Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.

ABSTRACT: The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solutio

SUBMITTER: Bradley PH 

PROVIDER: S-EPMC6084841 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature