ERC IDEM Interdisciplinary Workshop on Holobionts

November 6-8, 2017

University of Bordeaux

Bordeaux, France

Organizers: Derek Skillings and Thomas Pradeu

Workshop Description

Microbes play a significant role in the evolution, development, health, and ecological interactions of multicellular organisms. The importance of microbial interactions is now widely recognized and at the center of many new research initiatives across the life sciences. Part of this emerging research has focused on reconceptualizing all macroorganisms as “holobionts”, defined as a host and all its microbial symbionts, with the genomic complement of all partners becoming the “hologenome”. There has been extensive debate about the importance and need for such a reconceptualization, and how it will shape research and our understanding of the living world moving forward.

This workshop is the second workshop organized within Thomas Pradeu’s ERC-funded project IDEM (“Immunity, DEvelopment, and the Microbiota: Understanding the Continuous Construction of Biological Identity”). It will bring together researchers from diverse disciplines (microbiology, evolutionary biology, ecology, pathology, neuroscience, medicine, philosophy of science) working on holobionts and host-microbe associations, in order to foster interdisciplinary communication, investigate whether there are any particular insights or fruitful general principles that emerge from investigations across fields, and hopefully stimulate collaborative research for the future.

Megan Diddie

Credit: Megan Diddie


Downloadable Copy Here

Day 1: Monday Nov 6, 2017

The fundamental issue of, how to feed the world, has to be considered in the light of the forecasted 50% human population growth by 2050 and related consequences on deforestation and atmospheric CO2 increasing. In addition we know that current agricultural practices are not sustainable (e.g. fertilizer inputs, unpredictable water availability, and reached plateau of crop yields). Agriculture will thus have to make its revolution toward a more sustainable food production. Agriculture practices and plant-breeding strategy have led to the artificialization of agrosystems, this artificialization being in part a consequence of damaged ecological functions. So what might be the road to a new green revolution ?

From the knowledge about plant-microorganisms partnership accumulated since decades, we know the tremendous importance of symbiotic interactions for plant survival and reproduction. Because of their sessile lifestyle, the most important mechanism for plant survival is its ability to buffer environmental constraints . Plant-phenotypic changes induced are not solely genetically controlled but are also based on either epigenetic marks or plant microbiota by recruitment of mutualists. Both epigenetic and microbiota interactions allow plants to rapidly adjust to environmental conditions and subsequently support their fitness. The recruitment from the microbial reservoir of a single microorganism within the plant microbiome allows the mobilisation of a number of new genes associated to this microorganism. This recruitment has to be seen as a much more efficient and dynamic process than plant-genome changes. Hence, plants can no longer be considered as standalone entities but rather as a complex assemblage of organisms forming a single entity, a plant-holobiont. This new conceptualisation of what is truly a plant induces a novel understanding of evolution. Supporting this plant-holobiont concept, new findings clearly demonstrate co-evolution processes between microbiome and plants, filtering mechanism of microbiome components core microbiome heritability and active microbiome dispersal by plants.

Beside this fundamental understanding, this new conceptualization offers opportunities for the next agriculture.

Since the last decade, recurrent summer mortalities affect the exploited oyster, Crassostrea gigas. The pathology is multifactorial since it is induced by the combination of environmental factors (water temperature, development of viral and bacterial pathogens), physiological status and genetic backgrounds of oysters (Petton et al. 2013; Dégremont et al. 2015; Petton et al. 2015). Although microbiota play a crucial role for host fitness (according to the hologenome theory; Rosenberg et al. 2007), little is known concerning the structure of microbial communities associated to oysters, and whether they are affected by stressful conditions. To tackle these issues, we analyzed the microbiota (16S rDNA-metabarcoding) at the individual scale of five oyster families that showed contrasted phenotypes in terms of susceptibility to summer mortalities. First, we described the specific diversity of microbial communities, but also their functional diversity after inference of metagenomic profiles (Aßhauer et al. 2015). Then, we tested if the structure of microbiota were linked to (i) the genetic background of oysters (specificity), (ii) environmental conditions (infectious vs. non-infectious conditions), and (iii) if the fitness in terms of susceptibility status of families was positively linked to the stability of their microbiota in various conditions.


Dégremont L, Lamy J-B, Pépin J-F, Travers M-A, Renault T. New insight for the genetic evaluation of resistance to ostreid Herpesvirus infection, a worldwide disease, in Crassostrea gigas. PLoS ONE, 10(6): e0127917. doi:10.1371/journal.pone.0127917.
Aßhauer KP, Wemheuer B, Daniel R, Meinicke P. 2015. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics, 31: 2882-2884.
Petton B, Pernet F, Robert R, Boudry P. 2013. Temperature influence on pathogen transmission and subsequent mortalities in juvenile Pacific oysters Crassostrea gigas. Aquac. Environ. Interact., 3(3): 257-273.
Petton B, Bruto M, James A, Labreuche Y, Alunno-Bruscia M-A, Leroux F. 2015. Crassostrea gigas mortality in France: the usual suspect, a herpes virus, may not be the killer in this polymicrobial opportunistic disease. Front. Microbiol.,
Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. 2007. The role of microorganisms in coral health, disease and evolution. Nat. Rev. Microbiol., 5: 355-362.


Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still matter of debate. Especially, the relative contribution of host and environment in shaping the microbial communities should be examined carefully to decipher the potential role for symbionts in host adaptation in the context of global changes. As a sessile, long-lived, cosmopolitan and environmentally sensitive organism, the reef-building coral Pocillopora damicornis is an ideal species to address these issues.


We sampled Pocillopora damicornis sensu lato colonies (that corresponded to two different mitochondrial haplotypes) from thermally contrasted regions: Djibouti, French Polynesia, New Caledonia and Taïwan. To study the associated Symbiodinium and bacterial assemblages, we used high throughput sequencing of ITS2 and 16S respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter and Acinetobacter in all samples. While Symbiodinium clade C1 was dominant in Taïwan and New Caledonia, D1 was highly abundant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e. with abundances <1%) of A1, C3, C15 and G subclades. Using redundancy analyses, we found for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures (accounting for ~70% of the total variation of such assemblages), whereas host haplotype had a much lower effect. In contrast, the constraint of host haplotype was higher than temperatures on bacterial composition. Finally, the effect of biogeography was very low for both symbiotic communities.


Because Symbiodinium assemblages were more related to thermal regimes than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature modifications might be higher than bacterial microbiota input. Moreover, the link between Symbiodinium communities and minimal temperatures confirmed the low relative fitness of clade D at lower temperatures. This is particularly interesting in the context of climate change, since corals will face increasing temperatures, as well as much frequent abnormal cold episodes.

Numerous studies have highlighted the importance of microbial communities in the environmental adaptability and evolution of macroorganisms that host them (hologenome concept of evolution). The microbiota of most metazoans is located on external surfaces such as skin, teguments or in cavities in contact with the outside like the digestive tract. Moreover, it is generally accepted that the circulatory system of healthy animals is sterile. Nevertheless, some marine invertebrates such as oysters escape this rule and possess an internal microbiota associated with the hemolymph (the blood of invertebrates) called hemo-microbiota. The existence of this hemo-microbiota constitutes a paradox since the hemolymph contains circulating cells (hemocytes) that play a key role in the anti-infectious response of the oyster. The hemolymph can thus be considered as an ecological niche in which immune cells and micro-organisms coexist. An attractive hypothesis is that the hemo-microbiota could be the result of a coevolution process leading to the “domestication” of a microbial community participating in the holobiont fitness.

In order to explore this hypothesis, we have undertaken the characterization of the entire microbial community (viruses, bacteria and protists) living in oyster’s hemolymph using global analytical approaches (metabarcoding and metagenomics). In order to determine the impact of the oyster’s genetic background on the hemo-microbiota establishment and dynamics we used genetically differentiated oyster families, produced in hatchery and bearing contrasted phenotypes, especially in respect to summer mortality syndrome (i.e. resistant and susceptible). These animals were then transplanted in natural environments (infectious and non-infectious) in order to study the impact of the environment on the composition and dynamics of the hemo-microbiota.

Preliminary results showed that the hemo-microbiota is a complex microbial community composed of viruses, bacteria and protists. Moreover, the hemo-microbiota (bacteria and protists at least) is different from the whole oyster microbiota, suggesting that the hemolymph compartment could be considered as an ecological niche. Our results showed that the environmental factors play a major control on the composition and the dynamics of the hemo-microbiota whereas the genetic background of the animals does not seem to be significant in the shaping of microbial communities. Finally, only a viral population composition was positively correlated with the susceptibility of oysters to mortalities in the natural environment.

The world of living objects possesses a hierarchical nature. Genes are nested within chromosomes, chromosomes within cells, cells within organisms, organisms within groups, etc. This hierarchical attribute of the natural world is currently considered a consequence of the fact that evolution is a process that not only selects individuals, but also leads to the emergence of higher-level individuals. These events, called evolutionary transitions in individuality (ETIs), consist of mergers of autonomously reproducing units, to the extent that, after an ETI, such units no longer reproduce independently, but jointly, as a single entity. One of the most outstanding examples of an ETI is endosymbiosis, a process during which a host engulfs a free-living bacterium and subsequently (on an evolutionary time scale) transforms it into a part of its body, thus rendering it incapable of a free-living lifestyle. Although this might seem to be a rare event, it is currently established among biologists and philosophers that endosymbiosis has had a tremendous effect on the evolutionary history of species. For instance, the mitochondrion, one of the most important organelles within cells, has an endosymbiotic origin. Due to its extraordinary role in the evolution of species, endosymbiosis has recently been the object of careful study. Specifically, its genetic aspect has been studied intensively. However, the ecological aspect of endosymbiotic events is still poorly understood, especially the question of whether endosymbiosis is a kind of parasitism or, perhaps, mutualism for the endosymbiont. In other words, figuring out whether endosymbiosis reduces or enhances the fitness of the bacterium in comparison to its free-living relatives is a hard nut to crack. Therefore, the popular approach is to argue that endosymbiosis is a kind of slavery, i.e. the endosymbiont is a slave of the host. Although metaphorically this analogy sounds interesting, it has not provided much illumination. The aim of my speech is to show that science can obtain a more precise understanding of the ecological aspects of endosymbiosis, one that transcends shallow analogies. I will do this by using an idea of fitness incommensurability which basically states that it is not always possible to compare the fitness of two objects. As a case study, I will analyse the origin of aphids’ endosymbiotic bacteria, Buchnera sp., and show that, in this symbiotic system, inquiring about the fitness benefits to the endosymbiont is not theoretically justified. As a result, I will argue that asking whether endosymbiosis is beneficial or harmful to the bacteria is not always appropriate, and thus, before we start looking for an answer to such a question, we should first determine whether, in a given symbiotic system, it makes sense to pose it at all.

It has become increasingly clear that humans have on them and in them a vast array of non-human organisms, most notably microbes. Our microbial fellow travelers are known collectively as the Human Microbiome. The scale of our microbiome is extraordinary; for example, there may be more than three times more microbial cells in and on our bodies than human cells (Ravel & al. 2014; for a more recent estimate see also, Sender & al. 2016). The complexity of our microbial selves is also astounding; we are home to hundreds of species of microbes that vary from place to place on our bodies, and from human to human. As amazing as the number of microbial cells and species in a single human may be, the gene diversity that our microbes make available to us is even more impressive. While human cells contain approximately 22,000 genes (Pertea & Salzberg 2010), our microbiome contains more than 2 million genes (Xu & Gordon 2003; Turnbaugh & al. 2007). Thus most of the genetic variation among humans tends to be microbial, and our microbiome can even be used as an individual identifier (Franzosa & al. 2015). The biological complexity of a human body, made of different sets of microbial and human cells, varying from individual to individual, poses a serious challenge to any scientist who is striving to unravel something about the fundamental nature of human organisms. To the question “What are we?”, Tom Insel replies “We are, at least from the standpoint of DNA, more microbial than humans” (Smith 2015; see also, Sleator 2010; Relman 2012; Ray 2012; Brody 2014).

But the philosophical challenges posed by the human microbiome are even more profound than this. Not only are we host to a diversity of microbial species and their genes, but there is increasing evidence that our microbial component has a vital impact on our lives as humans. Our microbes feed us through digesting foods that we cannot, they stimulate our immune system so that we can resist organisms that could cause us harm, they influence the development of our tissues when we are young, and can even alter our behavior by changing the concentration of neurochemicals in our body. Such intimate interactions between human and microbial cells can blur the lines between what is “human” and what is “microbial”, and challenge simple definitions of an “individual” human (Gilbert, Sapp, Tauber, 2013; see also, Pradeau 2016). In part because of the philosophical challenges posed by our microbial selves, we struggle with how to think about them. They have been referred to as a “second genome,” as an “additional organ.” Our microbes have been divided into “self” and “non-self” components, as if they are human tissue. The human body has been called an “ecosystem” with human and microbial “communities”, or a “superorganism” made up of distinctly different organisms united for a common cause, or a “holobiont” of host and symbionts. These different metaphors have featured prominently in portrayals of the human-microbe system in the scientific and popular media.

The fact that we cannot yet decide on how best to describe our fundamental nature has very real consequences. As with all metaphors, these different views of the human-microbe system make very different assumptions, resulting in different views regarding how our human and microbial selves interact, the nature of these selves and their origins. These different assumptions ultimately lead to very different views regarding how to best manage the human-microbe system, with important implications for human health and wellbeing. There is currently a battle being waged in the scientific and popular media regarding which of these metaphors best captures the new view of our composite selves that science has provided us (see, Blaser & al. 2013; Gordon & al. 2013; Theis & al. 2016, Rosenberg & Zilber-Rosenberg 2016). The scientists who produce those explanations tend to assume that there is one correct and complete account of the human-microbe self, represented by one particular metaphor, and that the “correct” account could emerge if we engage in comparative evaluation of alternatives. We will present – one by one – a list of such metaphors and the accounts they represent, ranging from the holobiont view, to the organ view, the immunity view, the superorganism view and, last the ecosystem view. Along with John Maynard Smith, we believe that “our choice of models, and to some extent our choice of words to describe them, is important because it affects how we think about the world” (Smith 1987, 120). For each metaphor/model, we will first highlight the premises that sustain them. Second, in the light of the current evidence, we will assess the epistemic benefits of each metaphor in helping us design and further imagine possible therapeutics. Last, we will show the epistemic limitations of each metaphor and how it constraints our understanding of human-microbe systems.

Our goal is to show that the conceptual ecology of the human-microbe system presents us with a positive example of pragmatic pluralism, analogous to that proposed by Longino (2012, 2). Longino argues the multiplicity of successful approaches to the study of human behavior (genetic, neurobiological, social-environment) must be supplemented by a form of pragmatism that judges those alternatives in relation to practical goals of action. Similarly, we believe that alternative approaches to describing the human-microbe system should be judged in relation to practical goals such as the development of novel therapies. We show that monistic frameworks (i.e. a particular metaphor, and the account that it represents) produce reductive (partial) explanations that ultimately limit research and shape therapeutic agendas in biased ways. In the light of the complexity of the human-microbe system, we conclude that only scientifically pluralist approaches can push the boundaries of our understanding of what it means to be human in the post-microbiome era.

Holobionts are sometimes understood broadly to refer to any set of symbolically interconnected organisms, sometimes more specifically to refer to a macrobe and its associated symbiotic microbes.  For several reasons I suggest it is better to use the broader definition.  Because of the varying degrees of permanence and obligatoriness of symbiotic relations, the narrower definition is itself quite vague: it is not clear which microbial associates are parts of the holobiont.  Moreover, different theoretical purposes suggest different levels of inclusiveness. Functionally important symbionts may often be best considered as environmental factors in evolutionary models, for instance.  More generally, there is no reason to think that there is a uniquely correct way of dividing living material into distinct individuals; the best such division is purpose relative, a position I refer to as promiscuous individualism.  All of this becomes much easier to understand when we move from the still prevalent substance ontology in which biology is often understood, to a more satisfactory process ontology. Processes can be multiply intertwined and interconnected in ways that are excluded by traditional substance or thing thinking.

Day 2: Tuesday Nov 7, 2017


(work co-authored with Lynn Chiu, Marie-Elise Truchetet, Thierry Schaeverbeke, Laurence Delhaes and Thomas Pradeu) Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity”, where an organism is protected by both its own immune system and components of its microbiota.

The human gastrointestinal tract is inhabited by trillions of bacteria that collectively represent up to 35,000 different species. Loss of microbial richness in the western world is correlated with metabolic dysfunction, inflammation and obesity. To what extend these missing microbes are also impacting our resistance to pathogens and fueling antibiotic use remains unknown. What is becoming clear is that individual members of the microbiota can have large effects on the host immune status. In mice, the commensal bacterium segmented filamentous bacteria, or SFB, has been shown to strongly stimulate the host immune system very early during development, leading to pathogen resistance both in and outside of the gut. As SFB is present in a wide range of vertebrates, the data suggests that a selective advantage for the presence of SFB in the microbiota to prime the host immune system may have led to the co-evolution of SFB with its host.

The human body as a landscape of ecological communities is a novel perspective shaking up how we understand health and disease. As both sites of and barriers to infection, mucosal and skin tissues reside at the immunological frontier of self/non-self where countless diseases arise. Mucosa house rich ecological communities of microbes, viruses, and protozoa, and for this reason, cutting-edge evolutionary and ecological research is needed to understand their corresponding pathogenic states. I will discuss my on-going research into the ecological communities of the female lower-reproductive tract. As a community ecologist, I am investigating the three main ‘trophic’ levels of these cervicovaginal ‘food webs’ and the interactions between them. Beginning with resources themselves, we have combined ecological mathematical modelling with cell culture data to study epithelial cell dynamics with the aim to understand how these populations prevent or clear infections, such as Human papillomaviruses and Chlamydia. I will also discuss ongoing work on the vaginal microbiome, and how resource competition and fluctuating environments can shape the diversity of these communities. Finally, I will argue for a community ecology perspective, particularly drawing from biological invasion studies, as an exciting new direction for novel infection treatment or prevention.

Day 2: Tuesday Nov 7, 2017


Eukaryotic organisms are associated with a species-specific bacterial community. This close association between bacteria and its host is beneficial for both partners and forms a complex unit termed “holobiont”. Maintaining the composition of associated bacteria is crucial for the stability and function of holobionts, but the factors contributing to this host specific bacterial colonization are poorly understood. So far research has focused on the composition and control of host associated bacteria as key components of holobionts, while viruses as an important part of holobionts have been almost neglected. Viruses are compared to bacteria the most abundant and diverse entity in the world and are responsible to cause high mortalities in bacterial populations. Recently we have shown that the freshwater polyp Hydra is not only associated with a host specific bacterial community but carries also a host specific and diverse viral community, composed of both eukaryotic and prokaryotic viruses (phages). Moreover, we found first evidence that bacteriophages play an important role in the colonization control of Hydra by simple bacteria-bacteria interaction experiments. Genome sequencing of Hydra associated bacteria revealed that more than 50% of the associated bacteria feature an intact prophage sequence in their genome. The possession of a prophage not only protects Hydra associated bacteria from superinfection, we could also demonstrate that phages of Hydra associated bacteria can be induced and are able to cross-infect different bacterial strains. Surprisingly, we observed differences of prophage reactivation when bacteria were grown separate in liquid culture compare to bacteria living in association with their host. Phages could be induced by different environmental stressors and reactivation capacity was stronger when bacteria were associated with their host compared to bacteria grown in cultures. This observation suggests that the host environment interferes with bacteria-phage interactions. Furthermore, we could show that prophages can be induced by the presence of different bacterial strains. In conclusion, being associated with a prophage can protect bacteria from phage infections by superinfection exclusion. Switching from a lysogenic to a lytic lifecycle can be advantages for the bacterium but also for the eukaryotic host. On one hand reactivated phages can serve as weapon against different bacteria and eliminates competitors on the other hand induction of prophages can function as internal regulation of host associated bacterial community. For these reasons we expect Hydra associated phages to play an important role in holobiont maintenance.

Viruses, and particularly phage that infect bacteria, are the most abundant and diverse life forms on the planet. Given their success throughout the biosphere, it is expected that phage are essential members of the animal and plant holobionts. We have shown that phage form a bacterial selective, adaptive immune system that helps protect the mucosal surfaces of animals and establish the microbiome. Additionally, phage are actively transported across epithelial layers and provide a systemic protection against bacteria. These two findings strongly suggest that phage formed the first acquired immune system and they remain important in extant animal immunology.

Day 3: Wednesday Nov 8, 2017

Developments in the life sciences, as well as in philosophy of biology, are enriching the debate surrounding the notion of the “biological individual.” Moreover, such developments have contributed to a diversity of approaches with which we may wish to track biological individuals in nature. In recent literature (Godfrey-Smith 2012; Pradeu 2016), the pursuit of a pluralistic conception of biological individuality is focused at the interface of two independently fruitful categorizations: evolution by natural selection and physiology.

Physiological individuals, sometimes referred to as “organisms,” are traditionally understood through a lens that is not embedded in evolutionary theory (Godfrey-Smith 2012; Clarke 2011; Pradeu 2010). Within the confines of medicine and “reductionist” sciences, the physiological individual is a highly integrated whole, and is recognized when constitutive parts engage in metabolic cooperation. Pradeu, for example, suggests that, in order to reveal the physiological individual, we should look to the immune system: a ubiquitous policing mechanism that designates what is tolerated by the metabolic whole.

In order to understand evolutionary individuality, we look to Lewontin’s popular formulation of three conditions: variation, heredity, and differential fitness (1970). When present, these features equip a biological entity with the potential to undergo evolution by natural selection. This suggests a biological individual is a unit of selection, a thing with the “capacity to participate in selective competitions, and to respond to selection by evolving cumulative adaptations” (Clarke 2016). Furthermore, to be such an entity, according to Godfrey-Smith, is to be a Darwinian individual—an individual that reproduces, so that it is the product and producer of a distinct lineage.

If we accept these characterizations of biological individuality, we must further accept that there are many instances where perfectly good physiological individuals are not evolutionary individuals; sophisticated host-microbial symbiont associations, referred to as holobionts, are often subject to this distinction. In cases where hosts receive their microbiome through horizontal transmission, i.e., from the environment, they are not considered to possess evolutionary individuality, as they do not produce clear parent-offspring lineages. However, hosts that receive their microbiome through vertical transmission, i.e., from the parent, are considered good evolutionary individuals, as the host-symbiont associations reflect direct lineages from parent to offspring. There are, of course, varying degrees of evolutionary individuality and one vertically transmitted host-symbiont association may exhibit a higher degree than another host-symbiont association. In any case, according to this understanding of evolutionary individuality—with the onus of heredity on reproduction—a host-symbiont association with no clear microbial parent-offspring lineages, though it may be a paradigmatic physiological individual, will not exhibit evolutionary individuality.

There are very good reasons to pursue a proper account of evolutionary individuality—reasons that have legitimate consequences for scientific practice. However, we argue that, in pursuing a proper account of evolutionary individuality, limiting the scope of heredity to reproduction (i.e., vertical transmission) fails to account for the ubiquity of horizontal transmission of adaptations in nature that play an important evolutionary role. While we certainly acknowledge the incredible significance of genetic inheritance in creating lineages acted upon by natural selection, we aim to contribute to the development of an account of evolutionary individuality that recognizes myriad extra-genetic means of inheritance as well. We contend that the Extended Evolutionary Synthesis (EES hereafter) may assist in such a development.

The EES aims to amend the Modern Synthesis through “inclusive inheritance:” a systematic recognition of extra-genetic modes of transmitting adaptations from one generation to the next (note: not necessarily from one parent to its offspring). One aspect of the EES, ecological inheritance, is of particular importance with respect to holobiont individuality. Ecological inheritance (Odling-Smee, Laland, & Feldman 2003) is the legacy of niche construction, and may be defined as a process of heredity “through which previous generations as well as current neighbors can affect organisms by altering the external environment or niche that they experience” (Lamm 2012). Through niche construction, organisms modify their own selective environments, as well as others’. Classic examples include the building of mounds, burrows, nests, and dams; the ecological artifacts of niche construction are inherited by subsequent generations. Thus, according to niche construction theory, environments are not passive selective pressures. Instead, they are actively modified by their inhabitants and transmitted downstream. Furthermore, “ecological inheritance” as a means of heredity is also variable from population to population and can exhibit differential fitness. Adaptations acquired through ecological inheritance are subject to evolution by natural selection. Thus, we argue that organisms that participate in niche construction, thereby transmitting adaptations via ecological inheritance, are eligible for exhibiting evolutionary individuality.

In order to demonstrate the application of ecological inheritance to an assessment of evolutionary individuality with respect to holobionts, we will consider several classic “problem cases,” such as the squid-Vibrio association. Each new generation of squid acquires its bacteria from bacteria in its environment, not bacteria from its parent generation. However, the squid “seed” their ocean habitats by expelling bacteria each day (Godfrey-Smith 2012). New generations acquire their microbiome horizontally in specific habitats replenished by the preceding generations. According to an account of biological individuality with the condition of heredity limited to reproduction, the squid-Vibrio association is not an evolutionary individual, as there is a multitude of microbial lineages in the environment with no guarantee of one squid’s microbial symbionts transmitting their descendants to their host’s descendants. However, if we accept the premise of inclusive inheritance from the EES, we find that categorizations of evolutionary and physiological individuality are reconciled in holobionts with the recognition of ecological inheritance. The process of “seeding” certain parts of the squid’s habitat demonstrates a modification of its selective environment—one whose artifacts are passed down to the next generation via ecological inheritance, despite an absence of clear parent-offspring lineages. Considering extra-genetic means of inheritance in problem cases such as this may help us to reveal an otherwise overlooked compatibility between physiological and evolutionary individuality in holobionts. We believe this robust conception of biological individuality—that of the extended evolutionary individual—is an appropriate extension that reflects advancements in evolutionary theory.

Formulating an evolutionary account of the purported individuality holobionts poses a challenge, which pertains to the fact that the microbial and microbial organisms that compose them often do not form clearly unified lineages (Burke et al. 2011; Moran and Sloan 2015; Douglas and Werren 2016). In their article “It’s the song, not the singer”, Doolittle and Both (2017) elaborate an innovative way to meet this challenge. Their proposal is articulated around the idea that, although holobionts themselves—which they compare to singers, or more adequately to singers bands—are not evolutionary individuals, the interaction structures manifested by their interrelated activities—which they compare to (polyphonic) songs—can be conceived as evolutionary replicators. Thus, Doolittle and Booth’s proposal intriguingly contrasts with previous biologists and philosophers of biology’s (e.g. Zilber-Rosenberg and Rosenberg 2008; De Monte and Rainey 2014; Lloyd 2017) evolutionary accounts of holobionts as either Darwiniam individuals (Godfrey-Smith 2009) or interactors (Dawkins 1976; Hull 1980; Lloyd 2012). This presentation aims to assess Doolittle and Booth’s proposal and to highlight an important challenge that it faces.

This challenge is raised by the way in which Doolittle and Booth draw on Bateson’s (1978, 2006) and Sterelny, Smith and Dickison’s (1996) extension of Hull’s notion of interactor (or Dawkin’s notion of vehicle). Bateson, Sterelny and others argue that the notions of replicator applies as nicely to the physical structures built by organisms (e.g. birds’ nests) as to genes, such that nests can as much be viewed as using birds to replicate themselves, as genes can be viewed as using the organisms that carry them to replicate themselves. Drawing on this “extended replicator” perspective, Doolittle and Booth claim that the interaction structures realized by holobionts are essentially similar to nests as conceived by Bateson and Sterelny, Smith and Dickison. In the same way as nests replicate themselves through the activities of bird interactors, holobionts’ interaction patterns replicate themselves through the interactive activities of microbial and microbial interactors (the polyphonic songs get replayed through the collective singing of singers). Doolittle and Booth thus maintain that the interaction structures manifested by holobionts, if not the holobionts themselves, are subject to natural selection, qua interactors. Just like a variation on the architecture of a nest can increase the chances that nests exhibiting the new architecture will be rebuilt by other birds (either by being easier to build or by improving the survival and reproductive abilities of the birds that tend to build it), a variation on the architecture of a holobiont’s interaction structure can increase the chances that it will be re-exhibited by other microbes (either by being easier to realize or by improving the survival and reproductive abilities of the microbes that tend to collectively realize it).

Although Doolittle and Booth’s proposal offers worthy insights by shifting the attention from the holobionts themselves to the interaction structures that they realize, I will argue that it faces a serious challenge. This challenge, I will argue, concerns an important disanalogy between the way in which bird nests and other structures built by organisms are replicated by those organisms, and the way in which interaction structures are “replicated” by holobionts. While built structures (and genes) are numerically distinct from the organisms that build them and so can properly be conceived as products of those organisms, holobionts’ interaction structures are numerically identical with the organisms that collectively realize them and so supervene on those organisms (taken collectively). This implies that the interaction structures exhibited by holobionts are involved in evolutionary processes in a way more akin to traits than to classical interactors. What Doolittle and Booth call songs, in other words, are better construed as (possibly fitness-relevant) properties collectively exhibited by singers bands, than as entities which singers bands produce and through which they perpetuate themselves.

This disanalogy, I will argue, entails that, holobionts’ interaction structures may be construed as replicators at best in analogy with memes, thus potentially raising the standard issues raised by the concept of meme, and in this case, most obviously the issue of the type of transmission mechanism by which interaction structures could copy themselves from one holobiont to another. With this challenge in mind, I will close by assessing Doolittle and Booth’s proposal in comparison to two alternatives. The first alternative is to conceive the interaction structures realized by holobionts as collective traits which can be involved in evolutionary processes only through the evolution of the holobionts which realize them. This alternative thus construes holobionts as interactors (Lloyd 2017). I will observe that, given the importance of the lateral acquisition of microbes in the case of many holobionts (Burke et al. 2011; Moran and Sloan 2015; Douglas and Werren 2016), this first alternative can be successful only if one accepts a broadened understanding of evolution by natural selection which eschews reproduction and lineage formation as necessary conditions for its occurrence (Bouchard 2010, 2011; Dussault and Bouchard 2017). The second alternative is to conceive the interaction structures of holobionts as traits of non-evolutionary individuals, such as physiological or immunological individuals (Pradeu 2010, 2012, 2016; Godfrey-Smith 2013; Booth 2014a). This alternative, I will remark, seems promising in light of the importance that the holobiont perspective seems to have in the field of medicine (Costello et al. 2012). In line with what I argue elsewhere in the context of discussions of the individuality of larger-scale ecosystems (Dussault under evaluation a b), those considerations will lead me to favor the latter alternative, and to defend the philosophical and practical importance of thinking more pluralistically about biological individuality and of incorporating the theoretical perspectives of so far neglected biological sub-disciplines.

In the last three decades, studies in microbiology exposed a new world of diverse and dynamic interactions. Through metagenomics sequencing, complex bacterial communities became visible and proved important for many biological phenomena. As a result of discovering the connection between microorganisms and organisms’ survival, the notion of the Holobiont has become prominent and has been suggested as a biological individual. This view, commonly called the Hologenome Theory, focuses on the interactions and relations between the host and its symbionts and their relevance to the host’s development and evolution. Today the holobiont is in the heart of the debate on the nature of the biological individual that is connected to the same question about the nature of the individual organism.

I address the question of how should we understand the holobiont and offer to look at this question from the perspective of interactions. The debate about the nature of the holobiont centers on two questions: where to place the boundaries of the individual and what are the criteria to distinguish inside from outside. Two main views relate to these questions: one view is that the holobiont is indeed a biological individual and its borders include the symbiotic interactions and exclude the harmful interactions (Zilber-Rosenberg and Rosenberg 2008, 2013; Bordenstein and Theis 2015; Dupré and O’Malley 2009, Lloyd 2017). The other view excludes all interactions that are not considered obligatory (loyal) and inherited thus considering the holobiont as an individual only in these special cases. All other types of interactions between host and microorganisms should be considered as an ecological community mixed of different individuals (Godfrey-Smith 2013; Douglas and Werren 2016; Skillings 2016). Thus, the former sees the holobiont as a biological individual and the latter looks and the holobiont as an ecological community.

I argue for a third way of thinking about the holobiont as an individual that is also an ecological community. By shifting the focus from the degrees of the cohesion of the host-symbiont interactions to the heterogeneity of interactions, I suggest a different perspective on interactions and their role in shaping the character and nature of the holobiont. When thinking of interactions, we are used to thinking about the interacting agents and their characteristics that determine the nature of the interactions. I argue that it’s the other way around: the nature and characteristics of the interacting agents are determined by the interactions. Thus, interactions can be contextual (in the background) to the agents’ nature and characteristics, or they can constitute the agents, meaning that the agents’ nature and characteristics are determined by their interactions. This distinction is not a binary, rather we should think of it on a dynamic scale between the agents determining the interactions, to where the interactions determine the agents. The holobiont is an individual that is composed of other smaller individuals. Thus, we have a variety of interactions between different individuals: between the host and the bacteria, between the bacterial species, strands, groups, and cells, and between holobionts.

Looking at the holobiont through interactions, I offer a different set of questions to understand the nature of the holobiont. Instead of asking about the boundaries and, of the criteria to distinguish the inside from the outside, we need to ask a different set of questions. For example, how to think about the role of interactions in shaping the nature and characteristics of the interacting agents? Is the nature of the individuals composing the holobiont determined by their interactions with each other? Also, questions such as which interactions constitute, and which are contextual to the nature of the interacting individual? What are the environmental conditions influencing the interactions? As well as, how to understand the dynamics of the inside and outside connections? Here I also make the clarification of the distinction between interactions and relations and the possibility of confusing them. Interactions require a mutual exchange between two or more agents and relations refers to the different positions of the agents to each other (such as spatial or temporal relations). I argue that this view on the variety and heterogeneity of the holobiont’s interactions could help us better understand the holobiont in its specific environment and could highlight their role in the evolutionary process.

I demonstrate my perspective on interactions through studies about bacterial molecular interactions, particularly quorum sensing. Thinking about molecular interactions, I wish to show the role of the interactions in the determination of the bacterial function. Here the bacteria change their gene expression (and sometimes their genes!) in coordination with other bacterial cells through releasing and sensing molecules (Keller & Surette, 2006). Namely, the interactions occur through molecular exchange between bacterial cells. The molecules released from the bacterial cells to a small-scale environment create modifications that accumulate to influence the mode of bacterial proliferation and function. Thus, the diverse bacterial communities interact and coordinate to determine their gene expression and functions. These interactions are not only determined by the individual bacterium; rather they are determining the nature of each of the individual bacterium.

Thus, through this perspective, we can look at the interactions between the agents inside the holobiont as well as between holobionts. In each case, the focus on the interacting agent should be through its interactions with other agents. Looking at the interactions between individuals in the holobiont can help understand the holobionts’ nature and characteristics such as its immune system (i.e., immune tolerance and discrimination). Thinking about interactions and the way they constitute the agent’s nature, and characteristic will give a better understanding of the heterogenic nature of the holobiont and its relations with its environment.

Biologists and philosophers of biology are increasingly focusing on the ecological and evolutionary dynamics of host-microbial organization, integration, and emergent function. They are pursuing inquiries about organismality, individuality, levels of selection, fidelity of host-microbial transgenerational association, the scope and persistence of host-microbial cooperation and conflict, and the scales at which ecology and evolution intertwine in the context of host-microbial symbioses. Holobionts and hologenomes are tenable constructs that provide a vocabulary and framework for contemporary dialogue on hosts in light of their ubiquitous, complex, and phenotype-influencing microbiomes. These systems level, objective constructs, in concert with the hologenome concept of evolution, have practical ramifications for the study of host biology at each level of biological analysis. In this presentation, I will first discuss current debate over the hologenome concept and attempt a synthesis. I will then provide an example of its applied value, explaining how viewing medical syndromes through a hologenomic lens can translate to enhanced research in human disease and clinical care.

Recent empirical research has shown the crucial role that microbes play in the biology of multicellular organisms. The significance of this discovery has motivated a reconceptualization of macroorganisms as holobionts, that is, as multispecies units composed of a macro host and its microbial symbionts which together form a single hologenome. There is no consensus on what kind of biological unit the holobiont constitutes given the various degrees of macro-micro integration they exhibit. Some argue that the holobiont is a multispecies individual (Dupre and O’Malley 2009; Pradeu 2011), others that it is an ecological community (Godfrey-Smith 2013; Doulgas and Werren 2016) or both (Skillings 2016). But there is a wide spread conviction that the traditional conception of macroorganisms as organisms i.e. as functionally unified self-producing, self-organizing, self-regulated entities must be abandoned. For example, Bordenstein and Their (2015) tell us that “complex multicellular eukaryotes are not and have never been autonomous organisms, but rather are biological units organized from numerous microbial symbionts and their genomes.” This conviction is partly elicited by the standard reductionist conceptions of organisms in the philosophy of biology—e.g. as interactors (Hull 1992) or physiological individuals (Predau 2010)—most of which have resolutely denied the characteristic purposive nature of organisms and its role in biological explanation. Against this conception, a recent proposal argues that evolutionary developmental biology supports the view that organisms qua organisms are agents of evolutionary change that can respond in a purposive adaptive way to their conditions of existence as affordances (Walsh 2015; Fulda 2017). In this talk I want to explore the implications of the agential conception of organisms for the debate about the nature of the holobiont. I believed this approach allows us to critically assess the conviction that the rise of the holobiont is the end of the (macro) organism.

I will argue that the anti-organism conviction behind the holobiont conception is predicated on a conflation between the causal and the explanatory relations that hold between the macro host and its micro constituent symbionts. The holobiont conception has exposed the remarkable symmetry that holds between the causal contribution of the macro-host and that of its micro constituents in the realization of characteristic macro-organismal functions. However, by conceiving the macroorganism as a mere host—i.e. a passive locus of microbial interactions—the holobiont conception blurs the distinctive asymmetric role that the host plays in the explanation of its capacities and activities, including those supported by its microbe constituents. I submit that this explanatory asymmetry, not the underlying macro-micro causal symmetry, is the relation that constitutes the macro host as an organism in the full-blooded sense of a purposive system appropriately responding to its internal and external conditions of existence. To capture this asymmetry as such we must conceive the relation between the host and the microbes as an internal relation between a macro-agent and its reciprocally constituted micro-affordances, which together form a single, coupled dynamical system. Macroorganisms may be ecosystems from a microbial level of description. But macroorganisms are adaptive agents from higher-level ecological level of description. The microbial level of description captures the causal conditions that realize the functions that are constitutive of a microorganism. But the ecological level of description captures the constitutive conditions that specify the biological goals of the host to which the microbes are subservient. I conclude that while the holobiont conception has importantly altered our understanding of the complex conditions that are causally necessary for multicellular organismal capacities to emerge, it does not support the more radical call to abandon the traditional conception of macroorganisms as organisms. Instead, the holobiont conception, understood as a causal rather than as a constitutive hypothesis, is compatible with and complemented by, a robust conception of macroorganisms as agents.


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– Dupre´ J, O’Malley MA (2009) Varieties of living things: life at the intersection of lineage and metabolism. Philos Theory Biol 1:1–25.
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The rapid development of genomic technologies (e.g., prenatal testing, personalized medicine, gene editing) is raising important questions about their ethical, legal and social implications (ELSI). Genetic research and information are perceived by many as eminently sensitive, because they reveal the biological identity and specific vulnerabilities of individuals and populations that may be exploited by third parties, such as life insurance companies or racist movements, to motivate discriminatory attitudes, discourses and practices. Over the past decades, safeguards have been developed to regulate detection, access, communication and use of genetic information (e.g., guidelines for the conduct of genetic research, non-discrimination laws), in accordance with moral principles such as respect for privacy, medical confidentiality, and the protection of human diversity and minorities.

More recently, the field of environmental epigenetics has captured the attention of philosophers, social scientists, bioethicists and the media, since it is shedding light on the underlying molecular mechanisms through which the physico-chemical (pollutants), familial (parental behavior) and sociocultural (socio-economic status) environments to which individuals are exposed during their development can have long-term effects on gene expression, and thus increase their level of susceptibility to certain diseases later in life. Even though the biological processes leading to epigenetic modification, programming and inheritance are substantially different than those leading to the occurrence and familial transmission of genetic mutations, epigenetic information has been suggested to be as ethically sensitive as genomic information (if not more). Debates have emerged, for instance, around the pitfalls of biological neoreductionism, parental blame for ‘imposing’ epigenetic risks on their child, privacy protection in epigenetics research, and the level of protection (if any) offered by existing non-discrimination laws – that had been developed in the context of genetics – against epigenetic discrimination.

By contrast, the potential ELSIs of cutting-edge gene sequencing technologies, allowing better characterization of the human microbiome and further investigations at the molecular level of its interaction with a host’s genomic profile, have remained largely unexplored. How might the concept of “holobiont” affect perceptions of human identity, subjectivity, health and disease? How ethically sensitive should we consider research data and clinical information relating to a person’s “hologenome”? Should we expect the characterization of the human microbiome to raise similar or distinct ELSIs from those attributed to genetics? What can we learn from recent debates over the ELSIs of epigenetics? In this presentation, I will draw on my experience with the growing literature on the ELSIs of epigenetics, and try to anticipate some normative implications of scientific and conceptual turns toward “hologenomics” – and some traps that we might want to avoid when doing so.

Abstract Submission and Workshop Registration

Registration for the workshop is required, but free. Please email the conference organizers. 

If you would like to participate by giving a talk, please submit an abstract or prospectus (up to 1000 words) HERE. Submissions should be prepared for blind review and uploaded by July 16, 2017.

We encourage talks that are general or conceptual in nature, aimed at a high-level audience of experts across associated fields.

Questions? Please email Derek Skillings.

Workshop Supported By

This workshop is part of the Immunity, DEvelopment and the Microbiota (IDEM) project, an ERC-funded project located at the interface of philosophy of biology and biology (ERC Grant #637647, PI: Thomas Pradeu).