Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism

•Animal gut microbiomes impact diverse aspects of host physiology.•Functional metagenomics of gut microbiomes validate their in vivo roles within hosts.•Bacterial genes required for the use of local nutrients confer colonization ability in vivo.•Commensal alcohol dehydrogenase activity controls Drosophila development.

Accumulating data sets of gut microbiome by next-generation sequencing allow us to gain a comprehensive view of the functional diversity of the gut-associated metagenome. However, many microbiome functions are unknown and/or have only been predicted, and may not necessarily reflect the in vivo function within a gut niche. Functional genomic and metagenomic approaches have been successfully applied to broaden the understanding of invertebrate and vertebrate gut microbiome involved in diverse functions, including colonization ability, nutritional processing, antibiotic resistance, microbial physiology and metabolism, and the modulation of the host physiology. In this review, we discuss the recent knowledge obtained from the study of functional genomics and metagenomics of the animal intestine and its potential values for understanding gut microbiota–animal mutualism.