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Table 1 Plenary lectures from course leaders

From: “Microbiota, symbiosis and individuality summer school” meeting report

Presenter, Lecture title Description Associated
affiliation    references
Thomas Pradeu, Microbiota and Pradeu asked “what do we mean by microbiota?” and [2, 17]
The French National microbiome: a pointed out there is no single answer. He also argued that  
Center for Scientific conceptual analysis our understanding of microbiota impacts our conception of  
Research and University   individuality. Examining the history, meaning, and impact of  
of Bordeaux (France)   the microbiota is important when making ontological and  
   epistemological claims concerning individuality.  
  Interactions between Pradeu highlighted how the function of the immune system [5, 1820]
  the microbiota and the has been reconsidered in light of microbiota research. The  
  immune system: an immune response should be thought of as a dynamic  
  immunological point of equilibrium, regulated by activating and inhibitory signals as  
  view on biological a function of the ecological context and the encountered  
  individuality microbes. Pradeu proposed a physiological individual as a  
   unit of functioning, composed of the host and its microbiota,  
   where the immune system plays a crucial role in the  
   unification of this plurality.  
Scott Gilbert, Developmental symbiosis Gilbert argued that all metazoans have microbial symbionts [4, 21, 22]
Swarthmore College and the mapping of and these are important, sometimes essential, for normal  
(USA) and University novel evolutionary animal development and organ generation. For example, the  
of Helsinki (Finland) trajectories gut of cows has been transformed by symbionts and led to  
   the emergence of their herbivory diet. The close association  
   of organisms and their microbiota therefore opens novel  
   evolutionary trajectories. Organisms have been formed by  
   symbiotic interactions and these close associations open  
   novel evolutionary trajectories.  
Johannes Martens, Biological individuality: Martens provided philosophical context for the concept of [23, 24]
University Catholique a conceptual analysis biological individuality. He distinguished it from other  
of Louvain (Belgium)   concepts, such as unity, and argued that questions of  
   individuality primarily involve singling out the properties that  
   make an individual distinct. Productive theorizing about  
   individuality does, of course, require considering individuals  
   themselves, but it also involves considering their parts, as well as  
   the collectives they form.  
  Fraternal vs. Martens argued that there are two concepts associated with  
  egalitarian transitions in transitions in biological individuality. First, fraternal transitions  
  individuality: two involve a transition in Darwinian individuality (e.g., multicellularity  
  processes, one concept? and insect colonies). Second, egalitarian transitions involve a transition  
   in organismality, where the entities share a dependence and mutual  
   benefit (e.g., the eukaryotic cell). The identification of two concepts  
   for major transitions is helpful for exploring the influence of holobionts  
   on evolution at multiple levels of biological organization.  
Jan Pieter Konsman, Barriers and Konsman argued that we ought not confuse the existence of [25, 26]
The French National obstacles in relation a functional “axis” between the microbiota, host gut, and  
Center for Scientific to microbiota’s host host brain with the presence of precise mechanistic  
Research and effects interactions between the organisms involved in this axis  
University of Bordeaux   (which remain largely unconfirmed). The biological barriers  
(France)   have a dynamic nature and act more like borders, localized  
   areas over which complex regulation and interaction occurs.  
   Konsman concluded that methodologies and explanations  
   must consider host organization and other higher-level  
   features which can both inform and structure the  
   reductionistic methodologies present in biology.  
Thomas Bosch, The holobiont Bosch argued that biology and medicine have historically [11, 27, 28]
University of Kiel imperative: towards focused on the host, missing the important role of the  
(Germany) a holistic understanding microbiota. Using his experimental work on the Hydra  
  of complex life processes metaorganism as a model system for the evolution of  
   biological complexity, Bosch concluded that the  
   metaorganism perspective invites a more holistic and  
   integrative account of an organism.  
Rob Knight, Beyond the tip of Using his research investigating the impact of microbiota on [2933]
University of the iceberg: human health, Knight argued that microbiota research needs  
California, San discovering millions to focus more on determining causal pathways, examining  
Diego (USA) more “human” the transgenerational effects of microbiota and intervening  
  genes in our on the microbiota. On the other hand, even without these  
  microbiomes and possible advances, current microbiota research is already  
  their links to challenging classical philosophy of biology debates—  
  phenotype including debates about phenotypes and evolution, as well as  
   what counts as a unit of selection.  
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