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. 

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.

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.

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

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

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

• Diversity matters in planning journalism conferences by Steve Buttry
• show me the policy | cubist crystal by Jenny Martin
• Stop Agreeing To Be On All-Male Panels — Just Stop - Emily Peck the Huff Post.
• Increasing Diversity at Your Conference
• Promoting Gender Diversity at Conferences
• Encourage speaker diversity at synthetic biology conferences from Synberc 
• 6 Steps for Planning a Diverse Conference by Jessica Fleuti 
• White male lineup at medical meeting sparks 'public shaming' in STAT
• STEM Women: How Men Can Help, with Professor Jonathan Eisen ...
• Discussion of speaker diversity triggered by a #manel (Storify)
• Speaker gender balance at Society for the Neurobiology of Language conferences 2009–2015
• Countering gender bias at conferences Carrie Arnold in Science
• Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jenny Martin 
• How to Add More Women Speakers to Your Meetings by Michelle Russell in PCMA Convene
• Welcoming Women at STEM Conferences – and Beyond - the StoryExchange 
• To Get More Female Conference Speakers - GenomeWeb
• Female Scientists Turn to Data to Fight Lack of Representation on Panels NY Times
• How likely is an all-male speakers list, statistically speaking? A mathematician weighs in.

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

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.
-----------------------------

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

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.

Pleasantly surprised by the National Microbiome Initiative

So I got this email a few weeks ago inviting me to the White House.



Not every day that I get invited to the White House.  And I thought I was probably on their shit list after removing my name from the "Unified Microbiome Initiative" paper due to it being non open access.  So I asked a colleague if she could teach in my large introductory biology class for me on May 13 and she said yes.  So I RSVP to the meeting and told my mom I would be coming to the DC area (where I grew up).  And I told everyone, proudly "I am going to the White House".

I realized I had a tight schedule for flying in and out since I had to be back in Davis Saturday AM.  So I wrote to the White House to ask about the schedule for the event.  You see, I had no information as to what this event was going to be about.



And, they did tell me this would work although they would not tell me what the meeting was about.



I then bought my tickets and got excited to be going to the White House.  However, fate would not be so kind to me.  My daughter got sick last week (bronchitis, and multiple spin off issues) and so I started to wonder if I really should go away.  So I tried to find out what was happening at this event.  I wrote a few friends who I knew were going and one of them told me there would be a series of talks and another told me they did not know.  So - without much other information to go on, and with a strong desire to take care of my daughter as much as possible, I cancelled my trip.

Then yesterday I got an email from a NY Times reporter



And so we connected and talked for a bit.  I found out from the phone call that the White House was announcing their Microbiome Initiative (which I knew was in the works but for which I basically knew no details).  The reporter Gardiner Harris asked me how I felt about "Big Science" types of projects and, well, I did not say nice things about them.  And I stand by those critiques of Big Science.  I talked about how I disliked the Human Microbiome Project in many ways because it fed too much money to a few groups and was prone to the same problems of other Big Science projects.  And that they were generally a waste of money.  We also discussed how I thought science worked better when administrators got out of the way and let peer review have more of a role in determining what was important.  And I said that if the new White House initiative was another top down science effort, then this would likely be a bad thing.  Or something like that.  But I did also say that I had no idea what the White House was going to announce about and I hoped it was more supportive of small science.

So the article came out and I was featured in it



Definitely something I stand by.  I think top-down approaches to science do not work well.

I woke up early this AM and started posting about the evils of Big Science.  And then I finally found an announcement with actual details on the National Microbiome Initiative being announced today.  And I was pleasantly surprised.  This was not about a big, top down approach to science.  It was more about a collection of projects under one big umbrella theme of microbiome studies.



Yes there were some top down aspects to it.  But only a component. So once I saw this, I realized my quote in the NY Times was not ideal.  Yes Big Science is bad.  But this National Microbiome Initiative is not really the standard bearer of Big Science.  It is not really even Big Science.  It is more   of a "Organizing Distributed Science".

And I found one article out there about the project that captured this essence of it:  The White House Launches the National Microbiome Initiative  by Ed Yong in the Atlantic. He nails it with this section

The National Microbiome Initiative is not the Human Genome Project—a single project with a definitive goal. It consists of many organizations operating independently; to paraphrase Whitman, it contains multitudes.

So my quote in the NY Times was technically correct - Big Science is bad.  But it also not quite right in the context it is presented - since the NMI is actually not really (or at least not completely) Big Science.  I do wish the context of the quote had been presented a bit more  (well, more specifically that I did say I did not know the full details of what they were actually proposing).  Lesson learned.  Be really careful about commenting about things "generally" without knowing the details.  I definitely regret doing that here.  I did in fact say what is reported so can't complain about being misquoted.  But I should have been more careful regarding the caveats and context.

I note - it is unclear to me how much of these smaller distributed projects would have happened without the NMI.  My guess is most of them would have happened and that the NMI is a bit of a public relations effort.  Ed Yong also captured this issue in his piece:

A cynic might be forgiven for seeing this as an exercise in branding, encapsulating what microbiome scientists were already doing under a catchy umbrella.

And I also worry as always that "Microbiomania" (hype about the microbiome) will get worse with this announcement of the NMI.  And it probably will.

But in the end I am very happy that this is not a run of the mill top down Big Science project (like the Human Genome Project or the Human Microbiome Project or the Human Brain Project).  It is much more nuanced than that.  Much more distributive.  Much more likely to support small science and creative science and such.  And that is a good thing.

Would you try to vaginally "seed" your baby's microbiome after a C-section

Well, sadly I just accidentally deleted a whole post about this and cannot find it. So this is going to be way shorter than I would have liked.

I found this opinion piece to be very interesting and a really good case study for discussing the microbiome: Opinion: A Mother’s Microbes | The Scientist Magazine

About the piece

• Authors: Jack Gilbert and Rob Knight
• Topic: VMS. Vaginal Microbiome Seeding. Attempting to "seed" the microbiome of an infant born by C-section by collecting microbes from the mother's vagina and applying them to the baby. 
• Subtopic: A response to a BMJ editorial that seems to have said they do not at this time recommend VMS (I say seems to have said because the people at BMJ decided this was something to put behind a paywall). 

Why do I find it interesting?  Because I think the authors do a good job of showing how hard it is to make some decisions when the evidence is inconclusive.

Quibbles? Sure.  I like much of the approach of Gilbert and Knight but still find parts unconvincing and incomplete.  Some specifics are below:

The paragraph on the conditions associated with C-sections does not in my mind, go into enough detail on how such associations can be spurious and that those conditions could have no causal connection to C-sections.  Instead they simply say we do not know if these associations are due to lack of exposure to the vaginal microbiome of the mother.  That just is not sufficient in my mind.  For example, they mention the association between autism and C-sections.  However, they do not mention that some recent studies suggest that there may not be a causal association (e.g., see this). I think it is imperative when discussing such associations that one also mentions how such associations may have no causal relationship. 

It is unclear what the part near the end is that appears to be a quote from Rob Knight.  Not sure if this is a online formatting issue or what.  But in that section Knight writes "I seeded my newborn child with the vaginal microbes the baby would have received naturally had everything gone according to plan."  I have some quibbles with this as it seems possible that just doing an attempted seeding would not necessarily get the microbes that would have been received naturally

Finally, I have some more major quibbles with the last section.  On the one hand it it is good that they do discuss a risk that could come from VMS (exposure of the baby to pathogens from the mother).  However I think it would have been good in this discussion to also discuss other possible risks.  For example, it seems plausible that exposure to non pathogens from the mother could in fact do some harm (e.g., if one exposure the baby to the wrong non pathogenic organisms perhaps things could go wrong in terms of colonization).  In addition, it seems also plausible that by doing the sending, some parents and medical caregivers and others might be less vigilant at watching the infant for health issues assuming that the seeding made them healthy.  And I am sure there are others.  

It would in fact be good to lay out the possible risks somewhere in more detail.  Why?  Because I think Gilbert and Knight are actually spot on with their final recommendation:

But based on the evidence to date that your child’s microbiome at birth is important and modifiable, we think that parents should make up their own minds how much evidence is enough given the evolutionarily sound logic and clear health advantages of vaginal birth over C-section. 

And I am not just per se talking in the hypothetical.  If I could go back in time to when my daughter was born by a last minute C-section, I think I would have wanted to have done VMS.  And if I could go back in time to when our second child was born by a planned C-section, I definitely would have wanted to have been more aware of this issue and I think we would have seriously considered it.  I probably would have looked in more detail at the possible risks if I had the time but regardless, from what I know now, I think VMS is definitely worth considering in cases of C-sections if the mother's vaginal microbiome does not contain any known dangerous pathogens and if other risks can be considered and balanced.  

Bonus: BMJ did make available an audio commentary about their Editorial. See below:

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Made a Storify of some of the discussion around the topic

Some other questions of interest and or papers to look at

• Does length of stay in the hospital have any role in microbial colonization? See new PLOS Med paper for example about length of stay and health risks. 

Tony Rodriguez Illustration of Me for WiredUK

OK so I have not worn a tie in a very long time and I pretty much don't wear a lab coat too often either but I totally love this:

My illustration of Jonathan Eisen for Wired Magazine's UK edition is now in print. #editorialillustration #digitalillustration #illustration #wiredmagazine #tonyrodriguezillustration

A photo posted by Tony Rodriguez (@tonyrodriguezillustration) on Dec 30, 2015 at 8:50am PST

See the whole story here.

My personal thoughts on Bordenstein and Theis Holobiont Paper - part 2

See this The Tree of Life: My personal thoughts on Bordenstein and Theis: Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes for part 1 and background.  I note - part of why I wrote the previous post was Seth had complained in a blog post that some authors seemed to have not read his paper.  So I decided to read it.  And to comment on it publically.

My personal thoughts on Bordenstein and Theis: Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes.

There are many discussions going on about a paper from Bordenstein and Theis that was published in PLOS Biology in August 2015. The paper is Bordenstein SR, Theis KR (2015) Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biol 13(8): e1002226. doi:10.1371/journal.pbio.1002226

A few days ago a paper came out by Moran and Sloan that discussed an alternative view of Hologenomes: Moran NA, Sloan DB (2015) The Hologenome Concept: Helpful or Hollow? PLoS Biol 13(12): e1002311. doi:10.1371/journal.pbio.1002311.

I made some comments on Twitter when the 1st paper came out about how I was skeptical of the paper and in discussions with Seth Bordenstein I said I would try to write up my thoughts.  And when I was pointed to the second paper today I posted to Twitter that I thought it was important and got into a brief discussion with Seth about the paper. 

In thinking about the papers and science publishing and scientific discussions I have decicded to try and carry out a new experiment.  I am going to go, as fast as I can, line for line through the papers and post my thoughts in response to those lines.  And I will try to be honest even if my thoughts are not, well thought out or nice or helpful.  I am just going to post the thoughts.  And one reason I want to do this is I worry (or maybe realize) that my judgement may be being affected here by visceral responses to some of the lines.  In particular, I confess, some of the way the Bordenstein and Theis article is written really rubs me the wrong way.  Nothing personal against the authors.  But the text did not agree with me in parts.  And I think that may have affected my response to the article.  I do not know for sure but it seems possible.  

Regardless, I am going to try and go through this.  And for now I am going to just start with the Abstract.

Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable.

I personally find this to be a bit too extreme. Really - did they once seem untouchable? To whom?

To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology.  

I think it is overstating the "central importance of microbiology" to place it somehow in line with Darwin, Mendel and the modern synthesis

Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." 

While on the one hand I agree with part of this statement I think it is making a claim and stating it as a fact when this is what is being debated.

 As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. 

Certainly animal and plant biology has to account for microbes. But it is false logic to say that one can only account for microbes by following the hologenome concepts.

Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. 

No thoughts on this.

Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. 

Confession. Saying ones own principles "clarify" something rubs me the wrong way. I would really have preferred it if they said "attempt to clarify".

We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. 

I find this to be really overstated too. I don't think what you have presented in this paper is a roadmap. And for you to call it that sets up this essay as basically saying that everything else that has come before is limited and lame.

At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology. 

I do not think symbiotic microbes are fundamental to all aspects of animal and plant biology. I think this is actually a silly statement and makes me doubt the objectivity of the authors.

  UPDATE: See part 2 here.

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Removing my name from the author list of #closedaccess "Unified Microbiome Initiative" paper in Science

The ChuckNorrisMicrobiome will get you, and you, and you ...

Some Saturday fun ...

A night with Matt Groening and the importance of faeces, feces and faces

So - I participated in a fundraiser for Emily Levine's "The Edge of Chaos" film a week ago. And one of the key guests was Matt Groening. Not only did I get to hang out with him and discuss fecal transplants with him (really) but I had a front row seat to Matt discussing the history of how he came up with the general outline of the Simpson's characters.

And in addition to this being just awesome to witness, one part of it struck me. See the video below and in particular the part that struck me was the beginning:

  Groening
basically said that only a few simple changes in faces can be recognized by people very easily. This reminds me of Jenna Lang's talk at the Lake Arrowhead meeting this year where she discussed using facial drawings as a form of visualizing microbiome data.

 

Citizen Microbiology: Opportunities for Engagement and Data Visualization, Lake Arrowhead, 2014 from jennomics

So - since I discussed fecal transplants with Matt and since he gave a good description of facial characteristics being easy to identify, I think we should definitely (1) try and get him to include microbiomes on the Simpsons and (2) for our work we should use Simpsons characters as model faces for different microbiomes ...

Oh and I also showed Groening some of the pics of my kids reading his "Hell" books:

So - basically it was a night of feces, faeces and faces.  Seems ideal.

Today's YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015

Just got pointed to (by Elisabeth Bik) an announcement for a meeting: Home : Pharma-Nutrition 2015 with a focus on "Linking the Microbiome with Nutrition and Pharma".  And alas, the list of confirmed speakers is as follows:

• Keynote Speaker
• Martin J. Blaser, NY University Medical Center, New York, NY, USA
• Speakers
• Gregor Reid, University of Western Ontario, London, ON, Canada 
• Alain van Gool, Radboud University, Nijmegen, The Netherlands 
• David Hafler, Yale, New Haven, CT, USA 
• John F. Cryan, University College Cork, Cork, Ireland 
• André Marette, Laval University, Montreal, QC, Canada 
• Charles R. Mackay, Monash University, Clayton, Victoria, Australia
• Alan L. Landay, Rush University Medical Center, Chicago, IL, USA

Yay.  All men.  How wonderful.  Because, you know, there are no women working on the microbiome and nutrition right?  Ugg.

Seems like they are still working on getting more speakers.  I will send this blog post to the organizers and see what they say.  But suffice it to say I am very disappointed in them.  Oh, and shockingly, the two organizers are men: Johan Garssen and Alan Landay.

These YAMMMs (Yet Another Mostly Male Meeting) really have got to be killed.  People should not got to them.  People should not speak at them.  And the organizers should not be allowed to run other meetings unless they can explain themselves and provide evidence that they will work to not have this happen again.

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UPDATE A FEW MINUTES AFTER POSTING.

I found the program committee for the meeting.  Alas the gender ratio there is lame too.

• John F Cryan, University College Cork, Cork, Ireland
• Alain van Gool, Radboud University Medical Centre, Nijmegen, The Netherlands
• David Hafler, Yale School of Medicine, New Haven, CT, USA
• Charles R Mackay, Monash University, Melbourne, Australia
• André Marette, Laval University, Sainte-Foy, QC, Canada
• Gregor Reid, Lawson Health Research Institute, London, ON, Canada

And a bit strangely - all of the people on the program committee are speakers.  No bias there.

Microbiome topic of the day: radiation therapy and the microbiome

Just saw this interesting story in the Observer: Cancer scientists to classify gut bacteria to prevent the side-effects of radiotherapy | Science | The Observer.  It discusses an effort to give more consideration to protecting and / or repopulating the microbiome in relation to radiation therapy.  I think this is critically important.  I want to note - people should give some credit to DARPA for being ahead of their time on this issue.  I went to a workshop in 2004 organized by Brett Giroir and Manley Heather.  The topic was "Radiation Protection" and one of the points of discussion was the gut microbiome and the effect of radiation on it.

Anyway - since that meeting I have been following this topic on and off.  And I do think thinking about the microbiome in relation to radiation therapy (and any radiation exposure) is critically important.

Simple microbiome quiz and then mapping function from PGED

Just did this: Map-Ed Genetics: Pin Yourself on Our World Map! (the microbiome one - there are two right now - the other is personal genomics - and others coming).  Best part is browsing the map of other participants afterwards.

Love these QTL experiment where microbe relative abundance is the quantitative trait being studied

Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group.  I really really love this new approach of doing QTL experiments where the quantitative trait being measured is the relative abundance of various microbes.  The first paper of this kind I know of that did such a QTL analysis was Benson et al. 2010 in PNAS in mouse.  There have been a few others using this approach (e.g., Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits) and I am sure we will see many many more.  Basically this approach allows one to identify genes / polymorphisms / regions of the genome in a host that influence the relative abundance of specific microbes.  And such information will be critical in understanding the interactions of microbial communities with hosts.