Microbiota succession throughout life from the cradle to the grave

doi:10.1038/s41579-022-00768-z

Review

. 2022 Dec;20(12):707-720.

doi: 10.1038/s41579-022-00768-z. Epub 2022 Jul 29.

Microbiota succession throughout life from the cradle to the grave

Cameron Martino^#^{1

2

3}, Amanda Hazel Dilmore^#^{1

4}, Zachary M Burcham⁵, Jessica L Metcalf⁵, Dilip Jeste^{3

6

7

8}, Rob Knight^{9

10

11

12}

Affiliations

¹ Department of Paediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
² Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
³ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁴ Biomedical Sciences Program, University of California, San Diego, La Jolla, CA, USA.
⁵ Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
⁶ Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
⁸ Sam and Rose Stein Institute for Research on Aging, University of California, San Diego, La Jolla, CA, USA.
⁹ Department of Paediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA. robknight@ucsd.edu.
¹⁰ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
¹¹ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
¹² Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.

^# Contributed equally.

PMID: 35906422
DOI: 10.1038/s41579-022-00768-z

Review

Microbiota succession throughout life from the cradle to the grave

Cameron Martino et al. Nat Rev Microbiol. 2022 Dec.

. 2022 Dec;20(12):707-720.

doi: 10.1038/s41579-022-00768-z. Epub 2022 Jul 29.

Authors

Cameron Martino^#^{1

2

3}, Amanda Hazel Dilmore^#^{1

4}, Zachary M Burcham⁵, Jessica L Metcalf⁵, Dilip Jeste^{3

6

7

8}, Rob Knight^{9

10

11

12}

Affiliations

¹ Department of Paediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
² Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
³ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁴ Biomedical Sciences Program, University of California, San Diego, La Jolla, CA, USA.
⁵ Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
⁶ Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
⁸ Sam and Rose Stein Institute for Research on Aging, University of California, San Diego, La Jolla, CA, USA.
⁹ Department of Paediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA. robknight@ucsd.edu.
¹⁰ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
¹¹ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
¹² Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. robknight@ucsd.edu.

^# Contributed equally.

PMID: 35906422
DOI: 10.1038/s41579-022-00768-z

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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References

1. Chu, D. M. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med. 23, 314–326 (2017). - PubMed - PMC - DOI
1. Ward, T. L. et al. Development of the human mycobiome over the first month of life and across body sites. mSystems 3, e00140–17 (2018). - PubMed - PMC - DOI
1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). - PubMed - PMC - DOI
1. Abeles, S. R. et al. Human oral viruses are personal, persistent and gender-consistent. ISME J. 8, 1753–1767 (2014). - PubMed - PMC - DOI
1. Grice, E. A. & Segre, J. A. The human microbiome: our second genome. Annu. Rev. Genomics Hum. Genet. 13, 151–170 (2012). - PubMed - PMC - DOI

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[1] Chu, D. M. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med. 23, 314–326 (2017). - PubMed - PMC - DOI

[2] Chu, D. M. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med. 23, 314–326 (2017). - PubMed - PMC - DOI

[3] Ward, T. L. et al. Development of the human mycobiome over the first month of life and across body sites. mSystems 3, e00140–17 (2018). - PubMed - PMC - DOI

[4] Ward, T. L. et al. Development of the human mycobiome over the first month of life and across body sites. mSystems 3, e00140–17 (2018). - PubMed - PMC - DOI

[5] Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). - PubMed - PMC - DOI

[6] Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). - PubMed - PMC - DOI

[7] Abeles, S. R. et al. Human oral viruses are personal, persistent and gender-consistent. ISME J. 8, 1753–1767 (2014). - PubMed - PMC - DOI

[8] Abeles, S. R. et al. Human oral viruses are personal, persistent and gender-consistent. ISME J. 8, 1753–1767 (2014). - PubMed - PMC - DOI

[9] Grice, E. A. & Segre, J. A. The human microbiome: our second genome. Annu. Rev. Genomics Hum. Genet. 13, 151–170 (2012). - PubMed - PMC - DOI

[10] Grice, E. A. & Segre, J. A. The human microbiome: our second genome. Annu. Rev. Genomics Hum. Genet. 13, 151–170 (2012). - PubMed - PMC - DOI

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Microbiota succession throughout life from the cradle to the grave

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Microbiota succession throughout life from the cradle to the grave

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