Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples

shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of Golden Delicious apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The functional significance of the variations was explored using microbial network modeling algorithms to reveal the metabolic role of specific phylogenetic groups.