Food Science and Technology Department

 

ORCID IDs

http://orcid.org/0000-0002-2599-2937

http://orcid.org/0000-0002-0112-190X

http://orcid.org/0000-0003-4956-2429

http://orcid.org/0000-0002-8813-0816

http://orcid.org/0000-0002-5904-5436

http://orcid.org/0000-0001-7284-6767

http://orcid.org/0000-0002-1110-0096

Date of this Version

1-15-2018

Citation

2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Comments

Nature Microbiology | VOL 3 | MARCH 2018 | 356–366 | www.nature.com/naturemicrobiology

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.

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