microbiome – Jonathan Eisen's Lab

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:

reconstructed a genome from their samples of Methanobrevibacter oralis subsp. neandertalensis.
compared the genomes to other Methanobrevibacter genomes including just one other M. oralis (this one from humans)
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

//storify.com/phylogenomics/kissing-oral-anal-contact-or-maybe-just-maybe-neit/embed?border=false&template=grid //storify.com/phylogenomics/kissing-oral-anal-contact-or-maybe-just-maybe-neit.js?border=false&template=grid[View the story “Humans and Neanderthals – kissing, oral-anal contact, or maybe, just maybe, neither” on Storify]

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.

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:

Made a Storify of some of the discussion around the topic

//storify.com/phylogenomics/vaginal-microbiome-seeding-would-you-do-it-what-do/embed?border=false&template=slideshow //storify.com/phylogenomics/vaginal-microbiome-seeding-would-you-do-it-what-do.js?border=false&template=slideshow[View the story “Vaginal Microbiome Seeding – would you do it? what do you think about it?” on Storify]

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

//platform.instagram.com/en_US/embeds.js 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.

After I posted about this there was some back and forth with Seth on Twitter. Here is some of it:

//storify.com/phylogenomics/discussion-of-hologenomes-part-1/embed?border=false //storify.com/phylogenomics/discussion-of-hologenomes-part-1.js?border=false[View the story “Discussion of Hologenomes Part 1” on Storify]

Anyway, I am going through, sentence by sentence the paper.

I did the Abstract in the last post. Now on to the Introduction

“The time has come to replace the purely reductionist ‘eyes-down’ molecular perspective with a new and genuinely holistic, eyes-up, view of the living world, one whose primary focus is on evolution, emergence, and biology’s innate complexity.”—Carl Woese (2004) [1]

Nice quote.

At the end of the 19th century, the theory of evolution via natural selection was birthed with the appreciation that individual animals and plants vary in their phenotypes and that competition at the individual level drives gradual change in the frequencies of these phenotypes [2].

No comments.

From this early vantage point, fusing evolution with Mendelian genetics in the early 20th century was a seamless transition in biology, namely one based on the framework that phenotypes in the individual animal and plant are encoded by the nuclear genome under the laws of Mendelian inheritance [3–5].

I really do not feel comfortable calling this a seamless transition. From my reading and what I know of the history, it took a lot of work by people to both figure out how to make this transition, how to refine it and then how to convince others that it was correct.

In the mid-20th century, the modern synthesis grounded the nucleocentric foundation of zoology and botany in three areas: (1) the nuclear mutability and recombinogenic nature of organisms, (2) the sorting of this genetic variation by natural selection, and (3) the observations that macroevolutionary processes such as the origin of species can be explained in a manner that aligns with Mendelian genetics and microevolutionary mechanisms [6].

Calling zoology and botany “nucleocentric” seems unnecessary to me although I guess I am not sure what they point of this is.

The foundation of the modern synthesis remains as scientifically sound today as when it was conceived.

I am not sure I understand what this is saying. How would the scientific soundness of the synthesis change over time? Or do they mean here “the perception of the scientific soundness?”

However, it is critical to recognize that microbiology was largely divorced from these early epochs in the life sciences.

Agreed.

The modern synthesis commenced at a time when the germ theory of disease dictated the prevailing wisdom on microbes, and the molecular tools used to understand the microbial world and its influence were inferior to those available now [7–11].

This is true but the tools were also inferior for characterizing anything. Plus I do not think it was the molecular tools per se that changed things. It was also ideas and theories.

The theories of gradual evolution and the modern synthesis were thus forged during periods of eukaryocentricism and nucleocentrism that did not appreciate the centrality of microbiology in zoology and botany because of limitations in perspective and technology.

Yes, good to mention the “limitations in perspective”. But I am not sure what eukaryocentrism is exactly. Or what nucleocentrism is either. And I just do not feel comfortable with the “centrality of microbiology in zoology and botany statement”. This seems to be putting the cart before the horse. Are they central? I don’t actual know. Are they important? Absolutely. That is why I study host-microbe interactions. But are they “central” – I would not go that far. And I thought part of the point of this was that we need to test that, not posit it.

Today, there is an unmistakable transformation happening in the way that life is comprehended [12–16], and it is as significant for many biologists as the modern synthesis. Animals and plants are no longer viewed as autonomous entities, but rather as “holobionts” [17–21], composed of the host plus all of its symbiotic microbes (definitions in Box 1).

I find this to be an enormous overstatement. I for one do not believe we are even remotely near a point where understanding that plants and animals are “not autonomous entities” is getting to something akin to the modern synthesis.

The term “holobiont” traces back to Lynn Margulis and refers to symbiotic associations throughout a significant portion of an organism’s lifetime, with the prefix holo- derived from the Greek word holos, meaning whole or entire.

I was not aware of the history.

Amid the flourishing of host microbiome studies, holobiont is now generally used to mean every macrobe and its numerous microbial associates [19,22], and the term importantly fills the gap in what to call such assemblages.

I am not so sure that this is a useful term and I am not convinced that it “importantly” fills any gap. Whether it fills any gap depends entirely on whether many of the claims in this paper are supported by evidence. So stating this in the introduction seems awkward.

Symbiotic microbes are fundamental to nearly every aspect of host form, function, and fitness, including in traits that once seemed intangible to microbiology: behavior [23–26], sociality [27–30], and the origin of species [31].

I agree that microbes play more of a role than was thought. I don’t think they play fundamental roles in “nearly every aspect of host form, function and fitness.” What about vision? Xylem formation? Meiosis? Speech? Muscle contraction? Flight mechanics? And 100,000 other things. Sure, microbes play fundamental roles in many aspects of host biology. And that is awesome and why I study host-microbe interactions. But this “nearly every aspect” is just really way overboard.

The conviction for a central role of microbiology in the life sciences has been growing exponentially, and microbial symbiosis is advancing from a subdiscipline to a central branch of knowledge in the life sciences [14,32–35].

I don’t find this convincing.

This revelation brings forth several newly appreciated facets of the life sciences, including the testable derivation that the nuclear genome, organelles, and microbiome of holobionts comprise a hologenome [35–37].

Ok. This I am OK with. Because rather than overstating things this presents something, finally, as something to test.

The hologenome concept is a holistic view of genetics in which animals and plants are polygenomic entities. Thus, variation in the hologenome can lead to variation in phenotypes upon which natural selection or genetic drift can operate.

This seems to be presenting material as fact rather than hypothesis.

While there is a rich literature on coevolutionary genomics of binary host–microbe interactions, there have been few systematic attempts to align the true complexity of the total microbiome with the modern synthesis in a way that integrates these disparate fields [38–40].

I generally agree with this.

The object of this essay is to make the holobiont and hologenome concepts widely known. We clarify and append what they are and are not, explain how they are both consistent with and extend existing theory in ecology and evolutionary biology, and provide a predictive framework for evaluating them.

OK.

Our goal is to provide the main conceptual foundation for future hypothesis-driven research that unifies perceived divisions among subdisciplines of biology (e.g., zoology, botany, and microbiology) and advances the postmodern synthesis that we are now experiencing [41,42].

This rubs me the wrong way. To aim to “provide the main conceptual foundation” seems to be exceptionally bold and arrogant. And to, in this one paper provide such a conceptual foundation – I don’t think so. And then to advance the post modern synthesis too? How about we judge that AFTER the article is published not before?

We distill this topic with evidence-based reasoning to present the ten principles of holobionts and hologenomes (summarized in Box 1).

I guess I don’t really like this either. “The” 10 principles? How about just “10 principles”. As this is written it implies there are no other principles that could be hypothesized.

OK … so that is the Introduction. Will try to continue with the meat of the paper soon.

UPDATE: See part 3 here.

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.

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

//storify.com/phylogenomics/removing-my-name-from-the-author-list-of-closedacc/embed?border=false //storify.com/phylogenomics/removing-my-name-from-the-author-list-of-closedacc.js?border=false[View the story “Removing my name from the author list of #closedaccess “Unified Microbiome Initiative” paper in Science” on Storify]

The ChuckNorrisMicrobiome will get you, and you, and you …

Some Saturday fun …

//storify.com/phylogenomics/the-chucknorrismicrobiome-will-get-you/embed //storify.com/phylogenomics/the-chucknorrismicrobiome-will-get-you.js[View the story “The #ChuckNorrisMicrobiome will get you” on Storify]

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.