ISS Blog

The purpose of this blog is to provide perspectives on and information about symbiotic systems, to increase the awareness of these symbioses in the general public, and to engage readers in conversation and dialog.  We encourage the participation of the International Symbiosis Society's membership in crafting blog posts and/or suggesting topics to cover.  If you would like to become a contributor, or would like to nominate someone, please email the vice president for the website or the webmaster.
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  • 15 Nov 2016 9:11 AM | Anonymous

    52th European Marine Biology Symposium with a special session on Marine Symbiosis in Piran, Slovenia between September 25 - 29, 2017. 52_EMBS_flyer.pdf

  • 22 Mar 2015 4:07 PM | Anonymous

    Most (if not all) organisms engage in symbioses with more than one partner. Adding an additional partner to a one-to-one symbiosis may affect this interaction in many ways, as the new partner may interact with the host, the symbiont or both, at different levels.  

    This symposium aims to bring together current empirical studies on multipartite interactions involving symbionts. In addition to talks from our invited speakers (see below), we welcome contributions focusing on the mechanisms underlying these interactions, their organismal and ecological impacts, as well as on their evolutionary consequences. We hope you will join us!

    Marcia Gonzalez Teuber is Associate Researcher at University of La Serena, Chile. She did her PhD at University of Duisburg-Essen, Germany, under the supervision of Martin Heil, and later on was a postdoctoral research fellow at the Max Planck Institute for Chemical Ecology, Germany.

    She is interested in mutualistic symbiosis between plants and other organisms, and particularly in plant endophyte/plant pathogen interactions. At the International Symbiosis Congress in Lisbon she will tell us about the exciting recent advances in our understanding of the Acacia-ant symbiosis:

    Mutualistic Pseudomyrmex ferrugineus ants on an acacia plant. The ants love nectar from the plant's extrafloral nectaries.

    Copyright: Martin Heil, CINVESTAV, Irapuata, Mexico.

    Ants can form mutualistic associations with plants. Acacia plants provide food and shelter to ants, while in return ants defend plants against the action of herbivores. The defensive service of mutualistic ants also involves, however, protection against leaf microbial pathogens. Direct mechanisms provided by ant-associated bacteria would contribute to the protective role against pathogens. Some bacterial genera, widely known for their production of antibacterial substances, were found to live in ant legs. Thus, ant bacteria seem to be an additional partner in plant-ant interactions, which can contribute significantly to ant-mediated protection from plant pathogens.


    Christoph Vorburger is Assistant Professor for Evolutionary Ecology at ETH Zürich's Institute of Integrative Biology in Switzerland. He did his PhD with Prof. Uli Reyer at the Institute of Zoology at the University of Zürich, and later on moved to Melbourne, Australia, to work as a postdoctoral research fellow with Dr. Paul Sunnucks at La Trobe University. In 2004 he returned to Zürich's Institute of Zoology then moved to ETH/EAWAG in 2009 after being awarded a Research Professorship by the Swiss National Science Foundation.

    The main focus of his research lies on insect host-parasitoid interactions. In particular, his group tries to understand the role of microbial symbionts in host-parasitoid coevolution. To address this issue, the group uses aphids (important agricultural pests), aphid parasitoids (their natural enemies) and the bacterial endosymbionts associated with aphids as a model system. Both theoretical and empirical approaches are employed to tackle how the coevolution between aphids and their parasitoids is modified by such symbionts, especially those that provide protection against parasitoids and other natural enemies.

    The black bean aphids, Aphis fabae, and the parasitoid Lysiphlebus fabarum(photo by Christoph Vorburger).

    At the International Symbiosis Congress in Lisbon Christoph Vorburger will present exciting advances in the understanding of factors that determine the dynamics of host-parasitoid coevolution mediated by symbionts, and their consequences for the composition of parasitoid communities in the field.


  • 07 Mar 2015 7:54 AM | Anonymous
    Lichens represent the most convenient examples of symbiosis because they are easy to find in almost any environment with vegetation.  Yet there is still much we don’t understand about the dynamics of the fungus-alga relationship both within an established lichen and over generations of repeated separation and remarriage.   This session aims to bring together diverse contributions from current research on the lives of lichen symbionts with or without their partners.  We hope you will participate; bring a spouse if you wish.


    Want to find out more about this and other sessions? Check out the full list here. Then, submit and abstract here.

  • 07 Mar 2015 7:49 AM | Anonymous

    In the next few posts, we will highlight some of the upcoming sessions at the International Symbiosis Society Congress in Portugal.  These posts will give you an overall sense of the Congress, the science, and the thematic organization for the event.  

  • 20 Aug 2014 2:51 PM | Anonymous

    Symbiosis: the view from 100,000 feet

    January 30, 2014

    By Mary Beth Saffo

    It is a poor creature that doesn’t know its own inhabitants.

    The Farandola

          Madeleine L’Engle,  The Wind in the Door, 1973

    Some things seem never to change (Exhibit A: the political headlines of the day, so often so depressingly similar to those of the day, week, month, year or decade  before; Exhibit B: the tragicomic constancy of human nature, its fundamentals evidently so impervious to the veneer of technology and other accoutrements of  “civilization”).  But in some spheres, things really do advance.

    Symbiosis research in the last few years is one such tangible advance. In my own academic lifetime, symbiosis, especially mutualistic symbiosis, has been transformed from a marginal, esoteric, even vaguely disreputable topic into a mainstream field of research. Its practitioners have won wide recognition for their work.  Among American biologists alone (to cite merely a few recent examples, among many), Nancy Moran’s work on bacterial-insect symbiosis was recognized in 2010 by the prestigious Japan Prize.  Thanks to Margaret McFall-Ngai, Ned Ruby and their students, the bobtail squid Euprymna and its bacterial symbionts have graced the covers of high-impact journals worldwide. Symbiosis researcher and microbiologist Jo Handelsman now has the ear of the White House, as the newly chosen Associate Director  for Science at the White House Office of Science and Technology Policy. Finally, just a few weeks ago, the American popular science magazine Science News  cited the importance of animal microbiomes as the #1 science story for 2013 (

    In the United States, federal funds for symbiosis research have (however inadequately) grown in concert with increasing recognition of the field. In recent years, there have been special funding initiatives at the National Institutes of Health to support research on host-associated microbial communities and the human microbiome,  support of microbial symbiosis research by the Dept. of Agriculture, and creation of a long-term funding program for basic research on pathogenic, parasitic and mutualistic symbiosis, “Symbiosis, Defense & Self-Recognition,” at the National Science Foundation.

    As a particularly remarkable indicator of the growing influence of symbiosis research, progress in research on beneficial symbosis has begun to significantly influence everyday agricultural and medical practice.  Once firmly committed to the principle that “the only good microbe is a dead microbe”,  both enterprises have been enlivened by the belated understanding that beneficial (as well as  parasitic/pathogenic) microbial colonists have profoundly affected the ecology and evolution of both animals and plants and by the recognition that many of those fungal, protistan and bacterial microbes are not only a normal presence in their hosts, but even essential to plant and animal health. The widely reported examples of beneficial symbiosis have also penetrated popular understanding. (Do others besides me find it easier these days to explain to non-biologist friends what they do, now that everyone seems suddenly to know about “good bacteria”, and to understand the devastating biological consequences of coral bleaching?)

    Finally, growing interest in symbiosis research is reflected in the growing complexity and sophistication of the field itself. With the extra boost of technical advances in genomics, microscopy, and related techniques (many of those advances created by symbiosis researchers themselves), symbiosis research has been stimulated and challenged by the explosive growth of data on all fronts. Recent research has created a deeper and more nuanced understanding, often revealing surprising new dimensions of long-known symbiotic interactions. New symbiotic associations are described, it seems, almost every week, confirming with ever-increasing detail the notion that symbiosis is – literally - everywhere.  So prevalent are symbiotic interactions now known to be among multicellular organisms that microbial symbiosis seems best viewed as not only an important factor in animal or plant biology, but as essentially a property of multicellular organisms.  Counting the symbiotic heritage of chloroplasts and mitochondria, one can argue (as Lynn Margulis so forcefully argued) that the symbiotic identity of eukaryotes is quite literally true.   But even considering only contemporary symbiotic interactions, the word “individual” seems an increasingly inadequate term with which to describe a given protist, plant or animal, or especially to characterize the ecological, evolutionary and physiological context of the multiple symbiotic interactions that shape fundamental aspects of their biology (for an account of bacterial symbiosis in animals, see  MJ McFall-Ngai, MG Hadfield et al., 2013: Animals in a bacterial world, an imperative for the life sciences. PNAS: 110: 3229-3236.

    Similarly, as biologists with more and more diverse backgrounds are drawn into the field, more and more symbiosis researchers are drawn into mutually beneficial, multidisciplinary conversations and collaborations as they seek novel approaches to address the complex interactions that have caught their attention.  Animal physiologists and plant ecologists find themselves learning microbiology and genomics. Medical researchers investigating the human microbiome have incorporated the principles of microbial ecology into their work. Molecular biologists have begun to appreciate the scientific importance of “non-model” organisms. Physiologists now take into account the importance of genetic variation of symbionts in assessing metabolic interactions, and consider the environmental and evolutionary context of the symbiotic interactions that they study. Evolutionary biologists discover the need to learn biochemistry; marine invertebrate zoologists with research interests in reef-building corals or siboglinid polychaetes become experts on photosynthesis and chemoautotrophy. Plant pathologists and mammalian immunologists find common molecular pathways to discuss. Each meeting of the International Symbiosis Society increases in the taxonomic diversity and disciplinary reach of its meeting agenda. Seeing the increasing cross-pollination of  disciplines in this field makes it, for me, a thrilling time to be a symbiosis researcher.


    Despite the rapid, exciting growth in the field, there remains a symptom of the youth of this discipline, and a constant frustration: a continuing lack of clarity  about the definition of symbiosis.  Remarkably, 135 years after de Bary’s 1879 definition of symbiosis as “the living together” of two or more species (that is, an intimate inter-species interaction, regardless of the outcome of that interaction), there is still inconsistency in usage of “symbiosis”,  not only  in the popular press  but also even among the most distinguished researchers in the field. Is there any other example of a scientific discipline where even specialists in the field do not agree on what the field means? Perhaps most frustrating is the tendency for many researchers to pay lip service to deBary’s definition, while in practice, restricting  “symbiosis” implicitly to mean only “mutualistic symbiosis” in speaking and writing about their own research (see Saffo, M.B. 1993. Coming to terms with a field: words and concepts in symbiosis. Symbiosis 14: 17-31).

    This chronic problem – the  usage of  “symbiosis” in a way that suggests “beneficial symbiosis” alone -- is not just a semantic one.  It matters because it affects the way we think. Such restricted usage restricts our thinking, with at least two unfortunate consequences:

    a.     First, using “symbiosis” to imply only beneficial interactions deprives biologists of the most pragmatic use of the broader definition: as a vehicle to describe the many symbiotic interactions – arguably most of the symbiotic interactions thus far described -- where the outcome of the interaction is in fact unknown for one or more of the interacting partners or too complex or too variable to be neatly pigeonholed into a simple definition of “harmful” or “mutually beneficial”. It also blinds us to the complexities of mutualistic symbioses themselves, which can entail significant costs as well as benefits to both partners, and embed antagonistic elements within its overall benign veneer.

    b.     Second, restrictive word usage inhibits fresh thinking about other aspects of symbiotic interactions, especially about the many biological challenges of interspecies intimacy shared by all symbioses (particularly endosymbioses) regardless of fitness outcome. With a broader perspective of symbiosis, we are likely to ask additional questions about the evolution of symbiotic interactions, beyond that of interaction outcome. We are better poised to discover, and to appreciate the significance of, intriguing similarities in infection mechanisms between mutualistic  and pathogenic bacteria, fungi, and protists; the provocative interactions between immune defenses and mutualistic endosymbionts; the close genomic relatedness between many pathogenic and mutualistic symbionts; the common features of pathogenic and beneficial intracellular symbiosis;  the mechanisms and long-term evolutionary persistence of parasitic and mutualistic horizontally-transmitted symbioses, despite once-a-generation opportunities to “divorce”; and the evidence for variability of interaction outcomes depending on the environmental context of the symbiosis in question.


    All parasitic, mutualistic and commensal symbioses, especially endosymbioses, share a basic underlying question: how and why do symbiotic interactions exist at all? We know that symbiosis is essentially everywhere, so pervasive that it is virtually a universal feature of life. Yet symbiosis exists in the face of another universal feature of life: the ability of every organism to distinguish self from non-self, an ability almost always linked to mechanisms which exclude, excise, encapsulate or destroy foreign cells and foreign DNA. How can symbiotic associations exist in the face of the universality of recognition of, and defenses against, non-self? An explanation along the lines of “immune defenses aren’t perfect” seems a little thin, even as an explanation for the success of physiologically clever pathogens and parasites, when even the just-barely-metazoan sponges display exquisitely tuned allorecognition systems (WEG Muller and IM Muller, 2003; Integrative Comparative Biology 43: 281-292), ctenophores show evidence of an induced immune response (S. Bolte et al., 2013. Biol. Lett. 9: 20130864), and plant immune defenses rival mammalian immunity in their head-spinning complexity and sophistication (JDG Jones and JL Dangl, 2006. Nature 444: 323-329; JL Dangl, DM Horvath, and BJ Staskawicz, 2013.  Science 341: 746-751). Similarly, explaining the presence of (allegedly) beneficial symbionts solely by noting the selective benefits of such symbiosis for their host is equally unsatisfactory, as such explanations dodge the crucial mechanistic question as to how such symbionts can evade or survive their host’s immune defenses to colonize their hosts in the first place. For me, a resolution of this paradox lies in the notion that symbiotic interactions are made possible precisely because of the universality of organismal mechanisms for preservation of integrity of self (M.B. Saffo. Complexity, variability and change in symbiotic associations. Family Systems. 2001.6: 3-19). With increasing attention to the role of immune systems in shaping gut microbiomes and other symbiotic communities, current research seems likely to generate richly informative and provocative answers to this fundamental question.

    Mary Beth Saffo recently completed a three-year rotation as Program Director in the Symbiosis, Defense & Self-Recognition Program of the US National Science Foundation. Although part of this essay was written during her stint as Program Director, the views in this essay do not represent the official views of NSF. She is currently at work on a book for University of Chicago Press, “Lives of the Infectious and the Infected: perspectives on mutualistic and parasitic endosymbiosis”, and welcomes research updates and articles from her colleagues. Email: or

  • 20 Aug 2014 12:44 PM | Anonymous

    by Elisha Wood Charlson and Nicole Webster

    When you step back and look at the field of symbiosis research (see Mary Beth Saffo’s recent blog post for the ISS), one can see that the rapid growth and appreciation of our field is staggering. Perhaps we do not rival other research fields with respect to number of scientists per unit effort, but scientists and non-scientists alike are finally beginning to comprehend the true magnitude and importance of microbial symbiosis.  A Grand Challenge Article (GCA) for the recently established journal Frontiers in Microbial Symbiosis highlighted how we are increasingly seeing the terms ‘holobiont’, ‘metaorganism’ and ‘microbiome’ used by researchers from a range of scientific disciplines. However, despite this recent progress in appreciating the importance and ubiquity of microbial symbioses, many scientists still tend to view symbiotic partners as separate individuals, thereby limiting our ability to assess interactive mechanisms (including synergism and pathogenesis) within these systems.  As researchers we desperately need to overcome this perception of individualism to truly understand the ecology and evolution of microbial symbioses.  And whilst Mary Beth highlighted the need for clarity and consistency regarding the definition of “symbiosis,” it is equally important to recognize that the concept of symbiosis needs to remain fluid. The subcategories of “symbiosis” (pathogenic, mutualistic and commensal) are ultimately just idealized interaction states; whereas the actualized state may wander across these defined boundaries depending on evolutionary processes, changes in environmental conditions and/or health state of the host/symbiont. For example, the cnidarian-algal mutualism, a partnership where most of the symbiont transmission is horizontal (and should therefore theoretically favour parasitism) highlights the complexity of symbiotic interactions. A study by Sachs and Wilcox (2006) used sequential horizontal transmission to demonstrate that after only a few forced horizontal transmissions, the Cassiopea–Symbiodinium partnership began to display parasitic rather than mutualistic characteristics.

    The blurred lines between “mutualism” and “parasitism” get really interesting when we start to include the “new symbiont on the block” into our research questions – Viruses. Viruses are thought of as the nemesis to all cellular life since cells were formed, and there are many interesting theories with regards to the origin of cells and the role of viruses in the tree of life Moreira and Lopez-Garcia (2009) that are pertinent to symbiosis research , but how might viruses contribute to the future of symbiosis research?[1] As coral and sponge ecologists from the Australian Institute of Marine Science, we have focused on microbial symbioses in corals and sponges for over a decade.  However, through recent grants awarded by the Australian Research Council we are now starting to explore the potential role of viruses in coral and sponge symbioses including an assessment of whether they can enhance the adaptive capacity of their hosts during a rapidly changing climate. Whilst there are noticeably less virologists than bacteriologists in the field of environmental symbiosis, this may all be about to change.  Attendance at a Symbiomics meeting in Valencia, Spain in February this year was noteworthy for just how many symbiosis researchers were discussing their plans to embark on research to understand the role of viruses in their own model symbiotic systems. Exciting times of discovery!

    Viruses as the new frontier for symbiosis research?

    In many ways, viruses may be the ultimate symbiont. They have been around since cellular life began. They are basically dormant, inert particles until they interact with an appropriate host where they spring to “life.” And some viruses, under the right conditions, confer adaptive benefit to their host cell, such as resistance to other viruses, niche expansion, and production of novel toxins for defence. In addition, viruses are veteran drivers of evolution, in a literal sense as agents of horizontal gene transfer, to a more biological sense by acting as a strong selection pressure for immunity. These little genetic reservoirs may also be a source of hope for rapid adaptation under the current projections of climate change.

    As symbiosis researchers that have adopted viruses into our lives, we need to express a sense of caution to fellow symbiosis colleagues considering the jump. The data is not easy to come by, and the results are often mired in concerns about host contamination and determining what it is you are actually observing.  Are we describing the whole viral assemblage or just those easy to “see” by standard techniques, such as flow cytometry, epifluroescent microscopy, or even extraction kits that were all designed to work with dsDNA from cellular organisms. In addition, viruses are not like anything you have ever worked with before. It may be relatively easy to switch from one type of invertebrate or plant symbiosis to another, but viruses require an entirely different skillset to work with. We recommend getting a nice cup of tea and settling in with the Marine Aquatic Viral Ecology (MAVE, ASLO publishing 2010) chapters, as they outline basic steps used to work with environmental viruses. Finally, find a new friend. The research community working with environmental viruses is enthusiastic and generally very open to collaboration and new ideas.

    This may all sound a bit daunting but think about the novelty, the joy of exploring the unexplored. In many ways, that is why we were drawn to the field of symbiosis to begin with. So, are we ready for the new symbiont on the block?.

    [1] Have a read through this initial paper, but don’t miss the 7 correspondence articles that follow!


    Nicole Webster is well known as a sponge microbial ecologist, but she has recently ventured into the world of viruses with the award from the Australian Research Council. Her Future Fellowship looks at the role of viruses in sponge holobiont communities. (Add anything?) Nicole is a Senior Research Scientist at the Australian Institute of Marine Science and chief specialty editor for Frontiers in Microbial Symbiosis. Elisha Wood-Charlson came to work on viruses as symbionts in corals by initially working on the onset of coral-dinoflagellate symbioses, then open ocean marine cyanophages. The worlds collided when she took at postdoc at AIMS to work on another Future Fellowship grant (awarded to Madeleine van Oppen) to look at the potential role of viruses in corals - pathogens or mutualists? Together, Nicole and Elisha make up part of AIMS's " Team Virus", working to promote the recognition and consideration of viruses in all aspects of symbiosis and climate change research. Contact us at:

  • 12 Mar 2014 8:58 AM | Anonymous


    by Nicole Gerardo (lab link)

    For the past year and a half, I have had the fortune to learn from a great teacher. She did not teach me the difference between adaptive and innate immunity, or how to do a headstand in yoga, or how to make a soufflé. She instead reminded me of the beauty of our discipline, and she inspired me to expect more from my students.

    Over the course of the last four semesters at Emory University in Atlanta, Georgia, I have worked alongside Diane Kempler, who teaches ceramics to undergraduate students. We began a collaborative effort to incorporate scientific concepts into the ceramics studio. In the first semester, I taught the students about basic concepts of symbiosis and exposed them to images of many of the natural systems that symbiosis researchers eventually begin to consider routine. Yes, it’s true that squid actually glow. Yes, it’s true that fungus can infect an ant’s brain. Yes, it’s true that there are solar-powered sea slugs. Wait, what is routine about any of this? What we study, in the eyes of art students, business majors and undergraduates who thought ceramics would be an “easy A” can inspire awe. Students have made pieces based on coral symbioses, where the dinoflagellate symbionts are now on the outside, remaining hidden no more. They have made totem poles of aphids and bacteria and lichens -- so, so many lichens. It turns out ceramics is a perfect medium for making the delicate lichen layers. Who knew? I certainly did not.

    We have expanded the breadth of the scientific focus to include partnerships between student artists and scientists on campus. Other assignments have focused on microscopic images, with students starting in the introductory biology laboratory and ending up in the studio near the kiln. For the final assignment of this semester, we are delving into public art. Students are making pieces to be placed in a local community garden. The assignment is to make the unseen world of the garden seen to the many garden visitors who walk unknowingly amongst a complex microscopic world.

    Assessment of whether the students are learning science has been difficult as they are coming into this experience with extremely diverse knowledge bases. Many students, however, have had the opportunity to appreciate some aspect of the natural world that they had not been exposed to before. My hope is that they also appreciate the practice of science that underlies that knowledge.

    Unfortunately, Emory University is closing its Visual Arts Department, making this a piece of reflection rather than a starting point. However, there is much to take away from this and to build upon. Recently, Diane herself has created a whole series of pieces inspired by cordyceps fungi. In my mind, these pieces represent one of the finest legacies of this experience. And, I have changed my own teaching in the biology classroom in subtle ways. Diane entices her students, many of whom have never touched clay before, to work hard, to learn and to create works of art. These students, when pushed, find abilities that they did not know they had. I can strive to do the same for my students as well.  

    Above and left, living lichens; Above and right, artwork by Emily Pardue incorporating lichens.


    Nicole Gerardo is an Assistant Professor in the Department of Biology at Emory University. Her research focuses on the evolutionary ecology of interactions between microbes and their insect hosts.

  • 07 Oct 2013 3:39 PM | Anonymous

    by Seth Bordenstein (lab and blog)


    View From 32,000 Feet

    Darwin and the 20th century pioneers of biology would have been astonished to see the countless roles that microbes play in shaping eukaryotic life. From the origins of eukaryotic cells to pharmaceutical products, Life as we know it would be unrecognizable without microbes. Integrating microbes into all facets of the life sciences today is a vision that is not only driven by exciting questions at the perimeters of the biological disciplines, but one that seems more achievable today than ever before, at least from a our vantage point within the symbiosis field.

    Let us briefly look backwards in order to look forwards. The fusion of evolutionary biology and Mendelian genetics spurred a modern synthesis in which the biologist sees the world through a refined set of filters: the genome is stably inherited, subject to natural selection, and defines who we are as individuals and how species arise from descent with genetic modification. Yet there is a transformation occurring today in our capacity to understand who we are beyond our nuclear genes. Indeed, biologists take the archetypal examples of mitochondria, chloroplasts, and endosymbionts for granted, but the science of the microbiome has emerged in the last decade to massively widen the recognition, if not scope, of Life's dependency on microbes. One luminary in our field lost to history, Prof. Ivan E. Wallin, remarked in 1927:

    "It is a rather startling proposal that bacteria, the organisms which are popularly associated with disease, may represent the fundamental causative factor in the origin of species"

    Below I will summarize our most recent foray into speciation by symbiosis. This post is far too small to give a full and fair treatment of the topic, and I apologize to my colleagues in advance for not citing their work.

    From Many Genes and Microbes, One Species

    Approaches to studying the gut microbiome in animals have largely been diet- and disease-centric. Relatively little is known about the comparative structure and evolution of bacterial communities among closely-related host species, but this knowledge gap is starting to change. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the host-associated microbial communities parallel the divergence of the host's nuclear genes? (Brucker and Bordenstein 2012a link) We hypothesized that if host phylogenetic relationships, in part, structure gut microbial communities, then related species of animals reared on the same diet will not acquire the same microbiome, but instead host species-specific communities of microbes. We discovered that the gut microbiome was indeed different between closely related species of insects reared on the same diet, and the constituents and composition of the bacterial communities in each species changed in parallel with the genomic relationships of the host species (Brucker & Bordenstein 2012b, link) - a pattern we have since termed "phylosymbiosis" (Brucker and Bordenstein 2013 link, and Figure 1 below).The significance of phylosymbiosis is also evident in primates (Ochman et al. 2010, link) and hydra (Franzenburg et al. 2013, link).

    Figure 1.Phylosymbiosis. Like phylogenomics, phylosymbiosis is a total microbiome metric that retains an ancestral signal of the host's evolution. (a) The central prediction is that divergence in host genes is positively correlated with differentiation of the microbiome. (b) Parallel dendrograms between the host phylogeny and the microbiome relationships is one test of phylosymbiosis (c) Schematic of a real data example from our model study system.

    We recently tested the hypothesis that the gut microbiome assists animal speciation, even in the well-studied Nasonia genus where nuclear speciation QTLs were genetically mapped to chromosomes. First, we demonstrated that gut bacterial diversity in F2 hybrids goes markedly awry in comparison to that of pure species controls (Bordenstein and Brucker 2013, Science, link). Second, curing this altered gut microbiota eliminated hybrid lethality (Figure 2), the misexpression of immune genes associated with hybrid lethality, and marker ratio distortions away from Mendelian inheritance for speciation QTLs. Finally, we recapitulated hybrid lethality in germ-free hybrids by orally inoculating them with resident strains of the dominant bacteria within species. Thus, in a series of "gain" and "loss" microbiome experiments, we demonstrated that reproductive isolation in this genus is not dependent solely on genetic divergence, but also on the interactions between the host genome and gut microbiome. It is enticing to speculate that this phenomenon will be common in animals since they all have a gut microbiome that is increasingly seen to affect numerous aspects of fitness. Time and experimentation will tell. A simple experiment would be to test if hybrid inviability can be cured in diverse germ-free systems.

    Speciation by symbiosis has been subject to healthy skepticism. For example, one interpretation of the data above is that the gut microbiome is just an environmentally conferred stress on the wasps’ fitness, and hybrids are hyper-susceptible to this stress. So the presumed stress of microbiome colonization on hybrid wasps can be compared to a predator eating hybrids more than the vigorous parentals that escape predator detection. However, in this argument, the microbiome is seen as purely extrinsic to the host. Like all metazoans, Nasonia's gut microbiome is inevitable and plays a large beneficial role in host fitness - survival and reproduction. Thus, removal or suppression of the microbiome in Nasonia is quite maladaptive, causing a ~15% decrease in survival from egg to pupal stages (Brucker and Bordenstein, 2012, link) and delayed development into adulthood by two to three days. Thus, in contrast to an extrinsic predator, the narrative here is that microbiome is essential for within-species fitness. Similar to a beneficial set of genes, the microbiome is also causal to reproductive isolation in hybrids, much like the way a classical geneticist studies speciation genes that are adaptive within species but break down in hybrids.

    Figure 2. Hybrid lethality in Nasonia. Top: Non-hybrid 3rd instar larva. Bottom: Hybrid 3rd instar larva that is melanized and dead.

    The Gravity of Symbiosis

    The term "holobiont" is used to define the host and its collection of beneficial symbionts. It does not differentiate intracellular or extracellular symbionts as it is a lens to view the individual as an engineered collection of organisms. Therefore, the term "hologenome" naturally follows as a definition of the total genetic material of the holobiont. The hologenome emphasizes that the animal’s genome, mitochondria and beneficial microbiome are an aggregate of genes that together form a unit of natural selection (Zilber-Rosenberg and Rosenberg, 2008, link). To be historically accurate, the term hologenome was originally and independently proposed in 1994 by Richard Jefferson in a seminar on PCR technology (YouTube link). The evidence motivating these terms spans the essential roles of the microbiome in eukaryotic fitness (McFall-Ngai et al, 2013, link), including digestion, immunity, olfaction, organ and neuronal development, etc.

    However, the hologenome concept is controversial, perhaps more so than the holobiont. These terms are gaining attention but are still rather new to biology and should be subject to questions. Some view the individual solely through the refined filter of the nuclear genome. In this case, the microbiome is purely extrinsic to the host animal and therefore unable to co-evolve sensu stricto with the host genome. In order for the microbiome to change in parallel with the host genome, stability of the two genomic units by vertical transmission or host selectivity in microbiome community structure is required. Current evidence specifies multiple paths for stability that we must delve much further into.  For example, maternal microbial transmission may be universal in animals for some fraction of the microbiome (Funkhouser and Bordenstein, 2013, link) and specificity provided by the host immune system can further cement the essential foundation for host-microbiome stability and co-cladogenesis (as evident in phylosymbiosis).

    In Nasonia, the phylosymbiotic associations of parental host genes and microbes are both required for fitness within species, but are in negative epistasis in hybrids undefined comparable to nuclear-nuclear and cytonuclear gene interactions that function normally within species but cause hybrid incompatibilities.  In this light, the discovery of the phylosymbiotic gut microbiome can be understood as part of a co-adapted unit, which functions normally within species, but breaks down in hybrids between species.

    Of particular relevance is that the vital fitness traits conferred by the gut microbiome within species blurs the lines between what biologists conventionally define as the environment or the organism. And perhaps this point is the most salient. Intrinsic and extrinsic views of the microbiome are largely semantic filters placed on our definition of the individual. Nature may not care about this linguistic argument. What matters is stability of the associations, no matter if we define them as intrinsic genome-by-genome or extrinsic gene-by-environment interactions. Today, it is convention that mitochondria represent anciently acquired bacteria that have a fully integrated partnership with the animal genome. The continuum of symbiosis stretches from these obligate relationships of endosymbionts to the host farming the microbiome.

    I extend my thanks to the ISS board for asking me to write this blog post and for you reading it. I look forward to reading your future posts and extending this social medium to the symbiosis community.

    Warmest regards,



    Dr. Seth Bordenstein is an invited blogger for the International Symbiosis Society.  He is an Associate Professor at Vanderbilt University in the Departments of Biological Sciences and Pathology, Microbiology, and Immunology, where he studies the interactions between viruses, bacteria, and their animal hosts. 

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