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FEMS Microbiol Rev. 2013 Sep;37(5):830-48. doi: 10.1111/1574-6976.12022. Epub 2013 Apr 22.

Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales.

Author information

1
FAS Center for Systems Biology, Harvard University, Cambridge, MA, 02138, USA.

Abstract

Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small-to-moderate-sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single-cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities.

KEYWORDS:

human microbiome; metabolic activity; metagenomics; microbial ecology; microbiota; single-cell analysis

PMID:
23550823
PMCID:
PMC3729610
DOI:
10.1111/1574-6976.12022
[Indexed for MEDLINE]
Free PMC Article
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