Friday, May 18, 2018

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.

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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.

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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

and




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.






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