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Philosophy of Microbiology


16 February 2024


Dr. Diego Gonzalez, UNINE


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 only starting to be explored. Microbiome studies in particular have raised a number of questions around fundamental biological and biomedical notions that deserve to be addressed. The objective of this activity is to discuss some of these notions and the ways in which they have been impacted by recent findings about animal and plant microbiomes.

1. Holobiont. The holobiont concept has been used in microbiome studies to try and shift our attention from individual organisms to associations between hosts and their microbiota as a whole. Its application in microbiome studies is, however, controversial, some researchers recommending its elimination because of the confusion it brings to empirical research, others its application to only a subset of host-microbiota associations. Questions connected to the holobiont concept include: In what sense and to what extent can different host-microbiota associations be considered evolutionary units? In what sense are hosts and microbiota integrated? How does causality function between hosts and their microbiota, and among the different components of the microbiota?

2. Health. Health is usually attributed to organisms ("my dog is healthy"), to parts of organisms ("my heart is healthy", "I have a mitochondrial disease"), or to organic functions ("my digestion is impaired", "I have a mood disorder"). Biomedical approaches of the microbiome make use of the dysbiosis concept to name imbalances in the microbiota that can be assimilated to diseases. While in some cases a clear causative agent for those imbalances can be identified, like in the case of Clostridium difficile infections, dysbioses encompassing the whole microbiota or even the holobiont as a unit have been proposed. This raises fundamental questions about the relevance of attributing health to ecosystems or metaorganisms and calls for a broader and more critical definition of health.

3. 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 co-dependence between organisms and their microbiota impacts the concept of individuality. General questions around the concept of individuality include: What is a biological individual? What is the relevance of the metaorganism level of organisation? What is a biological individual in the first place? Are there individuals beside the level of the organism, either above it (populations, associations) or below it (genes, organelles, endosymbionts)? Do individuals in the evolutionary and the physiological sense always overlap?

The course includes presentations of the general conceptual space of the three main notions and collective discussions of relevant literature (empirical and theoretical biological research as well as philosophy of biology). The end goal of the workshop is to collectively build conceptual maps for the notions at play and to get a sense of their interest and limits when applied to the microbiome. At the very least, the participants should learn to make a better usage of these notions and define them more precisely and carefully, which should help decreasing the confusion load in the microbiological literature.






Introduction, the holobiont dispute

· What is "philosophy of (micro)biology" and when do we need it (if we ever do)?

· Does the holobiont concept bring clarity or confusion? - Two contrasted scientific views of the microbiome revolution


Coffee break EatEco


The problem of biological individuality in the microbiome era

· Different views on biological individuality:

o folk biology

o physiological and immunological individuality

o evolutionary individuality in single and multiple dimensions

o pluralism about individuality

· In what sense are holobionts or microbial communities biological individuals?

o case studies: Olavius and other gutless worms, biofilms, Dictyostelium / Myxococcus, insect-bacteria symbioses, essential insect microbiota, …

o frameworks: Queller & Strassmann, Godfrey-Smith…


Lunch EatEco


Microbes in health and disease: new paradigms of causation in microbiome studies?

· Problems around dysbiosis

· How should we establish causal relationships in medical microbiology?

o limits of Koch's postulates

o causation in an interactionist framework

o are communities or ecosystems acceptable causes?


Coffee break EatEco


Anthropological and metaphysical perspectives

· Health and self: are microbiome studies driving an anthropological revolution?

· Are microbiome studies changing our understanding of life itself?

o evolutionary and metabolic views of life

o substance and processual ontologies of life


UNINE - UniMail A317


Before the course, each one of the participants will have to:

  • prepare a short (3 minutes, 2 slides) presentation on a problematic case of individuality or infectious disease causation;
  • read a couple of articles introducing general knowledge about the microbiome and giving discussions a common ground.

> Instructions about the two tasks will be sent by email, latest on 2024/02/05.


Reimbursements for CUSO MPS Students:
Train ticket, 2°class, half-fare from your institution to the place of the activity 

Reimbursement of your travel tickets can be asked online through your MyCUSO. 


Registration close

Deadline for registration : 31.01.2024



Deadline for registration 02.02.2024
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