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Estimates of microbiome heritability across hosts

Nature Microbiology volume 9, pages 3110–3119 (2024)Cite this article

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Abstract

Microbiomes contribute to variation in many plant and animal traits, suggesting that microbiome-mediated traits could evolve through selection on the host. However, for such evolution to occur, microbiomes must exhibit sufficient heritability to contribute to host adaptation. Previous work has attempted to estimate the heritability of a variety of microbiome attributes. Here we show that most published estimates are limited to vertebrate and plant hosts, but significant heritability of microbiome attributes has been frequently reported. This indicates that microbiomes could evolve in response to host-level selection, but studies across a wider range of hosts are necessary before general conclusions can be made. We suggest future studies focus on standardizing heritability measurements for the purpose of meta-analyses and investigate the role of the environment in contributing to heritable microbiome variation. This could have important implications for the use of microbiomes in conservation, agriculture and medicine.

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Fig. 1: The heritability of microbiomes and microbiome-mediated traits.
Fig. 2: Mechanisms of microbiome heritability.
Fig. 3: Estimates of microbiome heritability.

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Acknowledgements

This work was supported by a grant from the Gordon and Betty Moore Foundation (award no. 10001). B.J.M.B. was also supported by awards from the Alexander von Humboldt Foundation (Alexander-von-Humboldt Stiftung) and the SETS Synthesis Center of the Swiss Federal Institute of Aquatic Science and Technology (EAWAG). We are grateful for input from B. Week, H. Schulenburg and K. Räsänen, which greatly improved this Perspective.

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    Andrew H. Morris & Brendan J. M. Bohannan

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B.J.M.B. conceived of the study, supervised the project and critically revised the paper. A.H.M. performed the research, wrote the initial draft of the paper and critically revised the paper.

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Supplementary Table 1

Supplementary Table 1. Microbiome heritability estimates. Note that we chose to present ‘number of individuals’, which represents the number of unique hosts sampled in the study. This may or may not align with the sample size for statistical purposes so we have indicated that in a footnote where necessary. Attributes must have both a significant test statistic and/or a heritability estimate above a chosen heritability threshold (such as >0.15 or >0.20) to be considered heritable. Percent heritable, % is the percentage of tested microbiome attributes that were considered heritable. Heritability range is the range between the minimum and maximum heritability estimates for this study.

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Morris, A.H., Bohannan, B.J.M. Estimates of microbiome heritability across hosts. Nat Microbiol 9, 3110–3119 (2024). https://doi.org/10.1038/s41564-024-01865-w

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