ERC IDEM Final Conference


— This event had to be canceled due to the global COVID-19 outbreak —




May 5-7, 2020

Microbiota and the Physiology and Evolution of Biological Individuals


Final conference of the ERC project: “Immunity, Development, and the Microbiota: Understanding the Continuous Construction of Biological Identity”

Bordeaux, France
Organized by: Wiebke Bretting & Thomas Pradeu
University of Bordeaux/CNRS

Recent research has shown that the microbiota (all the microbes that live in and on an organism) can have a major impact on the physiology of the host, and potentially on its health and behavior. This final conference of the ERC-funded project “Immunity, Development, and the Microbiota: Understanding the Continuous Construction of Biological Identity” (P.I.: T. Pradeu) will gather biologists, medical doctors, and philosophers who investigate the nature of the host-microbiota crosstalk and its consequences for our understanding of biological individuality and identity.

Questions that will be discussed at this conference include, but are not limited to:

  • How does current research on host-microbiota interactions impact our view about what a biological individual is and how it persists through time?
  • How does the microbiota influence host physiology?
  • How does the microbiota influence host development?
  • How does the host shape the microbiota?
  • What role does the immune system play in host-microbiota interactions? How does this put into question the traditional “self” and “nonself” concepts of immunology?
  • Is it possible to establish a causal link between characteristics of the microbiota and characteristics of the host? Which approaches to causality are better suited to account for this relation?
  • Can health and disease be associated with certain features of the microbiota? Can the microbiota be manipulated to improve health?
  • What kind of benefits and costs for each partner are associated with host-microbiota interactions? How can evolutionary biology shed light on such interactions?
  • Is the notion of “holobiont” useful to better understand the association between a host and its microbiota? Does the “holobiont” constitute an individual, a community, or an ecosystem? Does the concept of a holobiont invalidate the notion of a biological individual?
  • Can concepts and models developed in approaches such as niche construction theory, ecological developmental biology, or community ecology, for example, help elucidate the nature of host-microbiota interactions?



Thomas Bosch (Professor of General Zoology at Kiel University, Germany)

Nadine Cerf-Bensussan (Director of Research INSERM, IMAGINE Institut and University Paris Descartes, France)

Ford Doolittle (Professor Emeritus at Dalhousie University, Department of Biochemistry and Molecular Biology, Halifax, Canada)

John Dupré (Professor of Philosophy of Science at the University of Exeter, UK)

Gérard Eberl (Professor of Immunology, Institut Pasteur, France) – Setting the reactivity of the immune system early in life: the microbiota again

Scott Gilbert (Professor Emeritus of Developmental Biology at Swarthmore College, USA)

Paul Griffiths (Professor of Philosophy at the University of Sydney, Australia) – Part, Process and Pregnancy

Rob Knight (Professor at the University of California San Diego, Co-founder of the American Gut Project, the Earth Microbiome Project, and founding Director of the Center for Microbiome Innovation.

Margaret McFall-Ngai (Professor and Director of the Pacific Biosciences Research Center, University of Hawaii-Manoa, USA) – The role of small RNAs in the control of symbiosis

Sarkis K. Mazmanian (Luis & Nelly Soux Professor of Microbiology, Division of Biology and Biological Engineering, California Institute of Technology, USA) – The Gut Microbiome-Brain Connection to Animal Behavior

Samir Okasha (Professor of Philosophy of Science at the University of Bristol, UK) – On the very idea of ‘biological individuality’

Thomas Pradeu (CNRS Senior Investigator in Philosophy of Science, PI of the ERC IDEM project, CNRS & University of Bordeaux, France) – The Microbiome and Extended Physiological Individuality

Joan Roughgarden (Professor of Biology, Emerita, at Stanford University and Adjunct Professor at the Hawaii Institute of Marine Biology, University of Hawaii-Manoa, USA) – Holobiont Evolution: Mathematical Model for Vertical vs. Horizontal Microbiome Transmission, Microbiome Community Structure, and Host-Microbiome Coadaptation




(please click here)

Application procedure

We welcome applications to this conference by philosophers of science and conceptually-oriented scientists and medical doctors at any stage of their careers.

To apply, please submit two separate files:

i) a short CV (2 pages maximum)
ii) a detailed and anonymous abstract (between 300 and 1,000 words, references included)

The material must be sent to:


The deadline for application is: February 7th, 2020.

Decisions will be notified on February 24th, 2020 at the latest.


Travel grants

PhD and postdoctoral scholars can apply for financial assistance to travel costs, up to 1000€ are awarded per person. In order to apply please send a letter of motivation to




The conference is open to all. Attendance is free, but inscriptions are mandatory.

To sign up for the event please fill out the inscription form.




This workshop is part of the Immunity, DEvelopment and the Microbiota (IDEM) project, an ERC-funded project located at the interface of philosophy of biology and biology (ERC Grant #637647, PI: Thomas Pradeu).