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Microbiota succession throughout life from the cradle to the grave

Abstract

Associations between age and the human microbiota are robust and reproducible. The microbial composition at several body sites can predict human chronological age relatively accurately. Although it is largely unknown why specific microorganisms are more abundant at certain ages, human microbiota research has elucidated a series of microbial community transformations that occur between birth and death. In this Review, we explore microbial succession in the healthy human microbiota from the cradle to the grave. We discuss the stages from primary succession at birth, to disruptions by disease or antibiotic use, to microbial expansion at death. We address how these successions differ by body site and by domain (bacteria, fungi or viruses). We also review experimental tools that microbiota researchers use to conduct this work. Finally, we discuss future directions for studying the microbiota’s relationship with age, including designing consistent, well-powered, longitudinal studies, performing robust statistical analyses and improving characterization of non-bacterial microorganisms.

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Fig. 1: The succession of the human microbiota from conception to death.
Fig. 2: Measurements of bacterial diversity across age.
Fig. 3: Primary succession in utero and during early life.
Fig. 4: Secondary succession in adolescence and adult life.
Fig. 5: Late succession approaching the end of life.
Fig. 6: The microbiota after death.

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Acknowledgements

This work was supported by the US National Institute of Justice under award number 2016-DN-BX-0194 (to R.K and J.L.M.) and the US National Institutes of Health under award number U19AG063744 Project 1: Changes in Gut Microbiome (to R.K.). A.H.D. is supported by the Stein Institute for Research on Aging, the Natasha Josefowitz Predoctoral Fellowship and the Reiter Endowed Fellowship.

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A.H.D. and C.M. researched data for the article. All authors discussed the content, wrote the article, and reviewed and edited the manuscript before submission.

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Glossary

Keystone community members

Microbial species that have an exceedingly large impact on the stability, or recovery after perturbation, of the whole ecosystem.

Alpha diversity

A measure of within-sample diversity.

Beta diversity

A measure of similarity between samples.

Secondary bile acids

Bile acids that have been altered by the microbiota.

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Martino, C., Dilmore, A.H., Burcham, Z.M. et al. Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol (2022). https://doi.org/10.1038/s41579-022-00768-z

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