Holobiont

The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections.

It has become increasingly clear that there is a vast array of microorganisms on and in the human body, known collectively as the human microbiome. Our microbiomes are extraordinarily complex, and this complexity has been linked to human health and well-being. Given the complexity and importance of our microbiomes, we struggle with how to think about them. There is a long list of competing metaphors that we use to refer to our microbiomes, including as an "organ" containing our "second genome," as a "symbiont" in the human "holobiont," and as an ecological "community" in the human "ecosystem," among others. Each of these makes different assumptions about the fundamental biology of the human-microbe system, with important implications for how we choose to study microbiomes, and the therapies we envision for correcting microbiome-linked disorders. We believe that it is time to move beyond metaphors, and we propose a scientifically pluralist approach that focuses on characterizing fundamental biological properties of microbiomes such as heritability, transmission mode, rates of dispersal rates, and strength of local selection. Such an approach will allow us to break out of the confines of narrow conceptual frameworks, and to guide the exploration of our complexity as chimeric beings.

Symbiosis

Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines the philosophical assumptions that underlie recent proposal of the hologenome concept of evolution, and traces those debates back in time to their historical origins, to the moment when the connection between the topics of symbiosis and biological individuality first came to the attention of biologists. The review is divided in two parts. The first part explores the historical origins of the connection between the notion of symbiosis and the concept of biological individuality, and emphasizes the role of A. de Bary, R. Pound, A. Schneider and C. Merezhkowsky in framing the debate. The second part examines the hologenome concept of evolution and explores four parallelisms between contemporary debates and the debates presented in the first part of the essay, arguing that the different debates raised by the hologenome concept were already present in the literature. I suggest that the novelty of the hologenome concept of evolution lies in the wider appreciation of the importance of symbiosis for maintaining life on Earth as we know it. Finally, I conclude by suggesting the importance of exploring the connections among contemporary biology, philosophy of biology and history of biology in order to gain a better understanding of contemporary biology.
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It is now widely accepted that microorganisms play many important roles in the lives of plants and animals. Every macroorganism has been shaped in some way by microorganisms. The recognition of the ubiquity and importance of microorganisms has led some to argue for a revolution in how we understand biological individuality and the primary units of natural selection. The term " holobiont " was introduced as a name for the biological unit made up by a host and all of its associated microorganisms, and much of this new debate about biological individuality has focused on whether holobionts are integrated individuals or communities. In this paper, I show how parts of the holobiont can span both characterizations. I argue that most holobionts share more affinities with communities than they do with organisms, and that, except for maybe in rare cases, holobionts do not meet the criteria for being organisms, evolutionary individuals, or units of selection.

This short essay can be read as an introduction of the US-American biologist Lynn Margulis (1938-2011) and her groundbreaking work in symbiosis research, endosymbiosis and Gaia theory. Focus is laid on her definition and use of the term 'holobiont'.

According to a shared functionalist view in philosophy of mind, a cognitive system, and cognitive function thereof, is based on the components of the organism it is realized by which, indeed, play a causal role in regulating our cognitive processes. This led philosophers to suggest also that, thus, cognition could be seen as an extended process, whose vehicle can extend not only outside the brain but also beyond bodily boundaries, on different kinds of devices. This is what we call the ‘Externally Extended Cognition Thesis.’ This notion has generated a lively debate. Here, we offer a novel notion of extended cognition, according to which cognition can be seen as being realized (and expanded) outside the brain, but still inside the body. This is what we call the ‘Internally Extended Cognition Thesis’. Not only our thesis but also our approach while defending it is innovative. The argument we offer is supported by recent empirical findings in the life sciences and biomedicine, which s...

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INTRODUCTION.
  1. Living organisms can modify the limits of the habitability zone of an star by interacting with the abiotic environment of a planet in a region called the habitable zone of inhabited planets (inHZ) [1].
  2. These organisms can be considered as biological communities which behave as a single entity (holobiont) [2].
  3. Calcium is the main messenger that links physiological rhythms in microorganisms with the ecological cycles of energy of their environment [3,4]. 
  We have proposed that the response to astrophysical electromagnetism (light, heat, plasma) has an important role in the evolution of sensory receptors [5]. Calcium ions have two electric charges and it is an intracellular messenger that respond to electromagnetic fields and to the cellular membrane.  Here we extend previous computational studies [1][5] showing that calcium can play a role in climate regulation and habitability in a planet (levels of CO2, calcium carbonate, temperature and pH). We focus in the extracellular dynamics of calcium for holobionts.
 
  MATERIALS AND METHODS.
  1. We search of bibliographic resources using filters in academic data bases.
  2. We use of mathematical analogies and simple physical models (circuits, mechanical dynamical models [2]).
  3. We explore new concepts linking holobionts and rhythms in astrobiology.
 
  CONCLUSIONS.
  1. Fluctuations in the calcium levels, generated by holobionts, and coupled with cycles of rotation (circadian) and translation (circanuales) of a planet, can be able to form oscillations in habitability. 
  2. It is evolutionary advantageous for microorganisms to incorporate these rhythms in order to predict the calcium-dependent favorable phases for exploration/activation vs. the states of resting.

REFERENCES

[1] Zuluaga, J. I., Salazar, J. F., Cuartas-Restrepo, P., and Poveda, G.: The Habitable Zone of Inhabited Planets, Biogeosciences Discuss., 11, 8443-8483, doi:10.5194/bgd-11-8443-2014, 2014.

[2] Zilber-Rosenberg, I., and Rosenberg, E. (2008). Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32, 723–735. doi: 10.1111/j.1574-6976.2008.00123

[3] Anbu P, Kang CH, Shin YJ, So JS. (2016) Formations of calcium carbonate minerals by bacteria and its multiple applications. Springerplus.Mar 1;5:250. doi: 10.1186/s40064-016-1869-2. eCollection 2016.

[4] Williams R.J.P. (2006) The evolution of calcium biochemistry. Biochimicaet BiophysicaActa1763 1139–1146

[5]Gomez JF and Restrepo (2012). Electromagnetism and magnetoreception: Detection of astrophysical events by organisms and robots. 2nd international Congress in astrobiology. Medellin, Planetario Municipal.

NOTE (26/02/2017): Accepted Abstract #5 by the Academic Committee of the 3rd International Congress of Astrobiology

Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.

Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.

We review recent work at the interface of economic game theory and evolutionary biology that provides new insights into the evolution of partner choice, host sanctions, partner fidelity feedback, and public goods. (1) The theory of games with asymmetric information shows that the right incentives allow hosts to screen-out parasites and screen-in mutualists, explaining successful partner choice in the absence of signalling. Applications range from ant-plants to microbiomes. (2) Contract theory distinguishes two longstanding but weakly differentiated explanations of host response to cheaters: host sanctions and partner fidelity feedback. Host traits that selectively punish misbehaving symbionts are parsimoniously interpreted as pre-adaptations. Yucca-moth and legume-rhizobia mutualisms are argued to be examples of partner fidelity feedback. (3) The theory of public goods shows that cooperation in multi-player interactions can evolve in the absence of assortment, in one-shot social dilemmas among non-kin. Applications include alarm calls in vertebrates and exoenzymes in microbes.

From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasingappreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forminga metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms.Research on host–microbe interactions has become an emerging cross-disciplinary field. In both vertebrates andinvertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, itsdisturbance can contribute to the development of disease states. However, the molecular and cellular me-chanisms controlling the interactions within a metaorganism are poorly understood and many key interactionsbetween the associated organisms remain unknown. In this perspective article, we outline some of the issues ininterspecies interactions and in particular address the question of how metaorganisms react and adapt to inputsfrom extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.

According to a shared functionalist view in philosophy of mind, a cognitive system, and cognitive function thereof, is based on the components of the organism it is realized by which, indeed, play a causal role in regulating our cognitive processes. This led philosophers to suggest also that, thus, cognition could be seen as an extended process, whose vehicle can extend not only outside the brain but also beyond bodily boundaries, on different kinds of devices. This is what we call the 'Externally Extended Cognition Thesis.' This notion has generated a lively debate. Here, we offer a novel notion of extended cognition, according to which cognition can be seen as being realized (and expanded) outside the brain, but still inside the body. This is what we call the 'Internally Extended Cognition Thesis'. Not only our thesis but also our approach while defending it is innovative. The argument we offer is supported by recent empirical findings in the life sciences and biomedicine, which suggest that the gut microbiota's activity has a functional role in regulating our cognitive processes and behaviors. In doing so, we embrace the holobiont-perspective, according to which it is possible to claim that what we call biological individuals are not autonomous entities with clear boundaries, but should rather be seen as networks of multiple interactions among species. Thus, by analyzing different sets of evidence in light of the holobiont-perspective, we argue that the gut microbiota could be seen as a component of our organism. On the basis of the philosophical interpretation of this evidence, however, we also suggest that there are no impediments standing the way of considering the gut microbiota also as a functional extension of our cognitive system. If so, this amounts to extending cognition out of 'our skull', though still confining it within 'our body': to 'our gut'. This is an instance of the 'Internally Extended Cognition Thesis,' whose benefits for an original (biologically informed) theory of extended cognition are discussed.

Dietary changes can alter the human microbiome with potential detrimental consequences for health. Given that environment, health, and evolution are interconnected, we ask: Could diet-driven microbiome perturbations have consequences that extend beyond their immediate impact on human health? We address this question in the context of the urgent health challenges posed by global climate change. Drawing on recent studies, we propose that not only can diet-driven microbiome changes lead to dysbiosis, they can also shape life-history traits and fuel human evolution. We posit that dietary shifts prompt mismatched microbiome-host genetics configurations that modulate human longevity and reproductive success. These mismatches can also induce a heritable intra-holobiont stress response, which encourages the holobiont to re-establish equilibrium within the changed nutritional environment. Thus, while mismatches between climate change-related genetic and epigenetic configurations within the holobiont increase the risk and severity of diseases, they may also affect life-history traits and facilitate adaptive responses. These propositions form a framework that can help systematize and address climate-related dietary challenges for policy and health interventions.

Our digestive identity; we are what we digest, not what we eat!
Our digestion plays a distinctive role in our identity, our gut biome affects our total health and one could ask whether special diets like vegan or vegetarian influence more than an individual’s health, do they influence the way we deal with challenges, our initiative, ambition, agency and maybe point to an emerging social paradigm shift? The millennial generation seems to be different from the baby boomers in this respect and the link between autism and biome dysfunction is a case in point.
Identity is quite a fashionable term these days, used in politics and the media a lot. Usually it refers to personal identity, that what one is in totality, with the personality as the relational expression of it. But we also see it used in social identity, in identification and digital identity, while the mathematical identity A=B means an equality relation.
Here I introduce yet another identity type, the digestive identity pointing at a deeper level of who we are, in relation to what we eat and digest and including our biome, the life-forms that we host in our guts and skin. Those are in reality an inseparable part of who we are. Therapy and healing turns more and more to probiotics and biome transplants to cure all kinds of diseases.
Our food digestion and probiotics intake defines us, also in a social sense and this means that a different diet may lead to a different social attitude, and notably vegetarian and vegan diets are of interest here. Is the lack of ambition in millennials (often vegan) due to their diet, is the difference between Hindu and Muslim populations because of their diet?

From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host-microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme ...

Under natural conditions, plants are always associated with a well-orchestrated community of microbes—the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chlor...

From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host-microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme ...

‘White syndrome’ is considered to be the most prevalent coral disease on the Great Barrier Reef, characterised by rapid rates of lesion progression and high levels of colony mortality. This study investigated the production and translocation of photoassimilates towards white syndrome lesions (WSLs) and artificially inflicted lesions in healthy and diseased colonies of tabular Acropora spp. to determine the intra-colonial response to white syndrome using 14C labelling. Translocation of 14C labelled photoassimilates was preferentially orientated away from active WSLs, with minimal 14C activity observed in the lesion borders, whilst artificial lesions (ALs) created directly opposite WSL borders showed significantly higher 14C activity, suggesting active translocation of photoassimilates for tissue regeneration. Transport of photoassimilates in healthy coral colonies was preferentially oriented towards ALs with a higher perimeter–area ratio, although translocation towards WSL boundaries was minimal even though the lesion perimeter was often the width of the colony (>200 cm). We suggest that the preferential orientation of photoassimilates away from WSLs may represent a deliberate strategy by the colony to induce a ‘shutdown reaction’ in order to preserve intra-colonial resources within areas of the colony that are more likely to survive and recover.