An introduction to phylosymbiosis

Abstract

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.

Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities

“…In other words, as host genetic differences increase over time, differences in the structure of host-associated microbial communities will also increase [7]. Detailed descriptions of phylosymbiosis and how it is measured have been reviewed elsewhere [10]. Importantly, phylosymbiosis is different from codiversification in that the microbiome dendrogram is of microbial community structures, not of specific microbes (though this can be the case and will be discussed more below).…”

Ecological Specialization Within a Carnivorous Fish Family Is Supported by a Herbivorous Microbiome Shaped by a Combination of Gut Traits and Specific Diet

“…The abundant and diverse microbial communities present within and on the surface of animal bodies, i.e., the microbiomes, play a central role in the fitness of their host, providing benefits that include successful development of the immune system and protection against pathogens, but also enhanced food processing and nutrient absorption (McKenney et al, 2018a;Moran et al, 2019). These long histories of animalmicrobes interactions resulted for many clades in phylosymbiosis, i.e., the eco-evolutionary pattern where phylogenetically related hosts tend to have more similar microbiomes than distantly related ones (Brooks et al, 2016;Lim and Bordenstein, 2019). Further, phylosymbiosis signal in the gut microbiome was shown to be stronger when hosts share a recent common ancestor (i.e., intra clade) than when shared ancestry is more ancient (i.e., inter clades) (Groussin et al, 2017).…”

Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea)

“…Although many animals exhibit phylosymbiosis, the strength of the phylosymbiotic signature may differ (9,11,(15)(16)(17)(18). For example, both the gut bacterial community and the virome of Nasonia wasps have been shown to exhibit a strong phylosymbiotic signature and to exhibit functional phylosymbiosis, such that host development and survival are impacted by phylosymbiotic associations (9,16,(18)(19)(20). In contrast, Drosophila fruit flies exhibit mixed evidence for phylosymbiosis (9,(21)(22)(23).…”