Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples—one pair collected 24–72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics.

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We thank the participants who graciously participated in this research, K. Stewart and G. Gupta at the Massachusetts General Hospital (MGH) who assisted with recruitment for the study, and S. Sawyer (Brigham and Women’s Hospital), M. Atar (MGH), C. Dulong (MGH and the Harvard T. H. Chan School of Public Health) and T. Poon (Broad Institut) for their assistance with project logistics, sample handling, nucleic acid extractions and sequencing. This work was supported by National Institutes of Health grants U54DE023798, UM1 CA167552, U01CA152904, R01 HL35464, R01CA202704 and K24DK098311, as well as by the Starr Cancer Consortium. A.T.C. was in part supported by the Stuart and Suzanne Steele MGH Research Scholars Program. J.I. was in part supported by the Nebraska Tobacco Settlement Biomedical Research Development Fund. R.S.M. was supported by a Howard Hughes Medical Institute Medical Research Fellowship and an AGA–Eli and Edythe Broad Student Research Fellowship.

Author information

Author notes

  1. Raaj S. Mehta, Galeb S. Abu-Ali, Curtis Huttenhower and Andrew T. Chan contributed equally to this work.


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

    • Raaj S. Mehta
    • , David A. Drew
    • , Paul Lochhead
    • , Amit D. Joshi
    • , Hamed Khalili
    • , Gordon T. Brown
    • , Mingyang Song
    • , Long H. Nguyen
    •  & Andrew T. Chan
  2. Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA

    • Raaj S. Mehta
    • , David A. Drew
    • , Paul Lochhead
    • , Amit D. Joshi
    • , Hamed Khalili
    • , Gordon T. Brown
    • , Mingyang Song
    • , Long H. Nguyen
    •  & Andrew T. Chan
  3. Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    • Galeb S. Abu-Ali
    • , Jason Lloyd-Price
    • , Ayshwarya Subramanian
    • , Casey DuLong
    • , Himel Mallick
    •  & Curtis Huttenhower
  4. The Broad Institute, Cambridge, MA, USA

    • Galeb S. Abu-Ali
    • , Jason Lloyd-Price
    • , Ayshwarya Subramanian
    • , Himel Mallick
    •  & Curtis Huttenhower
  5. Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA

    • Kerry L. Ivey
    •  & Eric B. Rimm
  6. South Australian Health and Medical Research Institute, Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia

    • Kerry L. Ivey
  7. Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA

    • Eric B. Rimm
    •  & Andrew T. Chan
  8. University of Nebraska, Lincoln, NE, USA

    • Jacques Izard


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J.I., A.T.C. and C.H. designed and managed the study. R.S.M., D.A.D., K.L.I., G.T.B., C.D., E.B.R. and J.I. collected the samples and generated the data. R.S.M., G.S.A.-A., D.A.D., J.L.-P., A.S., P.L., A.D.J., H.K., G.T.B., M.S., L.H.N. and H.M. analysed the data. R.S.M., G.S.A.-A., D.A.D., K.L.I., J.I., C.H. and A.T.C. prepared and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Curtis Huttenhower or Andrew T. Chan.

Supplementary information

  1. Supplementary Information

    Supplementary Discussion, Supplementary Figure 1, Supplementary Table 1, Supplementary References.

  2. Life Sciences Reporting Summary