Probing the functional significance of wild animal microbiomes using omics data

Host-associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from studies of a handful of animal models and humans. To test the generality of this conclusion, studies in non-model and wild animals are needed. However, whilst microbiome taxonomic diversity has recently received much attention, characterization of its functional potential in wild animals is lagging behind. Functional “omics” approaches, such as metagenomics, metatranscriptomics, and metabolomics, represent promising techniques to probe the significance of host-associated microbiomes in the wild. In this review, we propose to (1) briefly define the main available functional omics tools along with their strengths and limitations, (2) summarise the key advances enabled by omics tools to understand microbiome function in human and animal models, (3) showcase examples of how these methods have already brought invaluable insights into wild host microbiomes and (4) provide guidelines on how to implement these tools to address outstanding questions in the field of wild animal microbiomes. To conclude, we suggest that functional omics tools represent a promising approach to probe the functional significance of wild host microbiomes once the presence of an abundant and resident microbiota has been established using more traditional (and less expensive) approaches such as qPCR and metabarcoding.