Results for 'Microbiome'

13 found
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  1.  59
    Holobiont Evolution: Mathematical Model with Vertical Vs. Horizontal Microbiome Transmission.Joan Roughgarden - 2020 - Philosophy, Theory, and Practice in Biology 12 (2).
    A holobiont is a composite organism consisting of a host together with its microbiome, such as a coral with its zooxanthellae. To explain the often intimate integration between hosts and their microbiomes, some investigators contend that selection operates on holobionts as a unit and view the microbiome’s genes as extending the host’s nuclear genome to jointly comprise a hologenome. Because vertical transmission of microbiomes is uncommon, other investigators contend that holobiont selection cannot be effective because a holobiont’s (...) is an acquired condition rather than an inherited trait. This disagreement invites a simple mathematical model to see how holobiont selection might operate and to assess its plausibility as an evolutionary force. This paper presents two variants of such a model. In one variant, juvenile hosts obtain microbiomes from their parents (vertical transmission). In the other variant, microbiomes of juvenile hosts are assembled from source pools containing the combined microbiomes of all parents (horizontal transmission). According to both variants, holobiont selection indeed causes evolutionary change in holobiont traits. Therefore, holobiont selection is plausibly an effective evolutionary force with either mode of microbiome transmission. The modeling employs two distinct concepts of inheritance, depending on the mode of microbiome transmission: collective inheritance whereby juveniles inherit a sample of the collected genomes from all parents, as contrasted with lineal inheritance whereby juveniles inherit the genomes from only their own parents. A distinction between collective and lineal inheritance also features in theories of multilevel selection. (shrink)
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  2.  52
    OHMI: The Ontology of Host-Microbiome Interactions.Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko & Jihad S. Obeid - 2019 - Journal of Biomedical Semantics 10 (1):1-14.
    Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI (...)
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  3.  73
    Methodology and Ontology in Microbiome Research.John Huss - 2014 - Biological Theory 9 (4):392-400.
    Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By (...)
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  4. "The Human Microbiome: Ethical, Legal, and Social Concerns" Edited by Rosamond Rhodes, Nada Gligorov, and Abraham Paul Schwab. [REVIEW]Nicolae Morar - 2014 - Environmental Philosophy 11 (2):362-366.
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  5. Explaining the Behaviour of Random Ecological Networks: The Stability of the Microbiome as a Case of Integrative Pluralism.Roger Deulofeu, Javier Suárez & Alberto Pérez-Cervera - forthcoming - Synthese:1-23.
    Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems (...)
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  6.  67
    What is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems.Javier Suárez & Vanessa Triviño - 2020 - Frontiers in Psychology 187 (11).
    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 (...)
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  7. A Metaphysical Approach to Holobiont Individuality: Holobionts as Emergent Individuals.Javier Suárez & Vanessa Triviño - 2019 - Quaderns de Filosofia 6 (1):59-76.
    Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in (...)
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  8. The Hologenome Concept of Evolution: A Philosophical and Biological Study.Javier Suárez - 2019 - Dissertation, University of Exeter
    The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight (...)
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  9.  38
    The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality.Javier Suárez - 2020 - History and Philosophy of the Life Sciences 42 (1):1-27.
    Bourrat and Griffiths :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 (...)
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  10.  50
    From Metagenomics to the Metagenome: Conceptual Change and the Rhetoric of Translational Genomic Research.Eric Thomas Juengst & John Edward Huss - 2009 - Genomics, Society, and Policy 5 (3):1-19.
    As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work – and for understanding who we are as biological organisms. In this essay we focus on the Human Microbiome Project as one such translational initiative. The HMP is a new ‘metagenomic’ research effort to sequence the genomes of human microbiological flora, in order to pursue (...)
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  11. What is an Organism? An Immunological Answer.Thomas Pradeu - 2010 - History and Philosophy of the Life Sciences 32 (2-3):247-267.
    The question “What is an organism?”, formerly considered as essential in biology, has now been increasingly replaced by a larger question, “What is a biological individual?”. On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection which tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory, which makes (...)
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  12. Big Dreams for Small Creatures: Ilana and Eugene Rosenberg’s Path to the Hologenome Theory.Ehud Lamm - 2016 - In Oren Harman & Michael Dietrich (eds.), Dreamers, Visionaries, and Revolutionaries in the Life Sciences. Chicago University Press.
    A biographical sketch of the Hologenome Theory.
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  13.  72
    Bioethics and the Hypothesis of Extended Health.Nicolae Morar & Joshua August Skorburg - 2018 - Kennedy Institute of Ethics Journal 28 (3):341-376.
    Dominant views about the nature of health and disease in bioethics and the philosophy of medicine have presumed the existence of a fixed, stable, individual organism as the bearer of health and disease states, and as such, the appropriate target of medical therapy and ethical concern. However, recent developments in microbial biology, neuroscience, the philosophy of cognitive science, and social and personality psychology (Ickes...
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