Microbiome epidemiology and association studies in human health

doi:10.1038/s41576-022-00529-x

Review

. 2023 Feb;24(2):109-124.

doi: 10.1038/s41576-022-00529-x. Epub 2022 Oct 5.

Microbiome epidemiology and association studies in human health

Hannah VanEvery^{1

2

3

4}, Eric A Franzosa^{1

3

5}, Long H Nguyen^{6

7

8

9}, Curtis Huttenhower^{10

11

12

13}

Affiliations

¹ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
² Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
³ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
⁴ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁶ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
⁷ Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
⁸ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
⁹ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
¹⁰ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.
¹¹ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.
¹² Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. chuttenh@hsph.harvard.edu.
¹³ Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.

PMID: 36198908
DOI: 10.1038/s41576-022-00529-x

Review

Microbiome epidemiology and association studies in human health

Hannah VanEvery et al. Nat Rev Genet. 2023 Feb.

. 2023 Feb;24(2):109-124.

doi: 10.1038/s41576-022-00529-x. Epub 2022 Oct 5.

Authors

Hannah VanEvery^{1

2

3

4}, Eric A Franzosa^{1

3

5}, Long H Nguyen^{6

7

8

9}, Curtis Huttenhower^{10

11

12

13}

Affiliations

¹ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
² Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
³ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
⁴ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁶ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
⁷ Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
⁸ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
⁹ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. lnguyen24@mgh.harvard.edu.
¹⁰ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.
¹¹ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.
¹² Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. chuttenh@hsph.harvard.edu.
¹³ Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.

PMID: 36198908
DOI: 10.1038/s41576-022-00529-x

Abstract

Studies of the human microbiome share both technical and conceptual similarities with genome-wide association studies and genetic epidemiology. However, the microbiome has many features that differ from genomes, such as its temporal and spatial variability, highly distinct genetic architecture and person-to-person variation. Moreover, there are various potential mechanisms by which distinct aspects of the human microbiome can relate to health outcomes. Recent advances, including next-generation sequencing and the proliferation of multi-omic data types, have enabled the exploration of the mechanisms that connect microbial communities to human health. Here, we review the ways in which features of the microbiome at various body sites can influence health outcomes, and we describe emerging opportunities and future directions for advanced microbiome epidemiology.

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References

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1. Peppercorn, M. A. & Goldman, P. The role of intestinal bacteria in the metabolism of salicylazosulfapyridine. J. Pharmacol. Exp. Ther. 181, 555–562 (1972).
1. Wilson, K. H. & Blitchington, R. B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62, 2273–2278 (1996). - DOI
1. Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005). - DOI
1. Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006). - DOI

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[1] Eiseman, B., Silen, W., Bascom, G. S. & Kauvar, A. J. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery 44, 854–859 (1958).

[2] Eiseman, B., Silen, W., Bascom, G. S. & Kauvar, A. J. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery 44, 854–859 (1958).

[3] Peppercorn, M. A. & Goldman, P. The role of intestinal bacteria in the metabolism of salicylazosulfapyridine. J. Pharmacol. Exp. Ther. 181, 555–562 (1972).

[4] Peppercorn, M. A. & Goldman, P. The role of intestinal bacteria in the metabolism of salicylazosulfapyridine. J. Pharmacol. Exp. Ther. 181, 555–562 (1972).

[5] Wilson, K. H. & Blitchington, R. B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62, 2273–2278 (1996). - DOI

[6] Wilson, K. H. & Blitchington, R. B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62, 2273–2278 (1996). - DOI

[7] Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005). - DOI

[8] Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005). - DOI

[9] Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006). - DOI

[10] Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006). - DOI

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Microbiome epidemiology and association studies in human health

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Microbiome epidemiology and association studies in human health

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