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Trends Microbiol DOI:10.1016/j.tim.2014.01.011

Functional and phylogenetic assembly of microbial communities in the human microbiome.

Publication TypeJournal Article
Year of Publication2014
AuthorsShafquat, A, Joice, R, Simmons, SL, Huttenhower, C
JournalTrends Microbiol
Date Published2014 May
KeywordsHumans, Microbiota, Phylogeny

Microbial communities associated with the human body, that is, the human microbiome, are complex ecologies critical for normal development and health. The taxonomic and phylogenetic composition of these communities tends to significantly differ among individuals, precluding the definition of a simple, shared set of 'core' microbes. Here, we review recent evidence and ecological theory supporting the assembly of host-associated microbial communities in terms of functional traits rather than specific organisms. That is, distinct microbial species may be responsible for specific host-associated functions and phenotypes in distinct hosts. We discuss how ecological processes (selective and stochastic forces) governing the assembly of metazoan communities can be adapted to describe microbial ecologies in host-associated environments, resulting in both niche-specific and 'core' metabolic and other pathways maintained throughout the human microbiome. The extent to which phylogeny and functional traits are linked in host-associated microbes, as opposed to unlinked by mechanisms, such as lateral transfer, remains to be determined. However, the definition of these functional assembly rules within microbial communities using controlled model systems and integrative 'omics' represents a fruitful opportunity for molecular systems ecology.


Alternate JournalTrends Microbiol.
PubMed ID24618403
PubMed Central IDPMC4008634
Grant ListR01 HG005969 / HG / NHGRI NIH HHS / United States
U54 DK102557 / DK / NIDDK NIH HHS / United States
R01HG005969 / HG / NHGRI NIH HHS / United States