Philosophy of microbiology

17 October 2025

Dr Diego Gonzalez, UNINE Ellen Clarke, University of Leeds, UK Thomas Pradeu, University of Bordeaux, FR

Over the last decades, we have come to realize that the physiology and evolution of multicellular organisms is deeply shaped by, and entangled with, the microorganisms they are associated with. The philosophical and theoretical consequences of this new perspective are however just starting to be explored. Microbiome studies in particular have raised a number of questions around fundamental biological and biomedical concepts that deserve to be addressed.

The objective of this activity is to discuss some of these questions and the ways in which they have been impacted by recent findings about animal and plant microbiomes.

1. Biological individuality. The concept of a biological individual is key for at least some interpretations of the theory of evolution. The definition of biological individuality is, however, quite controversial, some authors limiting it to individual organisms, others proposing to extend it to parts or collectives of organisms. One fundamental question for microbiome studies is how the close association and partial codependence between organisms and their microbiota impacts the concept of individuality and how this matters for empirical research. General questions around the concept of individuality include: What is a biological individual in general? When do individuals in the evolutionary sense and individuals in the physiological sense overlap? Are there individuals beside the level of the organism, either above it (populations, associations) or below it (genes, organelles, endosymbionts)? What is the relevance of the metaorganism level of organization?

2. The biological self and the immune system. The immune system plays a key role in the control and regulation of the microbiota of multicellular eukaryotes. However, how we think of the immune system and its function has changed dramatically over the last 70 years. First conceptualized as a "defense system" against pathogenic or parasitic microorganisms, the immune system has become, with the discovery of its role in transplant rejection and tolerance, the cornerstone of self-nonself distinction and delineation. Recent discoveries in microbiology and immunology emphasize that self-nonself distinction is a systemic, dynamic and never-ending process: the immune system is constantly probing and renegotiating what is or is not self and nonself. One of the aims of this activity is to get to understand how the regulation of microbiota, as we presently understand it, resonates with, and possibly further modifies, the flexible, epigenetic or metagenetic, definition of the biological self that has emerged from recent immunological research. The activity will take place over two days. The first day will cover the main theories of biological individuality and introduce the questions raised by recent research on multicellular eukaryotes-microbiota associations.

Format: The activity will mix: lectures to establish the broad context about the two main topics; short presentations of key papers or problematic cases by attending students; collective discussions about the core philosophical alternatives and their relevance to the present state of the scientific research.

UNINE

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