Table 1 Plenary lectures from course leaders

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, 18–20]

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

[29–33]

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.