Metatranscriptome of human faecal microbial communities in a cohort of adult men

Galeb S. Abu-Ali, Raaj S. Mehta, Jason Lloyd-Price, Himel Mallick, Tobyn Branck, Kerry L. Ivey, David A. Drew, Casey Dulong, Eric Rimm, Jacques Izard, Andrew T. Chan, Curtis Huttenhower

Research output: Contribution to journalArticle

37 Scopus citations

Abstract

The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome.

Original languageEnglish (US)
Pages (from-to)356-366
Number of pages11
JournalNature Microbiology
Volume3
Issue number3
DOIs
StatePublished - Mar 1 2018

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ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Applied Microbiology and Biotechnology
  • Genetics
  • Microbiology (medical)
  • Cell Biology

Cite this

Abu-Ali, G. S., Mehta, R. S., Lloyd-Price, J., Mallick, H., Branck, T., Ivey, K. L., Drew, D. A., Dulong, C., Rimm, E., Izard, J., Chan, A. T., & Huttenhower, C. (2018). Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nature Microbiology, 3(3), 356-366. https://doi.org/10.1038/s41564-017-0084-4