Australian Koala Foundation. 

“The solution is to reduce clearing of forests so that koalas do not get sick in the first instance.” 

Journal reference: PeerJ, DOI: 10.7717/peerj.4452 

And, well, it did not make me happy.  I kind of secretly wished nobody read the story and that it would just go away.  And then when I found out the story was picked up by IFLScience I was less happy.

So after festering for a while, Katie and I wrote an email to the reporter

Bob, 

Thank you again for your interest in writing about our team’s work on better understanding how antibiotics affect chlamydia-infected koalas. I am writing in regard to your recent article in New Scientist about this work. I am concerned because some of the wording in the article does not accurately reflect what we showed in our paper. We tried really hard to not overstate our findings in the paper and I believe that the way your article is written does not accurately reflect our findings. I would appreciate if the article could be changed such that it is less misleading for the audience. I offer comments on some sections of the article below: 

Re: ‘Curing chlamydia in koalas can be just as deadly as the disease itself, and now we know why.’ First of all, it has not been scientifically proven that curing chlamydia is deadly. Yes, there are reports that some koalas exhibit adverse side effects during antibiotic treatment, but it has not been shown that this is directly due to the antibiotics. We certainly did not show why Chlamydia cures might be deadly in our paper. Secondly, Chlamydia isn’t a lethal disease to koalas. It can kill koalas indirectly (e.g a lethal infection of an open wound caused by chronic incontinence because of Chlamydia infection; ramifications of vision loss caused by ocular Chlamydia infections).  

Re: ‘In humans, chlamydia is a common infection and can cause reproductive health issues. But for koalas it is more serious: the strain that infects them is often lethal. Koala chlamydia is transmitted during sex and, more commonly, through pap: a faecal product that females use to wean their joeys. A vaccine is in the works but it’s not ready yet.’ Again, Chlamydia is not directly lethal in koalas. It can cause urogenital issues and vision impairment; these aren’t lethal symptoms. Also, I think it is important to mention that the strain that infects humans is different from the ones that infect koalas. While it is true the Chlamydia can be sexually transmitted and spread during pap feeding in koalas, we don’t know statistics on disease transmission in koalas. It’s misleading to say Chlamydia is transmitted more commonly through pap because that hasn’t been shown.  

Re: ‘The team found that antibiotics had little effect on most of the friendly bacteria, but one species was often completely wiped out: Lonepinella koalarum.’ First, we did not show that antibiotics had “little effect on most of the friendly bacteria”. Instead what we showed was that broad diversity patterns did not show major differences in antibiotic treated vs untreated individuals. We do not even know how to ID friendly bacteria from others. Additionally, we did not show in any way that Lonepinella koalarum was “often completely wiped out” by antibiotic treatment.  Instead we found that koalas that died after antibiotics had lower relative levels of microbes related to Lonepinella koalarum.  

Re: ‘This species is crucial because it breaks down harmful chemicals called tannins, allowing the koalas to digest the tough eucalyptus leaves that make up almost all of their diet. Without L. koalarum to detox the tannin, the koalas seem to literally starve to death.’ We did not show that Lonepinella koalarum “is crucial” for survival of koalas. This is assumed likely to be true by some, but is has not been shown. It does degrade tannins in the lab, but we do not know how important it is to tannin degradation in the koala intestine. There could also be other tannin degrading microbes in the koala intestine that have yet to be characterized. Lastly, nobody has shown that the koalas starve to death after treatment nor that L. koalarum is involved in this. What is known is that joeys who don’t receive pap will not able to eat the adult koala diet of eucalyptus leaves (Caroline Monro is quoted in this article about this).  

Re: ‘It might be possible to feed koalas a probiotic diet to restore L. koalarum, but research on this is in its infancy.’ I do not know of this research, and in the context of the article it sounds as if that is work we are doing in the lab. It would be helpful to mention who is doing this work. 

I would really appreciate if you could update the article to more accurately represent the work we did for this project. I am happy to assist in the revision of this article.

Sincerely, 

Katie

And, well, it took a while.  But we just got back their response and they agreed to change many of the things we suggested should be changed.

Dear Katherine Dalhausen –  

Thank you for your communication about the koala story, which has been passed to me, and which I have finally digested. Numbering the points you raise: 

1)  We do say that “curing chlamydia in koalas can be just as deadly…” and, in the context of a popular weekly news magazine rather than a professional journal we believe this is reasonable and accurate.  

2)  Similarly, when we say that it is “often lethal”, in context this includes indirect lethality. (One might argue that cholera is largely indirectly lethal in humans, the dehydration and electrolyte disturbance being the thing: but for an audience that includes astronomers and accountants it’s certainly “often lethal”.) 

3)  We have corrected the online article to say only that chlamydia is transmitted through sex and by pap.  

4)   We have corrected the online article to say that antibiotics made little difference in overall diversity of gut bacteria, accepting what you say about being unable to enumerate “friendly” bacteria. 

5)   We have corrected the online article to say that “This species appears to be crucial” since that is the inference almost anyone would currently draw, but recognising that it is not a finding of yours.  

6)   We have corrected the online article to note that the work mentioned on probiotics is by others, since you request that we dissociate you from that.  

A printed correction notice is in press for the edition dated 26 May. 

I apologise for the time it has taken me to deal with this.  

Mike Holderness                

Readers’ editor

So - yay.  

As an aside - although I guess a big aside, we also worked with the UC Davis Press office to put out a press release where we tried to make sure the wording was really really careful about what was done. See "Treating Koalas for Chlamydia Alters Gut Microbes" by Andy Fell.  The text reads:

Koalas are one of Australia’s iconic animals, but they have been hard hit by an epidemic of Chlamydia infections contributing to a steep decline in numbers. Sick koalas brought to wildlife hospitals may be treated with antibiotics to clear up the chlamydia, but the antibiotics themselves can have severe side effects in the animals. 

KoalaKoalas feed almost exclusively on eucalyptus leaves. They depend on gut bacteria to make the leaves digestible. (Photo via Tourism Australia) 

A new study led by Katherine Dahlhausen, a graduate student at the UC Davis Genome Center, published in the journal PeerJ, shows that those antibiotics may be changing the balance of gut microbes thought to allow koalas to digest eucalyptus leaves.
Koalas rely on specialized gut microbes to break down tannins and other toxic compounds that would otherwise make eucalyptus leaves indigestible. Infant koalas pick up these microbes from their mothers by eating a specialized type of feces called “pap.”
Dahlhausen and colleagues studied the diversity of microbes in koalas treated or not treated with antibiotics at the Australia Zoo Wildlife Hospital, Queensland and the Port Macquarie Koala Hospital, New South Wales. They did not find a difference in gut microbes between treated and untreated animals, but did find that koalas that were treated with antibiotics and survived had a more diverse microbe population than animals that died during treatment. 

Health status was closely correlated with presence of bacteria related to Lonepinella koalarum, a microbe known to digest tannins. 

There have been other studies showing that antibiotic treatment can disturb gut microbes in other species, Dahlhausen and colleagues noted in the paper. But this might be especially important in animals like koalas where gut microbes are essential to their survival. 

The project highlights the possible need to restore a healthy balance of microbes in antibiotic treated koalas and for development of antibiotic-free treatments of koala chlamydia infections, such as as a koala chlamydia vaccine, under development  by Peter Timms’ lab at the University of the Sunshine Coast, Dahlhausen said. 

Other authors on the paper are Alana Firl and Jonathan Eisen at the UC Davis Genome Center, Ladan Daroud at the UC Davis Department of Computer Science, and Adam Polkinghorne at the University of the Sunshine Coast, Queensland, Australia. 

The work was funded by the Alfred P. Sloan Foundation as part of their “Microbiology of the Built Environment” program as well as by an Indiegogo crowdfunding campaign.

And amazingly this PR and Katie's paper became part of a fight of some kind between John Oliver and Russell Crowe: Everything You (and John Oliver) Need to Know About Koala Chlamydia. See this section where the author links to the PR

Antibiotics are also used to treat koalas, although they do not prevent re-infection and come with a host of unpleasant side effects. Research has shown that the treatment messes with the gut microbes that help them digest their leafy diet — meaning they can starve.

And they all seem to get the science better than the New Scientist -- which is good.

No Microbiome Santa Claus we cannot magically convert correlative studies into causal ones. And scientists dishing out medical advice about vaping based on such bad science is ridiculous.

Aaarrrrrrrg.  That is how I feel right now.

Many microbiome studies involve examining the microbiome in various samples and asking and answering "Are there differences in the microbiome between my sample types?".  This is a standard correlative analysis used in all sorts of areas of science. and it can be quite useful in many cases.

However, in most cases it is not OK to take information from a correlative study and infer that the microbiome was "changed" due to some factor that differed between the samples.  Generally this would only be possible to do in some sort of controlled experimental manipulation experiment.  But so so so many people make such inferences and I am going to highlight an example that relates to a new study of vaping and the microbiome.

There is a new paper on this topic and an associated press release:

• Press Release: Vapers and non-smokers have the same flourishing gut flora | EurekAlert! Science News
• Paper: Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study

Basically the researchers compared microbiomes in three groups of people who had different behaviors (some non smokers, some smokers, some papers vapers).  Note - they did not study people before and after vaping or smoking.  They compared different people who differed in these behaviors but also differ in 100s to 1000s of other things like diet, gender, age, activity, housing, childhood, and more.

And when they did comparisons in relation to the main variables of non smoker, smoker, vaper, they found some differences in microbiomes and some similarities.  Small study.  But potentially interesting.

However, the PR significantly misrepresents what they did and found. Here are some examples of wording I have a problem with:

Press Release:

• "Vapers and non-smokers have the same flourishing gut flora."
• OK this has nothing to do with the point of my post but they do not in any way show "flourishing" flora.
• "whilst smokers have significant changes to their microbiome".  
• No.  They show differences.  Not changes
• Significant changes were found in the gut bacteria of the smokers, with an increase in the Prevotella bacteria which is linked to an increased risk of colon cancer and colitis.
• Again.  No.  They show differences.  They do not know if they are changes since they do not know what these people had before smoking. And thus they cannot show "increases" either.
• There was also a decrease in the presence of Bacteroides in smokers, a beneficial bacteria or probiotic.
• No - no decrease shown.  And for that matter - not all Bacteroides are beneficial or probiotic. 
• More investigation is needed but to find that vaping is less-damaging than smoking on our gut bacteria adds to the incentive to change to e-cigarettes and for people to use them as a tool to quit smoking completely.
• Jesus #(@(@.  No.  They did not show this. 
• This revealed significant changes in the gut bacteria of the faecal samples.
• Again, no. 

This is one of the more problematic press releases I have seen in a while.  Really disappointing.  However, much more surprising is that many of these word choice and inference issues are also in the paper.  Here are some examples of problems with the wording in the paper (not all cases - just examples).

• Title: Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study
• No - they do not study effects of smoke or vapor at all. They study differences in people who do these activities.
• Abstract: In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls.
• No.  They are not able to determine if these "alter" anything. 
• Abstract: Tobacco smoking had a significant effect on the bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. 
• Noooooooo.  They did not show this.  
• Abstract: The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls
• No. They showed it was lower.  Not reduced.  To use "reduced" requires that they know what it was before.  But they do not.
• Abstract: From a microbial ecology perspective, the current pilot data demonstrate that the use of ECs may represent a safer alternative compared to tobacco smoking
• Oh Jesus ($(## again.  No they do not have any data that supports this claim. 
• Results: The Shannon diversity was significantly reduced in fecal samples collected from tobacco smokers compared to controls (P = 0.009), but the number of observed OTUs was comparable between all groups (Fig. 1A).
• No. They showed it was lower.  Not reduced.  To use "reduced" requires that they know what it was before.  But they do not.
• Results: showed tobacco smokers had significantly altered fecal bacterial profiles
• Again.  Different.  Not altered.
• Results: Prevotella had significantly increased relative abundance.
• No
• Results: Whereas Bacteroides showed significantly decreased relative abundance 
• No
• Discussion. We report, for the first time, that regular use of ECs does not measurably influence oral or gut bacterial communities
• No they do not show this.  They show that people who use ECs do not have significant differences from those that do not. 
• Discussion: Only the fecal microbiota was found to have specific genera significantly altered by exposure, with increased relative abundance of Prevotella, in accordance with existing data 
• Again. No.  They do not show ANY alteration by exposure.  Just correlations. 
• Discussion: Conversely, smoking tobacco cigarettes significantly decreased the relative abundance of Bacteroides compared to EC users and controls
• Nope. 
• Conclusions. In summary, we found that tobacco smoking significantly alters the bacterial profiles in feces, buccal, and saliva samples.
• Nooooooooooooooooo. Nooooooo. No.

So - you might ask -- why does this matter?  This is just a little bit of a word choice issue right?  Wrong. The press release and the paper mislead as to what was found here.  

You might then say "so what - what does it matter?".  Well, it does matter because when you make these types of misleading statements they might get picked up by the press or the public.  Like in the examples below:

Daily Mail: An incentive to switch to e-cigarettes? Smokers have more 'bad' and less 'good' bacteria than vapers putting them at greater risk of disease, finds study

Let's check out those bullet points:

• This puts them at higher risk of colon cancer, colitis, Crohn's disease and obesity
• E-cig users have similar microbiomes to those without the notoriously bad habit
• Scientists today labelled the study an 'incentive' for smokers to switch to vaping
• This is the first study to compare the microbiome between vapers and smokers

Wow.  This study provides incentive for people to switch from smoking to vaping.  Sorry - but the F@#$*)@#) it does.  Ridiculous.

And it shows that this puts people who smoke at higher risk of colon cancer, colitis, Crohn's and obesity.  The #(!@)($!@)( it does.

Just wait.  I am sure more news stories will come out with inaccurate information.  Sometimes that is the fault of reporters.  But in many cases, such as this one, the fault lies COMPLETELY with the scientists who use misleading statements in the papers and in the press releases.  Really sad and shameful.

UPDATE 5/1

And look.  What a surprise.  The pro- vaping community has picked up the bogus claims and is using them to say vaping is not bad for you.



UPDATE 2 - Another story saying vaping is not bad for your microbiome



UPDATE 3- - even more stuff on vaping and now it is not just not bad for you - it is good for you

Excellent podcast on #microbiomania - aka microbiome hype from Health News Review

Really well done Podcast on Microbiome Hype from Health News Review



Podcast: Gut Punch - Marketing Microbiome Hype - HealthNewsReview.org








Definitely worth a listen.

Retraction of paper on "Gut Makeover Diet" and the microbiome retracted for fundamental flaws including that it did not in any way look at the microbiome #overselling #hype #microbiomania

Made a Twitter moment that people may be interested in about a Buzzfeed article by Stephanie Lee on retraction of a deeply flawed paper supposedly connecting the Gut Makeover Diet to the microbiome and to beneficial health effects.

 See below

  "Gut Makeover" paper retracted for fundamental flaws #microbiome

Science Magazine publishes "opinion" piece targeting a specific student w/ sexist "critique" and then won't publicly discuss what happened or what they will do about it

Well, I can't even begin to explain how disappointed I am in AAAS and Science Magazine over their actions recently. An "opinion" article was published last week in the "Working Life" section of Science which was stunningly inappropriate for Science Magazine. I first found out about this when I saw a Tweet from a colleague and friend Rebecca Calisi Rodriguez.

I recently had a great experience publishing in @sciencemagazine's Working Life section on supporting mothers-in-science. Angry to see this now published- a personal, sexist attack on one woman (who is actually AWESOME at #Scicomm). A step back for #WomenInSTEM. Good thread here: https://t.co/KdVSqll3Rg

— Rebecca Calisi Rodriguez (@BeccaCalisi) March 15, 2018

And when I started to dig into the story I was nauseated.

 To sum up - the article was by a student who was apparently trying to express some thoughts about #SciComm activities by others that she did not like. And in the piece she named and mocked the activities of another PhD student at her own institution who does SciComm in ways she does not feel comfortable with. Fortunately, when I started looking at social media responses to this, they were overwhelmingly in support of this targeted student - Samantha Yammine who does really quite phenomenal SciComm work. (See for example her Twitter feed and her Instagram feed.

 I am really thrilled and proud of the community that came out in support of her.

There have also been a few news stories related to or directly about the topic which are worth reading.

• For example T. Ryan Gregory pointed me to this one Meet the PhD student who makes science accessible through social media 

• There is also this excellent piece in The Verge by Angela Chen "Scolding female scientists for embracing Instagram doesn’t solve the gender gap in STEM"

Also some of the Tweet streams about this are really worth reading. For example, this one from @christineliuart is a must read:

NEWS FLASH: my self-expression does not exist for you. Do not police the way I choose to interact with others and share my existence because it makes you bitter. You do you, but don't write an op-ed about why you dont want me doing me.
https://t.co/kAMulZJ6vV

— christine liu ✨ two photon art (@christineliuart) March 15, 2018

YAMMMM: Yet another mostly male microbiome meeting - Microbiome Therapeutics Europe Meeting

YAMMMM: Yet Another Mostly Male Microbiome Meeting:

Microbiome Therapeutics Europe Meeting

From their speakers page I estimated gender balance of speakers 

19:6 M:F 
or 75% male

YAMMMM - Yet another mostly male microbiome meeting - 2018 Translational Microbiome Conference

Uggh.

Here is a sad sad example of a YAMMMM - yet another mostly male microbiome meeting (a phrase first coined by Carly Rosewarne).

The 2018 Translational Microbiome Meeting.
https://www.microbiomeconference.com

From my estimates there are 47 speakers of which 41 are male (note - these are inferences of gender and may be inaccurate).  That comes out to an estimate of 87% male speakers.  That is just not good.  The microbiome field has a good sample pool of people of diverse backgrounds that could be speakers at meetings and thus meetings that are this skewed in diversity should not be supported.

  

-------------------
UPDATE 3/20/2018

The organizer of the meeting Mollie Roth has written to me to object to my post. She says she tried to have a more diverse collection of speakers. She says she invited many other women to speak, some who did not answer, and some who could not come, and some women who could not come sent men to replace them.

She wrote (I have removed names here)

• XXX from YYY was committed to speak and had to drop out due to work commitments, 

• that XXX of YYY was invited to speak and declined, 

• that XXX of YYY was invited to speak and choose to send a man instead, 

• that XXX committed to speak and had to drop out due to other commitments and is sending a man instead

• that XXX of YYY was invited and never responded

• that XXX andXXX of YYY were invited and never responded

That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats?

I responded that I did not feel this was in any way sufficient but she disagrees.  I pointed her to some suggestions for how to run a more diverse meeting that do not simply involve inviting more women to speak.

She also noted that she offended by my post and that I did not continue a private conversation we had on Linked In regarding this meeting.  I note I did not continue the private conversation, and chose to post this post, because her response to my private critique made it seem that she was not interested in having a private conversation about the meeting.

-----------------------------
UPDATE 2.  3/20/2018 3 PM PST.

The organizer of the meeting Mollie Roth apparently thinks that I have deleted her "comment" on this blog.  I have not done that.  The 1st comment made to this blog is the one where she is accusing me of deleting a comment.  I note - blog comments are open for anyone to post here for 2 weeks and then comments get moderated.  I checked the Blogger SPAM comment filter but there is nothing there.  So I can only conclude she did not make a comment.  I emailed her to try to find out what she meant but she did not answer directly.  I think what she may have meant is that she wanted me to post the full email of her communication with me to the blog but I am honestly not sure. I am pondering posting all my communications with her but am not sure if that is a good idea at this point.

So for now I am posting the entirety of her first message to me which I had edited a bit above.  I am still editing out identifying features of others however. See below.

Professor Eisen

XXX was kind enough to forward your email to me encouraging him not to participate in the Arrowhead conference. 

Really? Rather than engaging in a conversation with me on LinkedIn and learning more about this year’s gender imbalance, you are posting about it on your blog and reaching out to speakers encouraging them to drop out. 

Would you care to take a moment to learn that -

• XXX from YYY was committed to speak and had to drop out due to work commitments, 

• that XXX of YYY was invited to speak and declined, 

• that XXX of YYY was invited to speak and choose to send a man instead, 

• that XXX committed to speak and had to drop out due to other commitments and is sending a man instead

• that XXX of YYY was invited and never responded

• that XXX andXXX of YYY were invited and never responded

That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats?

I will ask, although I am sure you will neither respond nor do the right thing, that you primarily stop contacting speakers to ask them not to participate. But secondarily you should really if not retract your offensive post add some of this information to inform it and perhaps encourage the women to own some of this issue themselves this year.

I am sure you will do neither, unfortunately. I will be sure we do address this issue in our conference blog and in our social media channels.
----------------------------

UPDATE 3 3/20 11 PM PST

I guess my inclusion of this additional information was not enough for the organizer Mollie Roth.  She seemed to imply that I was hiding her explanations from the public.  So ... I am going to post them all here.

This all started with a Linked in message from her to me on March 5 telling me about this meeting.
I wrote back a few days later - obviously not enthusiastic about this meeting



She then wrote back, clearly not impressed with me.  I am not sure if she would be OK with me posting all of the comments she made in that thread so I am just posting the most relevant one here which is how she ended the discussion.

 

Sounded to me like she did not want anything to do with me ever again.  I pondered what to do for a while.  Was writing back a good or a bad thing?  I did not know.  But I decided to try. I wrote a response and tried to send it but the message would not go through.  I assumed she blocked me or disconnected / delinked me (I don't know what that is called on Linkedin).  I thought about emailing her back but the last message from her implied to me that she wanted nothing more to do with me.

So a few days later I wrote a blog post about YAMMMMs in relation to this meeting.  And then I wrote this blog post here.  And then I engages in some discussion about the post on Twitter and asked some of the speakers to not speak at the meeting.  I emailed one that I knew well and he forwarded the email to Mollie. She then sent me an email. I have deleted names and other identifying features of other people from this and other messages.

------------------------------

Professor Eisen 

XXX was kind enough to forward your email to me encouraging him not to participate in the Arrowhead conference. 

Really? Rather than engaging in a conversation with me on LinkedIn and learning more about this year’s gender imbalance, you are posting about it on your blog and reaching out to speakers encouraging them to drop out.  

Would you care to take a moment to learn that -
XXX from YYY was committed to speak and had to drop out due to work commitments,   

that XXX of YYY  was invited to speak and declined, 

that XXX of YYY was invited to speak and choose to send a man instead, 

that XXX committed to speak and had to drop out due to other commitments and is sending a man instea

that XXX of YYY was invited and never responded that XXX and XXX of YYY were invited and never responded 

That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats? 

I will ask, although I am sure you will neither respond nor do the right thing, that you primarily stop contacting speakers to ask them not to participate. But secondarily you should really if not retract your offensive post add some of this information to inform it and perhaps encourage the women to own some of this issue themselves this year 

I am sure you will do neither, unfortunately. I will be sure we do address this issue in our conference blog and in our social media channels. 

Mollie
Mollie Roth, J.D.Managing PartnerPGx Consulting

-----------------------

I wrote back

Mollie 

In our conversation on Linked In you basically told me you were not interested in discussing the issue. Your last message was "I am sorry I reached out to you and will not make the mistake of doing so again. Good day." 

Regardless, I tried to write back but was unable to respond to you via the messaging system.  I assumed that was because you blocked me in some way.  

Given that you did not seem to want to discuss it further in private, I decided to take it public.  I would be more than happy to add whatever response you want to my blog post or you can post there. I stand by my critique of your meeting.  It is not enough to just invite a few women to speak in my opinion and there is much literature on this out there if you are interested.  In order to achieve a diverse meeting one must work a bit more on it.  If you are interested in suggestions for how to do this, please see this part of my blog.
https://phylogenomics.blogspot.com/p/posts-on-women-in-science.html 

Jonathan

-----------------------

She then wrote back

Jonathan  

I neither blocked you nor impeded your communication in any way on LinkedIn or anywhere else. I have my doubts that you are so easily put off, I think you prefer the hype and hyperbole of being the individual who “outs” the bad actors, regardless of whether they are or they are not. 

I take offense at your characterization that I did no more than invite a few women, I do substantial research and go well beyond a bald faced email with no followup. I know many of these women personally from interactions over the years from prior conferences - where we have agreed women were well represented - but saying my conference fails on this front from a single year is a slant helpful only to you. 

I will be more than happy to have you demonstrate your acuity with gathering these women and getting them to the table next year. Writing about these issues from an academic perspective is one thing, actually driving engagement is quite another.  

In fact I will be more than happy to make a space for you on the podium this year if you would like to come speak about these issues and commit to lending your knowledgeable hand as a consultant next year to demonstrate how these “suggestions” work in practice. What say you Professor Eisen, willing to put your academic suggestions to the test in the real world? 

So I responded

Mollie 

In your 1st communication with me in September of 2015, you wrote 

"Let me start by applauding you for the commentary in your blog post on overselling the microbiome about the gender imbalance in Dr. Roizen’s conference. " 

So back then you supported a public critique of a meeting in relation to its gender balance of speakers.  This is why I wrote back to you privately on Linked In in such a shocked state regarding your current meeting. 

So -what has changed since then?  Your meeting has an unbalanced gender for speakers.  And I bogged about it.  Just like I did previously and which you applauded me for. 

Again, I stand by my critique of your meeting.  And no, I am definitely not interested in attending it in any way or for any purpose.  And I will continue to recommend other people not attend it or speak at it as it now stands.  If you run a meeting with a better gender balance I would be more than happy to participate in some way in a discussion of gender issues in STEM.

She wrote back

It is not until one is unfairly targeted that one understands how skewed people pointing these types of things out are. Knowing what I know now about your skewed attacks, I was perhaps unfair in assuming others were acting in bad faith. I d not believe you are acting in good faith, nor do I believe you will do so. I think you like the fight, I think you like the hyperbole and I think you like pointing fingers with no intention of trying to understand the other side. 

I wrote back

Ok. 

Believe what you want. 

I still welcome any comments you would like to make on my blog and whether you believe it or not I truly believed you did not want to hear a anything more from me in private.  I certainly could have made more of an effort to figure that out.  But your response led me to believe that that path was closed.

Molly wrote

If you were sincere Professor Eisen you would amend or include further information you have been provided on your blog post yourself. Of course I am going to contradict what you said or have a different perspective but it really only has substantial meaning if you are willing to say “ok hang on, here are some things I did not know” and further inform the conversation yourself. 

I will get in touch with our speakers and let them know the nature of your communications and how you have refused to take the information you have been provided and adjust your outrage. 

So I decided to do what she asked.  It seemed only fair.  And I updated my post with a summary of her comments.  I did not say I agreed with her but I did try to provide her perspective.

I thought I was doing what she asked.  To give her side of the story.  I did not think I was obliged to agree with her but she then wrote back something which I just do not understand.

I just went to remove my response to your post realizing the fact that you are not really interested din the reality of these situations to find you had removed it and, no surprise, recharacterized it all in your own words. That’s not open discourse Professor Eisen now is it, more evidence that you simply like being the finger pointer and are not actually interested in honest and open engagement. 

This was so strange because she never posted a comment to my blog.  I went and checked SPAM and comments awaiting moderation and -- nothing.  I was very very confused.  So I wrote back

Mollie 

I have no idea what you are talking about here. 

When did you write a response and post it to my blog?  Did you submit a comment? I have no record of that. How could you then remove it?  How could I then remove it?  You have not as far as I know posted any comment anywhere. I have certainly not removed a single thing you posted to my blog nor would I. 

She then wrote

Oh my goodness. You literally wrote on your blog that the organizer responded on your blog and then recharacterized what I said and you are now playing DUMB?

So so weird.  I did not delete any comment.  She never made any comment.  And now her explanation what that she was claiming I had written that she made a comment.  But I did not write that.  My guess is she either (1) thought that her email to me was automatically posted to my blog (seems unlikely that she thought that) or (2) that I had posted her comments to my blog directly and then deleted them.  Seemed like 2 was the only plausible option But since she had already told me she did not want me to post her comments directly to my blog this seemed weird. So I wrote back again.  

No Mollie 

I wrote "The organizer of the meeting Mollie Roth has written to me to object to my post"
I did not say you wrote on my blog. 

And when I asked you in email if I should post your comments to my blog directly you wrote 

"If you were sincere Professor Eisen you would amend or include further information you have been provided on your blog post yourself. Of course I am going to contradict what you said or have a different perspective but it really only has substantial meaning if you are willing to say “ok hang on, here are some things I did not know” and further inform the conversation yourself. " 

Clearly saying you did not want me to just post what you wrote.

I did not hear back immediately so I wrote a follow up:

Here is a proposal.  I will post the entire contents of these emails to my blog in the interest of transparency.  Are you OK with that?

And she wrote back:

It is your blog Professor, you are free to do with it anything you wish, clearly

So here we are.  I still do not know what she meant by me deleting her comments from my blog, which I did not do.  But in the interest of transparency I am posting all of our emails here.

--------------------------

UPDATE 4. 3/21/18

Mollie Roth, the organizer of the meeting sent an email to all the speakers of the meeting and cc'd me.  In the interest of transparency, especially since she accused me of deleting comments that she never posted here, I feel comfortable posting her email here.

Dear Speakers  

It has come to our attention that you may have received a message from a Professor Jonathan Eisen at UC Davis encouraging you to boycott the Arrowhead conference next month because of the lack of gender diversity on the speaking faculty. 

Unfortunately Professor Eisen is absolutely correct, the speaking faculty is predominantly male this year. Highlighting the role of women in this industry has been a top priority since I started this conference four years ago and prior years were much more gender balanced. Professor Eisen is well aware of this from our prior discussions on the issue. His dissatisfaction this year is equal to mine - in spite off having identified and invited numerous women to speak, they did not respond to my invitation or accepted and subsequently had to withdraw or in two cases decided to send men in their places.
Several of you have been in touch asking what WE are going to do to address this issue. I will turn that question around as gender diversity in the sciences is all of our responsibility - what are YOU going to do to address this?  

I encourage all of you to identify a women in your organization and send her to speak in your place if this issue is of concern to you. There is only so much I can do as an outsider to drive this issue, it requires everyone working together. 

If this is possible, please let us know as soon as possible and we will switch out her name and bio for yours on the online agenda and before it goes to press for printing. It would be my great pleasure to highlight this happening next month. 

And I will extend the same invitation to Professor Eisen who is copied here that I did privately, please consider lending your substantial knowledge and expertise on this issue to making this gender diversity happen not simply in your academic writing but in the real world. I welcome your time and assistance in pulling together the faculty for the conference next year. The experience will no doubt further inform your understanding of just how difficult this task is to accomplish in the real world. 

If you have any questions or continuing concerns, please do not hesitate to be in touch. 

Best regards
Mollie
Mollie Roth, J.D.
Managing Partner
PGx Consulting
Founder and Chair
Arrowhead Translational Microbiome Conference
www.microbiomeconference.com

I wrote back

Mollie (cc'ing speakers) 

Thank you very much for working to improve the diversity of speakers at this meeting. I think asking for help in identifying and selecting speakers that represent a broader sample of diversity is a great idea. In addition, I would be more than happy to help you organize a conference next year.   

Contrary to your comments, I have extensive experience planning and running conferences in various STEM area including the microbiome space.  And though it can be difficult to achieve, for these we have had excellent diversity of speakers.  You can see a partial list here.  

For each of the meetings I have organized in the last 5 or so years (I became interested to speaker diversity about 10 years ago but have been more committed to it in the last 5) we have been able to achieve a strong representation of diversity among the speakers.  This is however not easy in every case and takes a strong commitment to diversity and sometimes significant amounts of work. 

I would suggest that for your future meetings you do some of the things recommended in the articles I list at the bottom of my web page on Diversity at Conferences. One example article worth looking as is this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238945/.
Some examples of things that can improve the diversity of speakers include 

1. Develop a diversity policy and publicly post it stating your commitment to diversity for speakers. I would be happy to help you develop one.  Many people basically copy a template that has come up from the technology world. I note this should not just be about gender diversity but about diversity broadly (i.e., racial, ethnic, gender, career stage, background, country, type of institution, etc). An example is https://us.pycon.org/2017/about/diversity/
2. When people turn down invitations, ask them why and whether you could do anything to make it more likely the next time for them to accept.  It may be that some simple changes might make it more likely for people to accept.
3. Broaden the invitation pool by expanding topics or types of people you invite.  This could, for example, include having a student or post doc presentation in each session, or including sessions focused on related topics such as press coverage of the field, or such.
4. Ask people in the field for help in identifying speakers.  Ideally this would happen at the planning stage but could happen any time.
5. Record and share data about speaker diversity.
6. Make use of and contribute to diversity related lists for speakers.  For example Elisabeth Bik, now at uBiome maintains a great website and list of women in microbiome and related fields who could be invited speakers. See https://microbiomedigest.com/sample-page/women-in-microbiology-for-keynote-lectures/ . There are many other such lists around and they can be very useful. 

I would be happy to work with you on crafting a speaker diversity statement for your future meeting(s) and work with you on planning a meeting. 

Again, thank you for working to improve the diversity of this meeting.

Jonathan Eisen