Developing general principles of host–microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
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K.R.A. is supported as a fellow in CIFAR’s Humans & the Microbiome programme. E.K.M. is supported by the Vanderbilt Microbiome Initiative and was partially supported by CIFAR.
The authors declare no competing interests.
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Similarities in host-associated microbial community structure that mirror the phylogenetic relationships of the hosts.
- Vertical transmission
A pathway of transmission where a symbiotic organism is transmitted from the host parent to offspring.
Reciprocal genetic change in two species that occurs as a result of the selective pressures that each imposes on the other.
- Priority effects
A phenomenon in which species that arrive first at a site alter the abiotic and/or biotic conditions such that this impacts the colonization success of species arriving later.
- Ecological drift
The random fluctuation of species abundances in a community or population, often as a result of isolation from other populations.
- Horizontal transmission
A pathway of transmission where a symbiotic organism is transmitted between individuals via the social or physical environment instead of from parent to offspring.
- Oviparous animals
Animals that lay eggs and in which embryonic development does not occur internally in the mother.
Tubes through which a female animal lays or deposits eggs; most often refers to a structure found in insects.
- Viviparous animals
Animals characterized by live birth (viviparity) of offspring with embryonic development occurring internally in the mother.
- Innate immune system
A non-specific immune response to potential pathogens found in invertebrates and vertebrates. In vertebrates, the innate immune system has a role in activating the adaptive immune system.
- Adaptive immune system
The portion of the immune system that, in vertebrates, allows an organism to identify, learn about and respond to specific pathogens.
- Sacculated foregut
A multichambered stomach which allows microbial fermentation before food moves further into the digestive tract.
Diversification of two species at the same pace and that have a shared evolutionary history as a result of either co-evolution or a shared environment.
- Niche construction
When a species changes its local environment, altering the selective pressures acting on it and other organisms in its environment.
The process of change in the composition of an ecological community over time, often involving increasing community diversity.
Symbiotic, often mutualistic, organisms living inside the tissue of another organism. Symbionts are transmitted either horizontally or vertically, and the symbiosis relationship can be obligatory or not obligatory.
- Host specificity
Microbial ability to colonize a host depending on physiological interactions with the host and environmental requirements (for example, pH tolerance, biofilm regulation and polysaccharide utilization loci).
- Matrilineal species
Species in which females remain in their natal group, males disperse, dominance rank is inherited by females from their mothers and social bonds between closely related females are strong.
Dietary items which provide substrates for bacterial growth in the digestive tract.
- Sympatric terrestrial species
Distinct species living in the same terrestrial habitat.
- Sympatric arboreal species
Distinct species living in the same arboreal habitat.
- Host selectivity
Host ability to limit the microbial strains that associate with it via various physiological filters (for example, immune system, gut anatomy and diet/nutrients).
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Mallott, E.K., Amato, K.R. Host specificity of the gut microbiome. Nat Rev Microbiol (2021). https://doi.org/10.1038/s41579-021-00562-3