title: Functional and phylogenetic assembly of microbial communities in the human microbiome.
abstract: 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.
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA.
authors.forename: Afrah
authors.initials: A
authors.lastname: Shafquat
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA.
authors.forename: Regina
authors.initials: R
authors.lastname: Joice
authors.affiliation: Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
authors.forename: Sheri L
authors.initials: SL
authors.lastname: Simmons
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA; The Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 301 Binney Street, Cambridge, MA 02142, USA. Electronic address: chuttenh@hsph.harvard.edu.
authors.forename: Curtis
authors.initials: C
authors.lastname: Huttenhower
mesh_terms: D006801:Humans; D064307:Microbiota / Q000502:physiology*; D010802:Phylogeny
keywords: functional ecology; human microbiome; metagenomics; microbial ecology