Category Archives: microbiome

07Oct / 2019

Yet another mostly male microbiome meeting – #YAMMMM – a microbiome #manel in San Diego





Well, just when I thought the microbiome space was getting better about diversity of speakers.  I got called twice today from someone trying to get me to sign up for this meeting and I got an email about it too.

The meeting: "Gen-Next Probiotics and Microbiome - Advanced Therapeutics and Sequencing Congress” to be held on 6th and 7th February 2020 in San Diego, USA."

Speakers from the email:
• Maya Ivanjesku, Chief Scientific Officer, Dakota Biotech
• Bharath Prithiviraj, Senior Scientist, City university of New York
• Ross Youngs, CEO & Founder, Biosortia Pharmaceuticals
• Seth Crosby, Director, Research Collaborations, Washington University School of Medicine
• Elliot Friedman, Senior Research Investigator, University of Pennsylvania
• Peter Leighton, CEO, ProSperity Bioscience
• Tal Korem, Assistant Professor, Columbia University in New York City
• Chuck Collins, Professor, East Tennessee State University
• Joseph C Ellis, Sr. Staff Scientist, OAK Ridge National Laboratory
• Aubrey Levitt, CEO/Co-Founder, Postbiotics +
• M. Andrea Azcarate-Peril, Director, Microbiome Core Facility, University of North Carolina
• Arun Bhunia, Professor of Food Microbiology, Purdue University
• A. Bruce Johnson, PhD, Corporate Vice President, Business Development, Phibro Animal Health Corporation
• Michael Leonidas Chikindas, Microbiologist, Rutgers University

I looked up these people and their descriptions on various websites and with this information and other I assigned them to M vs F.  I realize this approach is imperfect.  I label my inferences below: M in yellow and F in green.

• Maya Ivanjesku, Chief Scientific Officer, Dakota Biotech
• Bharath Prithiviraj, Senior Scientist, City university of New York
• Ross Youngs, CEO & Founder, Biosortia Pharmaceuticals
• Seth Crosby, Director, Research Collaborations, Washington University School of Medicine
• Elliot Friedman, Senior Research Investigator, University of Pennsylvania
• Peter Leighton, CEO, ProSperity Bioscience
• Tal Korem, Assistant Professor, Columbia University in New York City
• Chuck Collins, Professor, East Tennessee State University
• Joseph C Ellis, Sr. Staff Scientist, OAK Ridge National Laboratory
• Aubrey Levitt, CEO/Co-Founder, Postbiotics +
• M. Andrea Azcarate-Peril, Director, Microbiome Core Facility, University of North Carolina
• Arun Bhunia, Professor of Food Microbiology, Purdue University
• A. Bruce Johnson, PhD, Corporate Vice President, Business Development, Phibro Animal Health Corporation
• Michael Leonidas Chikindas, Microbiologist, Rutgers University

So that comes to 11M vs 3F.

Or ~ 80% M.

No thanks.  I will skip this YAMMMM.  And you should too. 



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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in manel, microbiome, YAMMM, YAMMMM

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17Sep / 2019

Viome – trying to prove that my calling them "The Theranos of Microbiome Companies" was an understatement …

A month or so I wrote the post below that I thought was an example of really bad misleading advertising.  And it is indeed.  But keep reading past the discussion of this ad, because today I got a much worse example.

Post I drafted a month ago but did not actually make public:

Uggh.  This is just such BS.  I saw a Viome ad on Facebook.

 

Here is the text:
DNA tests can tell you a lot about where you came from.
Your past. Your family history, and your ancestry.
But that doesn’t help you right now.
That doesn’t help you today.
DNA tests also told her what foods were best for, but the recommendations never changed, even as symptoms got worse.
Just like you, Kelly wanted to know how to make the most of her health.
DNA tests told Kelly what diseases she was more at risk for genetically,
but they don’t give her any actionable advice on how to lower that risk.
Frustrated with generic guidelines like “exercise more and eat healthy,” Kelly finally found Viome, and it made all the difference.
That’s because Viome didn’t test her DNA. Viome tested the RNA of the microbes that make up Kelly’s gut microbiome to tell her what her microbes were up to and how they were affecting her.
The same microbes that are responsible for making most of the neurotransmitters, nutrients, and other compounds her body needs to be healthy.
Just like Kelly’s microbes eat what Kelly eats, your microbes eat what you eat, and if they don’t get the right foods at the right time, they begin making compounds that contribute to chronic inflammation.
That means:
Poor sleep,
Bloating,
Weight gain (the bad kind),
And a significantly increased risk for all kinds of chronic diseases.
Once Kelly got her Viome results, she knew which foods she needed in her unique personalized diet to boost the good guys (and which foods to avoid!) to take action to improve her health.
You can do the same thing as Kelly using the Viome Gut Intelligence Test.
End the guesswork and take charge of your health.
Order your Viome Gut Intelligence Test today.

And the key part that is completely bogus -
Once Kelly got her Viome results, she knew which foods she needed in her unique personalized diet to boost the good guys (and which foods to avoid!) to take action to improve her health.
There is simply no evidence that Viome can use microbiome analysis to tell anyone (Kelly or others) which foods you need and which to avoid to boost one's microbiome.

And I did not make the post public because, well, I was busy and really did not fell like picking yet another fight with what I consider to be the scam artists at Viome.  And then I saw another ad a few minutes ago that is even more egregious, also from Viome.

This one comes with some text and then a scrollable series of images.  And the sum total of it is just some absurd snake oil



Here are the scrollable images from the ad



And here is the text if you want to dig into it without looking at my screen captures.

Hate wrinkles?
Maybe it’s the rows of creams, gels, lotions, vitamins and mysterious liquids with ingredient names you can’t pronounce listed in fine print on the back, that you pay for every month, that you really hate.
They’re all part of a time consuming, morning, and evening ritual that seems to get longer every few months (with each new product added).
Sound familiar?
They pull you in promising “age-defying” or “anti-aging” effects that always fall flat.
And the products that actually do work seem to only work temporarily.
(But they always have a more expensive cream for you to buy that does just a little more).
The problem is that at best they only hide the symptoms.
Because they don’t address the actual problem.
Sound familiar? 
If you want your skin to be healthy, you need to take care of all of the different parts of your body that affect it, specifically your microbiomes. 
You have an entire ecosystem living on your skin.
Colonies of helpful microbes live on your skin, and they actively help fight against harsh environments and protect against allergens. 
And guess what directly affects your skin microbiome?
Your gut microbiome. 
An unbalanced gut microbiome can lead to **chronic inflammation.**
Chronic inflammation has been shown to cause **leaky gut syndrome.**
Leaky gut syndrome allows toxins and other harmful materials to escape from the gut into the body.
Then your immune system jumps in to fight the toxins being released by your gut.
That’s a problem for your skin,
Because your immune system helps repair the normal wear-and-tear your skin takes every day.
If your immune system is too busy fighting off toxins escaping your gut, it won’t be able to help repair your skin as much as it does when you’re healthy.
Gut Health = Skin Health
Your gut health is directly related to what you eat. Everyone’s gut microbiome is unique, and the only way to see what your little critters need to give you a healthy and balanced gut is to have a look in and see.
That’s what Viome does. 
The Viome Gut Intelligence Test sees exactly what’s in your gut, and what it’s doing. Then based on these results, provides customized diet recommendations designed to balance your gut microbiome in order to: 
Minimizing inflammation,
Protecting against leaky gut syndrome,
Allowing your skin to heal and glow, naturally.

This is just completely ridiculous.  For just $129 Viome is going to do some microbome mumbo jumbo magic and tell you what foods you should eat to make your skin glow.  There are two possibilities here - they don't use the microbiome analysis at all for this and tell you things you could have found out from a google search.  Or, they analyze the microbiome and make recommendations that have no basis in science.  Either way, this is true microbiomania. 


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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in hype, microbiomania, microbiome, viome

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05Mar / 2019

If a body wash falls in the forest, is it gentle on the microbiome?

Well, I guess I am happy Dove is interested in the microbiome. My exposure to Dove's thinking on the microbiome started with an ad that was shared with me by Christine Parks.




The ad claims that Dove is gentle on the microbiome.  OK.  I am not sure I get what that means completely.  But I think they are saying "Our product does not mess up your microbiome".  I guess this could be good for some people if it were true.  But for others, maybe you want to mess up the microbiome.  Regardless, I would love to see data, if it exists, behind such a claim because my guess is that any body wash affects up the microbiome in many ways.

So, if they were not going to show evidence for this claim, I wondered, what are the ingredients of this Dover product? Fortunately the company provides them readily: https://www.dove.com/us/en/washing-and-bathing/body-wash/deep-moisture-body-wash.html. And here they are:
  • Water (Aqua), 
  • Cocamidopropyl Betaine, 
  • Sodium Hydroxypropyl Starch Phosphate, 
  • Lauric Acid, 
  • Sodium Lauroyl Glycinate, 
  • Sodium Lauroyl Isethionate, 
  • Hydrogenated Soybean Oil, 
  • Glycine Soja (Soybean) Oil, 
  • Sodium Chloride, 
  • Glycerin, 
  • Fragrance (Parfum), 
  • Phenoxyethanol, 
  • Guar Hydroxypropyltrimonium Chloride, 
  • Stearic Acid, 
  • Citric Acid, 
  • Sodium Isethionate, 
  • BHT, 
  • Tetrasodium, 
  • Iodopropynyl Butylcarbamate (IPBC)
This last one, Iodopropynyl Butylcarbamate (IPBC), is interesting since there is a paper discussing its effect on the microbiome. See "Effect of cosmetic chemical preservatives on resident flora isolated from healthy facial skin". They report "MTI and IPBC displayed the strongest effect on all tested strains (MICs ≤0.01%), followed by EHG and MP (MICs ≤0.3%), and finally PE with the weakest effect (MIC ≤1%)."  IPBC apparently is a known antibacterial and anti fungal agent.  Unclear how that being in the product is consistent with being gentle on the microbiome.

BHT is also interesting as it has been known as an antimicrobial for a long time (e.g., see this 1980 paper). It is used widely as a "preservative" but one of the ways it works as a preservative appears to be that it is anti microbial. 

Phenoxyethanol is also an antimicrobial.  See for example this where they report things like:
The study reveals that the six preservatives-Phenoxyethanol, Methyl paraben, Propyl paraben, Sorbic acid, Potassium sorbate and Sodium benzoate shown antimicrobial activity with the three test organisms at various concentrations and time periods.
My guess is many of the other ingredients can also affect the microbiome.  This would not really be surprising as lots of things affect the microbiome.  So, sorry Dove, but just saying your product is "gentle on the microbiome" just does not cut it for me.

I decided to see if I could find out anything else about Dove's claim of being gentle on the microbiome so I did the usual thing and Googled "Dove microbiome" and found some of their material on the microbiome.  And I guess I could say I was pretty disappointed. For example see this:Introducing your skin’s microbiome – Dove Nothing there providing data on just how gentle Dove really is or is not on the sin microbiome.  And in addition there was a statement I was not so fond of:
"Think of it as an invisible eco-system that lives on the skin that’s working to help keep it healthy and in good condition. "
Umm -- no -- no evidence for this.  The microbes on your skin appear to mostly be working for themselves.  Some of the time they are harmful. Some of the time they are helpful.  Some of the time they are neither.  But they are certainly not "working" to keep skin healthy.

So - it seems like Dove wants to get in on the microbiome hype.  I guess I am glad they are interested in the microbiome.  But they cannot just make claims about things like "being gentle" on the microbiome without evidence.  Especially when their ingredient list contains a collection of known antimicrobial chemicals.

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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in Dove, microbiome, skin

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18May / 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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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in Chlamydia, John Oliver, Koalas, microbiomania, microbiome, news, Russell Crowe, story behind the paper

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26Mar / 2018

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

 

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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in BuzzFeed, Gut Makeover, microbiomania, microbiome, scams, Stephanie Lee

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30Jan / 2018

Engineered bacteria to detect gut inflammation

0000-0002-8715-28960000-0003-0319-5416 I wrote about engineered probiotics at the beginning of 2017, and the field continued throughout 2017 with more papers and startup news using engineered bacteria in the gut. For instance, one paper used engineered

Posted by in e. coli, engineered probiotic, featured, IBD, Inflammation, microbiome, synbio, synthetic biology

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21Sep / 2017

Genetics and microbiome of cattle methane production: 2017 PLOS Genetics Research Prize Winning Research

post-info AddThis Sharing Buttons aTTThe PLOS Genetics Editors-in-Chief and Senior Editors would like to congratulate: Rainer Roehe, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, Nest McKain, Dave W.  Ross, Jimmy J. Hyslop, Anthony Waterhouse,

Posted by in announcement, community, environment, featured, genetics, Metagenomics, Microbiology, microbiome, news, open access, PLoS Genetics, Research, Research Prize

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24Jul / 2017

Another white men’s microbiome meeting from Kisaco #YAMMM #manel #STEMDiversity

Well, this is really unpleasant.

Last year I blogged about a what I called "The White Men's Microbiome Congress." The gender balance of the meeting was so bad I called for a boycott. And my call seemed to have some impact as many people refused to participate and then the meeting organizers from Kisaco Research responded, apologized for the gender bias, and made some attempts to at least try to fix things. For example they posted on my blog:
We recognize that it is our responsibility to help ensure that the speaker faculty reflect the diversity and culture of the field and science as a whole. In this instance we failed to live up to our own standards of sensitivity and diversity, for which we sincerely apologize. Kisaco Research is deeply committed to producing events that represent the diversity of the scientific fields we work with. We are embarrassed that this has been previously overlooked and are currently working to make this, and all other programmes, ones that the top scientists are proud to be a part of. 
And they did seem to try to make the meeting I critiqued less biased.

And thus it was really disturbing to me when someone sent me the invite they received to a microbiome meeting organized by this group and pointed out that it had the same issue. I went to the web site for this new meeting - the "3rd annual European microbiome congress (see The Microbiome Congress – Europe – Kisaco Research). And it confirmed my fears.



95% of the highlighted speakers are male (as always, I note, assessing the gender balance of a meeting is not always straight forward.  In this case I looked at the web sites of the speakers and other descriptions of them to see what pronouns were used to describe them.  I think my assessment is accurate but I apologize if I made mistakes). And all of them appear to be white.  It is a meeting for white men to speak at.  The field of microbiome studies is rich and diverse in many ways - including in the scientists and others who work on the topic.  It would not have been hard to come up with a more diverse set of speakers.  In fact, the field is so diverse in terms of researchers that I think this speaker line up - especially in light of the previous meeting - is evidence for bias.   I am not sure where that bias comes in (it could be at invitations, at acceptances, or other places) but it is pretty clear this is not a random selection of top microbiome researchers.

As this is a pattern from Kisaco Research I am calling for the following
  • People should boycott this meeting. That is, do not attend this meeting.
  • People should Boycott all Kisaco meetings. This is a pattern for Kisaco, and not a good one.  Nobody should attend any of their meetings
  • The meeting sponsors should withdraw support for this meeting. The listed sponsors include Synthetic Biologic, Qiagen, ProDigest, Affymetrix and Zymo Research. I encourage people to contact them about this and pressure them to rescind their sponsorship.  I have already contacted Zymo, for which I am an advisor.  I will let people know how they respond. 
  • The speakers should cancel their participation.  A meeting cannot go on without the speakers. The listed speakers include:
Of course, it would be better to prevent such things from happening in the future.  Some things to consider that will start to shift away from meetings with poor diversity of presenters:
  • Make diversity of presenters one of the factors you consider when deciding whether or not to accept invitations to speak at or attend a meeting. Some ways to make an informed decision here include
    • looking at past meetings by the same organizers
    • asking for a list of presenters for the meeting one is invited to
    • asking if the meeting has any policies on diversity
  • When you are involved in organizing a meeting work to make it a stellar meeting that also happens to have a diverse collection of presenters (diverse in background,  race and ethnicity, kills, perspectives, gender, types of institutions, careers stages, country of origin, and more). 
  • Develop diversity policies for meetings in which you are involved
  • If you are on the sponsorship side of things - require meeting organizers to have a diversity policy and to show their prior track records before you offer support
  • Develop and support practices and policies that would help make meetings more diverse 

Also check out some of these articles and posts

It is entirely possible to run meetings where there is no bias against particular groups in the presenter line up.  It is also possible to embrace diversity and all of its benefits and make a meeting that is simply better than a meeting where diversity is not embraced.  It does take some effort.  But it is worth it.

UPDATE. Making a Storify of some responses




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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in diversity, kisaco research, manel, microbiome, racism, Sexism, STEMWomen, YAMMM

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09Mar / 2017

Kissing between humans and Neanderthals? Could be oral – anal contact too. Or neither.

Umm - I really do not know what to say here. There is a new incredibly exciting paper out on Neanderthal oral microbiomes.

I saw some news stories about a new study on Neanderthal oral microbiomes. And one thing caught my eye - a claim about how the data provided evidence that Neanderthal's and humans were kissing each other.
See for example the LA Times: Vegetarian Neanderthals? Extinct human relatives hid a mouthful of surprises - LA Times
The scientists also managed to sequence the oldest microbial genome yet — a bug called Methanobrevibacter oralis that has been linked to gum disease. By looking at the number of mutations in the genome, the scientists determined it was introduced to Neanderthals around 120,000 years ago — near the edge of the time period when humans and Neanderthals were interbreeding, Weyrich said 
There are a few ways to swap this microbe between species, she pointed out: by sharing food, through parental care, or through kissing. 
“We really think that this suggests that Neanderthals and humans may have had a much friendlier relationship than anyone imagined,” Weyrich said. “Certainly if they’re swapping oral microorganisms — or swapping spit — it’s not these brute, rash-type encounters that people were suspecting happened during interbreeding. It’s really kind of friendly interactions.”
And Redorbit: Neanderthals were vegetarian– and probably kissed early humans



Another surprise was the discovery of the near-complete genome for Methanobrevibacter oralis, a microbe known to live between the gums and teeth of modern humans, in the dental calculus of the Neanderthals. Weyrich said that this organism is the oldest of its kind to ever be sequenced, and that its existence in Neanderthals means that it had to have been spread to humans somehow – likely through kissing, which supports the growing notion that humans and Neanderthals were known to become intimate with one another on occasion.
And the Washington Post Neanderthal microbes reveal surprises about what they ate — and whom they kissed



And there is this doozy of a quote in the Post article
“In order to get microorganisms swapped between people you have to be kissing,” Weyrich said.
And many others.  Now - this seemed like it would be really hard to prove.  After all, it is really hard to prove from microbiome data that two people have been kissing even when we have high quality data from many samples and even when we have data from both the possible donor and recipient.  So how could one show that humans and Neanderthals were kissing with data from ancient samples and only from one of the partners in the putative exchange?  Well, as far as I can tell, you cannot.

Sadly the paper is not open access and I generally avoid writing about closed access papers here. But I am making an exception here because the media has run with what I believe to be an inaccurate representation of the science.

So I went to the paper.  Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.  I have access to it at UC Davis but if you do not have access to it, you could search for it in SciHub (for more about SciHub see Wikipedia).  I am not encouraging you to use SciHub - a site that makes papers available view what may be illegal means in some countries.  But if you want to see the paper, and you have determined that you are OK with using SciHub, well, that is an option. This is a link that might get you access in SciHub, if you wanted to do that.

Anyway - I read the paper.  And it really is quite fascinating.  It has all sorts of interesting information and really does represent an incredible tour de force of both lab and computational work. Kudos to all involved.  But alas, there is nothing in the paper about kissing. If you search in the paper for the word kiss - it is not found. The possible transfer of microbes between Neanderthal and humans is briefly discussed however.

From what I can tell, what they did here was the following:


  1. reconstructed a genome from their samples of Methanobrevibacter oralis subsp. neandertalensis.
  2. compared the genomes to other Methanobrevibacter genomes including just one other M. oralis (this one from humans)
  3. Inferred a possbile possible date range for the split between their M. oralis and that from humans 


It is cool and very interesting stuff.  See this figure for example.



And then based on this they write:
Date estimates using a strict molecular clock place the divergence between the M. oralis strains of Neanderthals and modern humans between 112–143 ka (95% highest posterior density interval; mean date of 126 ka) (Fig. 3b; see Supplementary Information). As this is long after the genomic divergence of Neanderthals and modern humans (450–750 ka)29, it appears that commensal microbial species were transferred between the two hosts during subsequent interactions, potentially in the Near East30.

So they are inferring transfer of commensal microbes based on molecular clock dating from one single M. oralis genome from Neanderthal and one from humans and a comparison of the inferred dating of their common ancestor versus the timing of supposed divergence between humans and Neanderthal. Personally it seems like a big big stretch to make that inference here. What if the dating from their analysis is off (such dating estimates are generally highly debated and unclear how accurate they are)?

But let's just say that this is in fact good evidence for some sort of more recent common ancestry of the M. oralis found in their sample and the M. oralis found in a human than one would expect based on knowledge of Neanderthal and human common ancestry. Does that mean swapping of the microbes between humans and Neanderthal? Not at all. Maybe the M. oralis comes from food. And if it is living in some sort of food source (could be animal, or plant or something else) and it comes into both humans and Neanderthal separately, then one could easily have a way for the one found in their Neanderthal sample to have a more recent common ancestry with the one found from humans than the common ancestry of the "hosts" here.

Interestingly, the genome they used to compare to Methanobrevibacter oralis JMR01 actually came from a fecal sample and not an oral sample - see Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from the Human Intestinal Microbiota. So this microbe is not solely found in the mouth and it apparently can survive transit between the mouth and another orifice, and may even be a gut resident (i.e., not just transiting).

So anyway - it seems woefully premature to conclude that the data they have here provides evidence for exchange between humans and Neanderthals of M. oralis. Could have occurred. But also could be separate colonization from similarly environmental sources.

And finally, even if we assume that the M. oralis was exchanged, which again there seems to be no good evidence for, what is to suggest that this was do due to kissing? Nothing as far as I can tell. How about sharing utensils? How about contact with fecal contaminated water (since M. oralis seems to do OK in feces)? Or I guess would could go extreme and say this could be evidence for oral anal contact between Neanderthal and humans, if we wanted to sensationalize this even more. After all, we do know many cases of microbes getting exchanged by oral - anal contact. But we don't do we? How about we stick to what we have good evidence for and then carefully discuss possibilities, of which kissing is one, but it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best.


This There is really amazing science in this work. But the kissing claims are premature as far as I can tell (I honestly hope I am wrong and that there is more data than presented in the paper, but if there is it should be presented somewhere - or maybe I have misinterpreted the paper - but I don't think so). If the claims are as premature as they seem to be, this is damaging in my mind to the field of microbiome science.
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UPDATE 3/10/17

Thanks to Ed Yong for updating his Atlantic article on this story to add a reference to my concerns.

He wrote
But after the paper was published, and several publications noted Weyrich’s suggestion about kissing in their headlines, Jonathan Eisen from the University of California, Davis, expressed skepticism about the claim. “Maybe the M. oralis comes from food,” he wrote in a blog post. It could have been picked up independently from the environment, or from water contaminated with feces, or from other kinds of sexual contact. A kissing route “it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best,” Eisen said.

UPDATE 2 - Made a Storify of some responses


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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in anal, kissing, microbiome, Neanderthal, oral

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06Oct / 2016

The White Men’s Microbiome Congress #YAMMM #Manel #Boycott

So I got this email this morning inviting me to attend a conference: the Second Annual Human Microbiome Congress in San Diego. (also called the North American Microbiome Congress).



And it struck me that all the featured speakers were men.




 Great.  So I decided to give them the benefit of the doubt, hoping that maybe if I looked at the rest of the speakers it would be better.

So I had to register on some web site to download the full agenda for the meeting.  And there were the featured speakers, rippling with diversity



So then I went to scroll through the document looking for the other speakers.

OMFG - what a joke.



27 speakers featured.  25 of them male.  That comes to a whopping 93% male lineup.  In a field where there are a massive number of well known, well regarded female researchers.  What a f$&(#()@ joke.  This meeting should be boycotted.  I am going to write to all the speakers I know and ask them to cancel participating.




Update 10/6 1 PM

Got an email from a meeting representative asking me what I thought about the program.  I guess I got this because of my signing up to get the program.



And I wrote back



I guess we will see where this goes.


Update 10/6 1:10 PM

I also have begin writing to people I know who are speaking at the meeting.



I am hoping many of them cancel participating.  I will update when I get more answers but so far the two people who have responded have now withdrawn from the meeting.

UPDATE 10/11

The meeting organizers have responded and appear committed to improving / fixing their diversity issue.  See comments here and also the meeting web site.





That's the good news.

Now the bad news.  A commenter pointed me to the same Group's European Microbiome Congress.  It is a bit better than the US one but not much.



I think this group needs to make a broader statement about diversity than just focusing on one meeting.


For other posts on STEM Diversity see here.


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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in gender bias, manel, meetings, microbiome, YAMMM

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