associations depend on tight regulation via signaling secretion systems (Schmitz and
Harrison 2014; Nelson and Sadowsky 2015), but only Rhizobium–legume associations are known for strict sanctions to cheater microbes (Kiers et al. 2003; Sachs
et al. 2010; Oono et al. 2011).
Microbial communities in the animal gut break down complex polymers into
digestible molecules, and provide essential vitamins and amino acids otherwise
unavailable from the host’s diet (Koh and Bäckhed 2020). In humans, the gut
microbiome assists in the breakdown of dietary products, like complex polysaccharides, and production of essential nutrients, such as short-chain fatty acids, vitamins
(B and D), and essential amino acids (Ley et al. 2008b; Qin and MetaHIT Consortium 2010; Kamada et al. 2013). More generally for mammals, the highest gut
diversity is attributed to herbivores, particularly ruminants and fermenters, where
these functions are essential to the breakdown of a plant diet, the host’s sole source
of nutrients (Ley et al. 2008a; Godon et al. 2016). These microbial communities are
generally very diverse, ranging from hundreds to thousands of species (Reese and
Dunn 2018), indicating that microbes may complement each other in their metabolic
pathways leading to more effectively break down of food and more diverse production of metabolites (Henson and Phalak 2017; Coyte and Rakoff-Nahoum 2019).
Nonetheless, some animals with defined diets hold species-poor communities in
their gut, potentially limiting membership to those that provide effective transformation of specific molecules. For example, bees host five to nine core bacterial
species in their guts (Engel et al. 2012; Raymann and Moran 2018), while aphids
consuming sap have been reported to have 8 core species (Smith et al. 2015) and up
to 21 facultative bacterial symbionts (Gauthier et al. 2015). An extreme example is
the lack of resident microbiota in caterpillars, suggesting that the host benefits from
producing the necessary enzymes instead of hosting potentially dangerous microbes
(Hammer et al. 2017).
17.2.2 Disease Prevention
In the context of human health, microbes were regarded solely as pathogens for a
very long time, and understanding their role in preventing disease is a relatively
newer perspective (Casadevall and Pirofski 2015). It is clear now that microbial
ability to prevent and combat disease has direct applications in human health, such as
combating Clostridium dificile infections with fecal transplants (Eiseman et al. 1958;
Bojanova and Bordenstein 2016; Ooijevaar et al. 2019; Jin Song et al. 2019).
Applications extend into other areas like agriculture, where inoculations of protective microbes in crops have the potential to increase yield and block phytopathogens
while reducing the use of toxic compounds (Pérez-García et al. 2011; Busby et al.
2017). Whether in animals or plants, these defensive properties rely on interactions
between protective microbes and invasive pathogens (García-Bayona and Comstock
2018). Those interactions include competition for resources, competitive interference, modification of abiotic conditions, and priming of the host immune system.
17 Diversity–Function Relationships and the Underlying Ecological Mechanisms in. . .
301
Harrison 2014; Nelson and Sadowsky 2015), but only Rhizobium–legume associations are known for strict sanctions to cheater microbes (Kiers et al. 2003; Sachs
et al. 2010; Oono et al. 2011).
Microbial communities in the animal gut break down complex polymers into
digestible molecules, and provide essential vitamins and amino acids otherwise
unavailable from the host’s diet (Koh and Bäckhed 2020). In humans, the gut
microbiome assists in the breakdown of dietary products, like complex polysaccharides, and production of essential nutrients, such as short-chain fatty acids, vitamins
(B and D), and essential amino acids (Ley et al. 2008b; Qin and MetaHIT Consortium 2010; Kamada et al. 2013). More generally for mammals, the highest gut
diversity is attributed to herbivores, particularly ruminants and fermenters, where
these functions are essential to the breakdown of a plant diet, the host’s sole source
of nutrients (Ley et al. 2008a; Godon et al. 2016). These microbial communities are
generally very diverse, ranging from hundreds to thousands of species (Reese and
Dunn 2018), indicating that microbes may complement each other in their metabolic
pathways leading to more effectively break down of food and more diverse production of metabolites (Henson and Phalak 2017; Coyte and Rakoff-Nahoum 2019).
Nonetheless, some animals with defined diets hold species-poor communities in
their gut, potentially limiting membership to those that provide effective transformation of specific molecules. For example, bees host five to nine core bacterial
species in their guts (Engel et al. 2012; Raymann and Moran 2018), while aphids
consuming sap have been reported to have 8 core species (Smith et al. 2015) and up
to 21 facultative bacterial symbionts (Gauthier et al. 2015). An extreme example is
the lack of resident microbiota in caterpillars, suggesting that the host benefits from
producing the necessary enzymes instead of hosting potentially dangerous microbes
(Hammer et al. 2017).
17.2.2 Disease Prevention
In the context of human health, microbes were regarded solely as pathogens for a
very long time, and understanding their role in preventing disease is a relatively
newer perspective (Casadevall and Pirofski 2015). It is clear now that microbial
ability to prevent and combat disease has direct applications in human health, such as
combating Clostridium dificile infections with fecal transplants (Eiseman et al. 1958;
Bojanova and Bordenstein 2016; Ooijevaar et al. 2019; Jin Song et al. 2019).
Applications extend into other areas like agriculture, where inoculations of protective microbes in crops have the potential to increase yield and block phytopathogens
while reducing the use of toxic compounds (Pérez-García et al. 2011; Busby et al.
2017). Whether in animals or plants, these defensive properties rely on interactions
between protective microbes and invasive pathogens (García-Bayona and Comstock
2018). Those interactions include competition for resources, competitive interference, modification of abiotic conditions, and priming of the host immune system.
17 Diversity–Function Relationships and the Underlying Ecological Mechanisms in. . .
301