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Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies

Nature Protocols volume 16, pages 2724–2731 (2021)Cite this article

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A Publisher Correction to this article was published on 13 May 2021

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Abstract

A lack of prospective studies has been a major barrier for assessing the role of the microbiome in human health and disease on a population-wide scale. To address this significant knowledge gap, we have launched a large-scale collection targeting fecal and oral microbiome specimens from 20,000 women within the Nurses’ Health Study II cohort (the Microbiome Among Nurses study, or Micro-N). Leveraging the rich epidemiologic data that have been repeatedly collected from this cohort since 1989; the established biorepository of archived blood, urine, buccal cell, and tumor tissue specimens; the available genetic and biomarker data; the cohort’s ongoing follow-up; and the BIOM-Mass microbiome research platform, Micro-N furnishes unparalleled resources for future prospective studies to interrogate the interplay between host, environmental factors, and the microbiome in human health. These prospectively collected materials will provide much-needed evidence to infer causality in microbiome-associated outcomes, paving the way toward development of microbiota-targeted modulators, preventives, diagnostics and therapeutics. Here, we describe a generalizable, scalable and cost-effective platform used for stool and oral microbiome specimen and metadata collection in the Micro-N study as an example of how prospective studies of the microbiome may be carried out.

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Fig. 1: Overview of the Nurses’ Health Study II cohort.
Fig. 2: Workflow of the Micro-N project generalizable by the BIOM-Mass platform.

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Acknowledgements

This work was supported by the Massachusetts Life Sciences Center (MLSC), the National Institutes of Health (U01 CA176726, R24 DK110499, R00 CA215314, R35 CA253185, R01 CA202704 and R01 CA243454) and the Harvard T. H. Chan School of Public Health. J.I. is supported by Nebraska Tobacco Settlement Biomedical Research Development Funds. We thank staff at the Harvard T. H. Chan School of Public Health for their assistance (A. Spickard, M. Sinunu and S. Branstrator) and the investigators of other cohort studies for their participation of the microbiome working group and contribution to the questionnaire development. These investigators include J. Ahn (New York University), B. Blot (Vanderbilt University), R. Burk (Albert Einstein College of Medicine), M. Hullar (Fred Hutchinson Cancer Research Center), R. Kaplan (Albert Einstein College of Medicine), J. Lampe (Fred Hutchinson Cancer Research Center), L. Le Marchand (University of Hawaiʻi), K. Meyer (University of North Carolina at Chapel Hill), Q. Qi (Albert Einstein College of Medicine), T. Randolph (Fred Hutchinson Cancer Research Center), H. Sesso (Harvard Medical School/Brigham and Women’s Hospital), M. Shrubsole (Vanderbilt University), R. Sinha (National Cancer Institute), E. Vogtmann (National Cancer Institute), L. Wilkens (University of Hawaiʻi) and W. Zheng (Vanderbilt University). We also thank the participants and staff of the Nurses’ Health Study II for their valuable contributions—in particular, B. Hall, A. Scott, S. Al-Shanniek and E. Cornacchio for their dedication to sampling processing and handling and M. Atkinson for his database programming.

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Author notes

  1. These authors contributed equally: Christine Everett, Chengchen Li, Jeremy E. Wilkinson, Andrew T. Chan, Wendy S. Garrett, Curtis Huttenhower, Eric B. Rimm, Mingyang Song.

Authors and Affiliations

  1. Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    Christine Everett, Chengchen Li, Jeremy E. Wilkinson, Long H. Nguyen, Lauren J. McIver, Natalia Palacios, A. Heather Eliassen, Walter C. Willett, Alberto Ascherio, Qi Sun, Andrew T. Chan, Wendy S. Garrett, Curtis Huttenhower, Eric B. Rimm & Mingyang Song

  2. Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA

    Christine Everett, A. Heather Eliassen, Walter C. Willett, Alberto Ascherio, Qi Sun, Andrew T. Chan & Eric B. Rimm

  3. Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    Chengchen Li, Jeremy E. Wilkinson, Lauren J. McIver & Curtis Huttenhower

  4. Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA

    Long H. Nguyen, Andrew T. Chan & Mingyang Song

  5. Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA

    Long H. Nguyen, Andrew T. Chan & Mingyang Song

  6. Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    Kerry Ivey, Natalia Palacios, Walter C. Willett, Alberto Ascherio, Qi Sun, Eric B. Rimm & Mingyang Song

  7. South Australian Health and Medical Research Institute, Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia

    Kerry Ivey

  8. Department of Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia

    Kerry Ivey

  9. Food Science and Technology Department, Institute of Agriculture and Natural Resources, University of Nebraska, Lincoln, NE, USA

    Jacques Izard

  10. Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA

    Jacques Izard

  11. Department of Public Health, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA, USA

    Natalia Palacios

  12. Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    A. Heather Eliassen, Walter C. Willett, Alberto Ascherio, Shelley S. Tworoger, Eric B. Rimm & Mingyang Song

  13. Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA

    Shelley S. Tworoger

  14. Broad Institute of Harvard and MIT, Cambridge, MA, USA

    Andrew T. Chan, Wendy S. Garrett & Curtis Huttenhower

  15. Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    Andrew T. Chan, Wendy S. Garrett & Curtis Huttenhower

  16. Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    Wendy S. Garrett

  17. Department of Medicine, Harvard Medical School, Boston, MA, USA

    Wendy S. Garrett

  18. Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA

    Wendy S. Garrett

Authors
  1. Christine Everett
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Contributions

Study concept and design: A.H.E., W.C.W., A.T.C., W.S.G., C.H., E.B.R., M.S. Acquisition of data: C.E., C.L., J.E.W., L.H.N., L.J.M., K.I., J.I., N.P., A.H.E., W.C.W., A.A., Q.S., S.S.T., A.T.C., W.S.G., C.H., E.B.R., M.S. Drafting of the manuscript: A.T.C., W.S.G., C.H., E.B.R., M.S. Critical revision of the manuscript for important intellectual content: C.E., C.L., J.E.W., L.H.N., L.J.M., K.I., J.I., N.P., A.H.E., W.C.W., A.A., Q.S., S.S.T., A.T.C., W.S.G., C.H., E.B.R., M.S. Funding acquisition: A.H.E., W.C.W., A.T.C., W.S.G., C.H., E.B.R. Administrative, technical, or material support: A.T.C., W.S.G., C.H., E.B.R., M.S. Study supervision: A.T.C., W.S.G., C.H., E.B.R., M.S.

Corresponding author

Correspondence to Mingyang Song.

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Peer review information Nature Protocols thanks Muriel Derrien and John Penders for their contribution to the peer review of this work.

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Supplementary Methods 1, Table 1, Methods 2 and 3 and Discussion.

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Everett, C., Li, C., Wilkinson, J.E. et al. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc 16, 2724–2731 (2021). https://doi.org/10.1038/s41596-021-00519-z

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