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

Nat Microbiol. 2018 Mar;3(3):347-355. doi: 10.1038/s41564-017-0096-0. Epub 2018 Jan 15.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Bacteria / classification
  • Cohort Studies
  • Feces / microbiology*
  • Follow-Up Studies
  • Gastrointestinal Microbiome*
  • Gene Expression Profiling
  • Gene Expression*
  • Health Personnel / statistics & numerical data
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Male
  • Metagenomics
  • Microbiota*
  • Middle Aged
  • Prospective Studies