Multispecies individuals

Scrutinizing microbiome determinism: why deterministic hypotheses about the microbiome are conceptually ungrounded

This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call "host-microbiome determinism". Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the expression of certain phenotypic traits, which I call "microbiome-phenotype determinism". Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits.

Do heritable immune responses extend physiological individuality?

Immunology and its philosophy are a primary source for thinking about biological individuality. Through its discriminatory function, the immune system is believed to delineate organism and environment within one generation, thus defining the physiological individual. Based on the paradigmatic instantiations of immune systems, immune interactions and, thus, the physiological individual are believed to last only for one generation. However, in recent years, transgenerationally persisting immune responses have been reported in several phyla, but the consequences for physiological individuality have not yet been explored. In this article, I will introduce an invertebrate immune system that is RNA-based and operates through a heritable silencing/licensing paradigm. I will discuss how such a perspective on immune systems can illuminate our conceptions of individuality. I will particularly introduce an account of immunological individuality that is not restricted to one generation.

Unifying heritability in evolutionary theory

Despite being widely used in both biology and psychology as if it were a single notion, heritability is not a unified concept. This is also true in evolutionary theory, in which the word 'heritability' has at least two technical definitions that only partly overlap. These yield two approaches to heritability: the 'variance approach' and the 'regression approach.' In this paper, I aim to unify these two approaches. After presenting them, I argue that a general notion of heritability ought to satisfy two desiderata-'general applicability' and 'separability of the causes of resemblance.' I argue that neither the variance nor the regression approach satisfies these two desiderata concomitantly. From there, I develop a general definition of heritability that relies on the distinction between intrinsic and extrinsic properties. I show that this general definition satisfies the two desiderata. I then illustrate the potential usefulness of this general definition in the context of microbiome research.

Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity

Biofilms are organised heterogeneous assemblages of microbial cells that are encased within a self-produced matrix. Current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms. Since biofilms are the main mode of microbial life, understanding their biology and functions is critical, especially as controlling biofilm growth is essential in industrial, infrastructure and medical contexts. Here we discuss biofilms both as collections of individual cells, and as multicellular biological individuals, and introduce the concept of biofilms as unique incubators of diversity for the microbial world.

Vaginal Microbiota: Age Dynamic and Ethnic Particularities of Algerian Women

The composition of the vaginal microbiota is a key element for maintaining gynecological and reproductive health. With the aim of obtaining an accurate overview of the vaginal microbiota of Algerian women, in terms of their age and ethnic group, we conducted a 16S rRNA gene targeted metagenomic analysis of 100 vaginal samples taken from healthy childbearing and menopausal women. These data were used to establish the pattern of the vaginal microbiota during reproductive and postreproductive phases. Hormone levels were correlated to changes in microbial composition for menopausal women. The ethnic comparison revealed a particular microbiota profile for Algerian women, with a dominance of CST III and CST I. A rapid qPCR method developed by the authors was successfully used to identify the vaginal bacterial pattern for a customized gynecological management.

Interactions of host-associated multispecies bacterial communities

The oral microbiome comprises microbial communities colonizing biotic (epithelia, mucosa) and abiotic (enamel) surfaces. Different communities are associated with health (eg, immune development, pathogen resistance) and disease (eg, tooth loss and periodontal disease). Like any other host-associated microbiome, colonization and persistence of both beneficial and dysbiotic oral microbiomes are dictated by successful utilization of available nutrients and defense against host and competitor assaults. This chapter will explore these general features of microbe-host interactions through the lens of symbiotic (mutualistic and antagonistic/pathogenic) associations with nonmammalian animals. Investigations in such systems across a broad taxonomic range have revealed conserved mechanisms and processes that underlie the complex associations among microbes and between microbes and hosts.

Holobionts: Ecological communities, hybrids, or biological individuals? A metaphysical perspective on multispecies systems

Holobionts are symbiotic assemblages composed by a macrobe host (animal or plant) plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to their account, the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl's account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host's microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective.

Modeling the evolution of interconnected processes: It is the song and the singers: Tracking units of selection with interaction networks

Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re-produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re-production but also the evolution and fitness of biological and ecosystemic interconnected processes.

Individuals, Boundaries, and Graft-versus-Host Disease

Hematopoietic cell transplantation generates new individuals, transplant chimeras, composed of 2 genetic partners-the patient and donor-derived cells-no longer restricted by their original genomes. Interactions of donor-derived and recipient cells occur prominently at the boundary of the recipient with a third partner, the microbiome, in particular skin and intestinal tract, leading to disruption of microbiome homeostasis. These interactions of donor and patient cells at the boundary set the stage for the development of graft-versus-host disease, an expression of the defense of individuality by recipient and donor. Establishment of tolerance and return of homeostasis at the boundary will allow for the survival of the new integrated, physiologic individual.

"Microbiota, symbiosis and individuality summer school" meeting report

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.

Sources of epigenetic variation and their applications in natural populations

Epigenetic processes manage gene expression and products in a real‐time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet‐hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation.

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

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.

The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality

Bourrat and Griffiths (Hist Philos Life Sci 40(2):33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths' arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats (Nat Ecol Evol 2:659-668, 2018), I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics.

Evolutionary transitions in heritability and individuality

With a few exceptions, the literature on evolutionary transitions in individuality (ETIs) has mostly focused on the relationships between lower-level (particle-level) and higher-level (collective-level) selection, leaving aside the question of the relationship between particle-level and collective-level inheritance. Yet, without an account of this relationship, our hope to fully understand the evolutionary mechanisms underlying ETIs is impeded. To that effect, I present a highly idealized model to study the relationship between particle-level and collective-level heritability both when a collective-level trait is a linear function and when it is a nonlinear function of a particle-level trait. I first show that when a collective trait is a linear function of a particle-level trait, collective-level heritability is a by-product of particle-level heritability. It is equal to particle-level heritability, whether the particles interact randomly or not to form collectives. Second, I show that one effect of population structure is the reduction in variance in offspring collective-level character for a given parental collective. I propose that this reduction in variance is one dimension of individuality. Third, I show that even in the simple case of a nonlinear collective-level character, collective-level heritability is not only weak but also highly dependent on the frequency of the different types of particles in the global population. Finally, I show that population structure, because one of its effects is to reduce the variance in offspring collective-level character, allows not only for an increase in collective-level character but renders it less context dependent. This in turn permits a stable collective-level response to selection. The upshot is that population structure is a driver for ETIs. These results are particularly significant in that the relationship between population structure and collective-level heritability has, to my knowledge, not been previously explored in the context of ETIs.