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Stability of the human faecal microbiome in a cohort of adult men


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

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.

Correspondence to Curtis Huttenhower or Andrew T. Chan.

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Further reading

Fig. 1: Experimental design.
Fig. 2: Inter-individual differences in organismal composition and functional potential appear to be preserved, unlike the more variable metatranscriptomes.
Fig. 3: Stability of individual species, genes and transcripts over 6 months is correlated with average baseline relative abundance and prevalence.
Fig. 4: Relating metagenomic and metatranscriptomic stability over time.
Fig. 5: Exploring the stability of gene expression.