where theyfind nutrients and protection from competitors, among other things
(Donaldson et al. 2016). Microbes can also manipulate their host in many
different ways (Sansonetti and Di Santo 2007). Finally, it is crucial to understand
that the interaction between host and resident microbes is the product of
a complex equilibrium, in which the nature of the ecological relationship can
change through time depending on the circumstances and switch from mutualism
to commensalism to parasitism (microbes that switch from the status of symbionts
to pathogens have sometimes been called“pathobionts”(Chow et al. 2011)).
Recent work on immunological tolerance and the intimate dialogue between
host and microbes across the living world invalidates the claim that the immune
system eliminates foreign (nonself) entities. In the last two decades, symbiosis
in general and symbiotic interactions with microbes more specifically have been
recognized as ubiquitous and essential phenomena in nature. The specific
contribution of immunology to this literature is to ask how symbiotic entities
can be tolerated by the immune system and how they interact with this system in
several central physiological processes (seeBox 3.1).
BOX3.1 THEIMPORTANCE OFRESEARCH ONSYMBIOSIS INRECENTBIOLOGY AND
PHILOSOPHY OFBIOLOGY AND THEROLE OFIMMUNOLOGY INTHATRESEARCH
Although research on symbiosis has a long history, the last two decades
have seen a burst of investigations on this topic, at the crossroads of
different domains, largely as a consequence of new technological
advances (McFall-Ngai et al. 2013), particularly high-throughput sequen-
cing and metagenomics. A key discovery was that virtually all living
things harbor myriad microorganisms, many of which are beneficial to
the host for activities as diverse as nutrition, development, and metabolism
(Xu and Gordon 2003).
Recent work on symbiosis has also been of central interest to philoso-
phers and conceptually interested biologists. Among the central issues,
one can emphasize the degree of individuality displayed by host–microbe
associations (Gilbert 2002; Pradeu and Carosella 2006b; Gilbert et al.
2012 ), the marriage of ecology and developmental biology (Gilbert 2002),
an enrichment of the major transitions in evolution framework (Kiers and
West 2015), the impact of symbiotic interactions on traditional views
about evolutionary processes and the“tree of life”(Bouchard 2010)as
well as debates about the concept of“holobiont”(Zilber-Rosenberg and
Rosenberg 2008), and the long-recognized challenge of the transition from
correlation to causality in microbiome studies (for example, if the micro-
biome composition in patients with inflammatory bowel disease differsPhilosophy of Immunology 19