The talk was introduced by Illahee’s Director, Peter Schoonmaker.   In his  blog post, Peter described his summary of my presentation.

I used the occasion to wax lyrical about the congruence of the hologenome theory of evolution with our work on creating an open and transparent innovation cartography tool.

I tried to find a common thread of ‘biological innovation’ that can guide not only the practical realities of improving health, agriculture, environment and energy, but also the formation of productive and equitable economic and social structures and tools.

The full video of this presentation is available on Vimeo:   Enabling Innovation

Jan Huygens van Linschoten

The world’s greatest disruptive act of  Open Access Publishing.

The Dutch are pragmatists.   If there’s a more practical, hard-nosed, outcome-oriented culture that is steeped in business and trade, it might be the Chinese.  But the Dutch are (in so many ways) giants in the history of trade and commerce.

So it may be surprising that what is arguably history’s most disruptive act of creating a ‘commons of knowledge’ that opened up global trade to competition and fair-play came from a Dutchman,   Jan Huygens van Linschoten.

van Linschoten managed in a single act of sharing – in his case the pilfered Portuguese portolans and charts – to open the world of maritime commerce up to free and open competition, stimulating an era of growth and innovation in technology – shipbuilding, sailing, logistics, cartography and navigation – and in business – insurance, investment tools, financial instruments – that changed civilization for ever.

In 1596 or thereabouts, van Linschoten published what had for over a century and a half, the state secrets of Portugal – the maritime cartography of the Indies – West and East.

I’d like to share an email exchange I had some months ago with Eugene Rosenberg, one of the authors of some extremely interesting papers outlining the hologenome theory of evolution.   He and his wife, Ilana Zilber-Rosenberg apparently completely independently from me articulated the hologenome theory from their experiences in microbiology and nutrition, and coral microbiology in particular.

Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I.

Nat Rev Microbiol. 2007 May;5(5):355-62. Epub 2007 Mar 26. Review.PMID: 17384666 [PubMed - indexed for MEDLINE]

http://www.ncbi.nlm.nih.gov/pubmed

Email thread:

from: Eugene Rosenberg <eros@post.tau.ac.il>

to: Richard Jefferson <raj@cambia.org>

date: Wed, Mar 10, 2010 at 7:25 PM

subject: Re: Hologenome theory, microbiome / holobiont

Dear Richard,

Wow. What a joy to read your e-mail and blog. Before commenting, let me inform you that I am a young 75 year old general microbiologist that has published 250 scientific articles, almost exclusively on experimental studies on myxobacteria, hydrocarbon degradation by bacteria and more recently bacterial diseases of corals. My wife, Ilana, is the best nutritionist in Israel, with a strong background in biochemistry and microbiology. We came to the concept of the hologenome (I now include you in the “we”) from am attempt to explain how a particular coral became resistant to bacterial bleaching. Clearly, we share your view of the holobiont as a unit of selection in evolution of animals and plants.

Where do we go from here? Your clear discription of the glucuronide conjugate system is a fine example of how the microbes are an integral part of host metabolism. Furthermore you speculate that these reactions can lead to mating selection. Now to blow your mind- We have been working on the role of bacteria in mating selection for the last two years. It started when my wife found a paper in Evolution, published 20 years ago by Diane Dodd. She took a population of Drosophila from Bruce Canyon and raised half of them on a starch diet and the other half on maltose. After a year, she mixed them, and found the “starch flies” perfered to mate with ”starch flies” and “maltose flies” perfered to mate with “maltose flies.” Although they offered no explaination for this mating selection, my wife and I immediately thought bacteria. So, I put a graduate student, Gil Sharon, on the problem. He first repeated Dodd’s experiment using the standard laboratory strain of D. malanogaster and sucrose instead of maltose. Mating selection occurred after two generations and was maintained for 30 generations. When we added antibiotics, mating selection was abolished, indicating bacteria were responsible. Furthermore, we infected the antibiotic-treated flies with their homologous bacteria (isolated prior to antibiotic treatment) and mating selection was reestablished. We sent a manuscript to Nature and they rejected it, saying they would reconsider if we identified the specific bacterium responsible for the mating selection. This has not been an easy task, but we are still working on it.

Regardless of the particular bacterium, what is the mechanism? We have been extracting flies with pentane and doing GC-MS. There are differences between the “starch flies” and the “sucrose flies”.

Maybe the glucuronide system is involved.

It was a pleasure to hear from you. Let’s keep in contact.

Shalom

Eugene

Eugene Rosenberg, Professor Emeritus
Dept. of Molecular Microbiology and Biotechnology
Tel Aviv University
eros@post.tau.ac.il
+972-3-6409838

—– Original Message —–

From: Richard Jefferson

To: eros@post.tau.ac.il

Sent: Wednesday, March 10, 2010 8:27 AM

Subject: Hologenome theory, microbiome / holobiont relationships etc

Dear Professor Rosenberg,

I am writing firstly to compliment you and Professor Zilber-Rosenberg on your clear, lucid and compelling writing in the last years on the hologenome theory.

I have read these with great interest and pleasure.  I particularly commend you for the fine exposition in the FEMS and the Environmental Microbiology review and opinion piece, respectively.

I am a molecular biologist, and now as well innovation system strategist, currently with funding from the Gates Foundation.    I started work in molecular biology in 1974, and in the late 70′s and subsequently I began working with the glucuronide metabolism pathways of commensal vertebrate microbes, including E. coli.   It became very clear to me fairly early that the suite of capabilities to import, metabolize and ‘share’ the products of xenobiotic and endobiotic metabolism by gut microbes was central to the selective performance of the host and microbiome – the holobiont.

As I became involved in the earliest days of agricultural biotechnology, my focus on systems-level understanding and intervention continued to be informed by this awareness.   I was convinced that the model system approaches which were and are so joyously productive, may not have been as joyously instructive as to the workings and logic of natural systems as embedded through natural (or in agriculture, human) selection.

I’ve written about this approach a little, but I’m not very prolific as a writer (I would make a terrible academic, alas).  I have however been speaking and promoting this work for many years as part of my work as founder of Cambia – an international non-profit institution.

I attach to this a link to my blog (rarely visited, rarely updated) in which I wrote down some of my thoughts.  ( http://blogs.cambia.org/raj/index.php/2007/09/06/the-hologenome-hologenomics/ ).  I also have in my blog (the top of the blog) links to videos of lectures I”ve given at Cold Spring Harbor in 1994 on the hologenome, and its implications; and presentations in South Africa in 1997 (I’d love to share with you my old powerpoint if you’re interested) in which I refer to our molecular work on glucuronide metabolism and the logic of applying eco-therapeutics and the understanding and adjustment of the hologenome to health challenges.     Term ‘hologenome’ and ‘holobiont’ and its critical role in evolution were proposed by me at that CSH lecture and since, and I was overjoyed to read your parallel and independent articulation of their importance, especially with regard to the critical horizontal inheritance opportunities for the fitness of the selected holobiont in a complex environment.

This has continued to be my intellectual focus for much of the last 30 years, but most of my work has been focused on democratizing science-enabled innovation through ‘open source’ type approaches, and through increasing the transparency and fairness of intellectual property systems.

I would be thrilled to be in correspondence with you about these ideas – they shape my thinking in many fields, and I’m musing very hard about setting up experimental systems to test the hologenome theory, which to me is compelling.  My laboratory has been in storage now for over a year since our institute moved from Canberra to Brisbane, but within a year I expect I may be back to full steam.  I’ll likely be doing a ‘sabbatic’ of sorts at Berkeley  from July – December and look forward to getting back into the game, as our Initiative for Open Innovation goes to scale and can be taken over by other champions.

Again, my warmest wishes and congratulations for some of the best science writing I’ve read in a long time.  That we have arrived at virtually identical conclusions from such different perspectives is itself most gratifying.

Best wishes

Richard

Richard A. Jefferson PhD
Chief Executive Officer, Cambia
Director, Initiative for Open Innovation (IOI)
Professor of Science, Technology & Law
Queensland University of Technology (QUT)
G301, 2 George St, Brisbane 4000, QLD Australia
+61 419 499 753 (mobile)  +61 7 3138 4419 (work) +61 7 3138 4405 (fax)
www.bios.net |  www.cambia.org |  www.patentlens.net  | www.openinnovation.org
e: r.jefferson@cambia.org

Cambia\’s Youtube Channel, including Cold Spring Harbor presentation

At that time (September, 1994)  I was trying to set the scene for why studying, understanding and manipulating complex systems with tools and approaches of reductionism would not be enough.

I started in part one with the concept of getting ‘Beyond the Model System’, and used real-world agriculture and environment as the entry point for that discussion.

I then went on in parts II & III to discuss the complexities of crops that were really not ‘model systems’ by any measure, sugarcane and cassava being exemplars. For this I referred to the excellent work of my friend and colleague Bruno Sobral, then at the California Institute of Biological Research and affiliated with Cambia.

Next I outlined the Hologenome concept and the idea that the microbial constitution of the entire ‘selected unit’ was the Great Unknown but perhaps – I argued – the biggest opportunity to create sustainable and robust interventions that were congruent with the logic of natural selection and evolution.

Finally in part V I discussed our thoughts on forming an international activity to create the technologies and thought framework for understanding genetic and organismal diversity. I called this the GRIT initiative at the time, but alas, for all the promotion and exhortation we were unable to secure the momentum necessary to make it happen.

Perhaps we were way before our time? Shortly after this, huge sums of money were spent on DNA sequencing and genome analysis facilities. Probably money well spent in that now we have solid data that supports the contention that the majority of the biosphere is the microbiome, and that most of the ‘visible’ biosphere is itself comprehensively populated with such a microbiome.

Maybe now we can start asking how to go from this observation and from the ability to sequence and describe the numbers and diversity of these microbes to a new ability to grok their role in biological system performance and robustness.

In the last few years our lab has been getting more deeply into Type IV Secretion Systems. We set out some years back to ‘re-invent’ the Agrobacterium tumefaciens plant gene transfer capability in other families and genera of bacteria.

The reasons were twofold. First to invent around a very egregious and complex patent ‘thicket’.

Agrobacterium had been discovered to be capable of transferring genes from itself into higher plants, using a mechanism that is very similar to that used by virtually all bacteria to transfer genes (and proteins) from one bacterial cell to another, and often from one bacterial species to another. This observation was the first prominent inter-kingdom gene transfer described, and was the foundation of plant genetic engineering. So of course, it was patented up and down, backwards and forwards; every improvement, every species of plants…obscene greedfests of patenting. Until no one could actually use Agrobacterium to create crops (not just plants) that were improved. Except of course for a very few multinationals that had acquired strong portfolios and were willing to cross license them narrowly.

Anyway, we found that all the patents referred to this biologically unique (now there’s an oxymoron) capability of Agrobacterium tumefaciens. We reasoned that nothing in biology is unique. (Or as Jeff Goldblum’s darkly prescient character in Jurassic Park opines “Nature finds a way”). So we looked at moving this capacity to diverse bacteria and thus rendering the patents interesting and informative, but not legally restrictive.

It was surprisingly easy! And every one of the bacteria we tried it in worked, and in every plant species combination. Hmmm… so interkingdom gene transfer wasn’t hard? Well….

The other reason we set out to do this work-beyond, which we called Transbacter, was to make the process better. To use bacteria that had evolved a benign and symbiotic relationship with plants (and hence did not induce a pathogenesis response) to do our gene transfer, nicely.

Well, all that is pretty well described. But as we get more into these natural gene transfer capabilities, which are loosely clustered as ‘Type IV secretion systems (T4SS)’ I start to realize that the movement of genes between bacteria and likely, between bacteria and fungi, protists, plants, animals, you name it, is probably hugely more common than previously supposed.

The antibiotic resistance factors that are so promiscuously shared on broad host range plasmids (like the ubiquitous RK2) are moved around with T4SS’s, and of course the first system I cut my teeth on – the E. coli ‘F’ factor (fertility factor) is yet another of these. No self-respecting bacteria seems to lack such a capability.

If our observations about how the Ti-encoded Agrobacterium system can be so effective inother bacteria can be generalized, I think it may mean that a very serious force in metazoan and plant apogenome evolution will be from horizontal gene transfer from microbes. Note I say ‘microbes’ not bacteria, because I bet these types of systems pop up in fungi, protists, archae…etc.

Ok…my fingers are sore from typing this little blog. But there’s the convergent evolution in my scientific thinking – from glucuronide metabolism (and GUS the Wonder Gene) to horizontal gene transfer…now coming full circle.

What fun this period of life sciences could be. I really find 99% of molecular biology boring as bat shit these days. I can’t bear reading journals. But these ideas are much more envigorating, as they seem to smell of a pervasive logic. And as usual, I adore going where the metrics are tough. If you can’t see it and measure it, its not there? No way.

Still, there are new fields that are breathtaking in their implications (to me at least) and which do not lend themselves to being ‘owned’, but – at least at this stage in their development – rather shared.

The single most exciting development in the biological sciences to occur in my lifetime is the idea that microbes are not only ubiquitous but that they may be the most important component that drives the evolution of macro-organisms.

In fact, I’d venture to say that multicellular eukaryotes only exist in nature as complexes of organisms in which microbial genomes are critical, essential contributors to the fitness of the overall ‘individual’ (which itself needs redefining).

Back in September of 1994 I gave an invited presentation at a Symposium at Cold Spring Harbor sponsored by Perkin Elmer Corporation: “A Decade of PCR“.   The symposium was only a couple of days, was a celebration of the impact and future of PCR on life sciences, and featured Jim Watson, Kary Mullis, and a number of other prominent speakers. I was given the task of talking about Agriculture, Environment and the Third World. Rather dauntingly broad marching orders. But I decided that I’d try something fun out on the audience, which was a pretty substantial group of scientists.

While setting the scene with our observations about the complexity of agricultural systems, I wanted mostly to talk about ‘Hologenomics’, a term I coined and defined for that seminar.   As with most of my ideas, I’ve never written it down, but I have spoken about it alot, and thought about it even more. (This comment is a response to a quote from my PhD thesis advisor, who wrote in my letters of recommendation that “Jefferson thinks incredibly quickly, but speaks even faster”….sigh).

For years I’ve been studying the metabolism of glucuronide conjugates by Escherichia coli, and many other microbes associated with vertebrates. Vertebrates, including many humans (!) have a remarkable mode of turning over small molecules from their systems. Most small molecules, including steroid hormones, vitamins, xenobiotics (including most pharmaceuticals and dietary secondary metabolites) are excreted from the body as conjugates of glucuronic acid known as ‘glucuronides’ .

Glucuronic acid is simply glucose in which the 6-carbon is in the form of a carboxylic acid or carboxylate. The conjugates are typically (but not always) beta-1-O-linked glycosides of the aglycone. This conjugation is done in many tissues of the body, including of course the liver, but also epidermis and almost everywhere we look. The conjugates so generated tend to be much more water soluble than the aglycone (for instance, testosterone), and thus can more readily be transported in the aqueous circulatory system, where they can be transfered (recognizing the highly stereospecific glucuronic acid moiety) to an excretion pathway. The conjugates find their way to the kidneys for excretion in urine; the pancreas/bile ducts where they are dumped into the upper intestine; and the axils where they are excreted in apocrine and merocrine excretions (eg. sweat).

Turns out that the majority of steroid hormones are excreted this way, into the bile, where they end up feeding the enormous diversity of bugs in the upper and lower intestine. E. coli is just one of the myriad microbes there, and not even the most prominent one.

But it seems that the excretion of the hormone conjugates (and you can substitute almost any word for ‘hormone’ there, including ‘drug’, ‘toxin’, ‘metabolite’ etc) does not see the story end. Rather, the microbial populations have evolved the ability to transport these compounds selectively (in our own work, through a glucuronide transporter we call glucuronide permease, encoded by gusB locus of E. coli), where the aglycone (the steroid for instance) is cleaved off (by glucuronidase, encoded by gusA) and the sugar (glucuronic acid) metabolized by the microbe. The freed aglyone is then available for re-absorption in the gut.

Thus, thousands of compounds actually cycle through the intestine of vertebrates. Conjugated in the body, transported by circulatory system to a distal site of excretion, imported into microbial systems, cleaved to free the aglycone, which is then reabsorbed into the body. This has been called enterohepatic circulation, back when it was thought that the liver was the only site of glucuronic acid conjugation. I’ve read that as much as 65% of the circulating testosterone, for instance, has already passed through an enterohepatic circulation route.

Glucuronidation, and sulfation to a lesser extent (though this depends on species of molecule and species of macrobiont), are used on most steroids and most drugs to excrete. Hence the cleavage and re-presentation of the aglycone by the microbial populations are critical to controlling the level of these compounds.

Well these compounds include the entire range of steroids that have seminal impacts (excuse the pun) on reproduction, and reproductive fitness, including fertility, fecundity and mate choice. Estrogens, progesterone, testosterone, estradiols, all of them are excreted as glucuronides, and reabsorbed after microbial cleavage. Even the pheromones excreted from the armpits (or legpits…axils…) are generally non-aromatic. Some would say VERY non-aromatic. Perhaps better to say, they are excreted as water soluble, non-volatile compounds. It is the skin microbes that cleave the compounds to release the volatile steroids, such as androstenols, which impact on mate selection and population behaviour of the macrobiont (the big animal we see, for instance the human, mouse, fish, etc)..

Ok, so what is it about hologenomics and evolution? Well any sensible student of evolution will note that the traits that I mentioned, which are hugely impacted by steroid balance, which itself is determined (!) by the turnover of the glucuronide conjugates, are the very core traits that are key to natural selection, namely fertility, fecundity and mate choice.

Holy Cow! The evolutionarily most important traits of a mouse (or human) are encoded by bacteria!

And more importantly, by the balance of extraordinarily complex populations of bacteria in diverse settings. As anyone who has read this far (ie no one) would know, as we get better at looking for microorganisms we get much better at finding them – and it seems that the vast majority of the genomes associated with a human are non-human. Or are they? They are microbial (including eubacteria, but also protists, fungi, archae perhaps) but why are they not ‘human’?

They are causally associated with the behaviour and performance characteristics that have allowed us (or indeed any macrobiont) to persist and flourish under natural selection. So really, that means they are integral to ‘human’. In fact, I would argue they’re as ‘human’ as ‘we’ are. You see, we’re used to seeing our big sloppy nucleus and chromosomes and thinking ‘Yup, that’s the human genome; the book of life’…well, it seems that that’s only the scaffold! The real genome is what I call a hologenome. The apobiont (that would be what looks like me, if I had NO microbes associated with me) is not a holobiont (a complete organism) until the population structure makes it so. So the human genome hasn’t been sequenced, just the parts in a bag that replicates slowly. The little bags that replicate, migrate and reassort rapidly, and which clearly have mission critical functions, are only now being discovered.

And their importance is not yet appreciated. And its not just animal! All macrobionts (big multicellular organisms), including plants, are also a pastiche, an amalgam of many genomes. And so a rice plant is not really a rice plant in the absence of the microbial populations that allow it to perform in the environment.

This concept has big implications for our world view. For science. For medicine and agriculture. It is the tip of a very big iceberg. Its has been said in the last ten years by many scientists that most of the microorganisms in the world are unculturable (some would say that about humans too). Its true that as we begin our exploration of the microbiome we find vast numbers and diversity of microbes that have never been cultivated on media in the laboratory. The likelihood is that they never will. I guess that’s part of why I think they are a part of a hologenome that contributes to the overall natural selective fitness of the holobiont (and perhaps a holosystem?), and can only be thought of in that light.

So if we drop a mouse in a blender, we get (besides a visit from the site bioethics committee) more ‘bacterial’ than ‘mouse’ genomes. By a factor of nearly a hundred! This is the new wisdom. But its wrong. We definitely get more ‘microbiont’ than ‘macrobiont’ genomes. But the mouse is not the macrobiome. The mouse is the sum of these genomes – the holobiont expressing the hologenome – and it is that sum that contributes to the success of the mouse (not of course the blender mouse itself, who would not look at its role as a big success) under evolutionary selection.

And what gets very exciting about this is the following: If I were a macro-genetic-engineer (eg. teleologically speaking) I’d design most of the dull, workaday, scaffold functions to be encoded by slowly evolving, slowly replicating packets – ie nuclear genes. But I’d put the really critical, environmentally responsive functions in packets that could amplify quickly and specifically, could be traded (or not) through well crafted horizontal transfer mechanisms, which could replicate, and hence evolve, very rapidly. In short, I’d put the really cool important stuff in the microbial genomes, and leave the big macrobiont nucleus as a pretty pedestrian framework.

So are we really doing a great job yet at studying human (or mouse, or rouse – isn’t that the singular of rice?) genomics? Nope. Not until we think of the suite of genomes – the apogenomes and their aggregation into a hologenome – as the performance unit of natural selection. A nd therefore of the repository of the logic of life.

It would mean that the logic of ‘eukaryotic’ genomes will be incomplete, maybe even dead wrong, in the absence of the full appreciation of the impact of populations of microbes, which are lynchpins.

So I’m wondering, how do we set up experimental systems to prove this beyond a shadow of a doubt? How do we show that evolution works at that hologenome? Or doesn’t.

I’m rather optimistic that the glucuronide system may afford a model. And the new tools of massive high-throughput environmental sequencing will be a platform. I will be musing on this rather alot.

So let’s keep talking about hologenomics, and even its practical implications.

In a talk in South Africa at the 14th Conference of the South African Society of Biochemistry and Molecular Biology in 1997, in Grahamstown South Africa,  I called this Ecotherapeutics.

The idea that adjusting the balance and constitution of the microbial populations would have huge repercussions on disease and health. Both plant and animal. And that this could constitute the next revolution in life sciences, in which the interventions could be intrinsically ‘un-ownable’, context dependent and robust.