An introduction to phylosymbiosis

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1 Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States
2 Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
3 Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, Tennessee, United States
4 Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States
DOI
10.7287/peerj.preprints.27879v2
Published
Accepted
Subject Areas
Biodiversity, Bioinformatics, Evolutionary Studies, Microbiology
Keywords
symbiosis, phylosymbiosis, microbiome, host-microbe interactions, natural selection, microbial ecology, speciation
Copyright
© 2019 Lim et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Lim SJ, Bordenstein SR. 2019. An introduction to phylosymbiosis. PeerJ Preprints 7:e27879v2

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.

Author Comment

This article is revised in response to comments by the reviewers

Supplemental Information

Figure 1. Sequential overview of bioinformatic methods commonly used for phylosymbiosis analyses

DOI: 10.7287/peerj.preprints.27879v2/supp-1

Figure 2. Representative diversity of phylosymbiosis across host species, tissues, habitats, and functions. The * symbol denotes taxa with mixed evidence for phylosymbiosis

DOI: 10.7287/peerj.preprints.27879v2/supp-2