Holobiont metagenomics

Recent advances in microbiology have revealed the importance of the relationship between multicellular organisms and their microbiome. The links between host and micro-organisms (both prokaryotes and eukaryotes) are so strong that they can drive the development of host traits normally not associated with aspects of microbiology, such as behaviour. In addition, a consistent fraction of the eukaryotic cell derives from ancient associations between prokaryotes, which makes the study of such links crucial for the study of the evolution of life on Earth.

Two concepts have been developed to tackle this issue: the holobiont (an independent entity composed of the host and all its associated micro-organisms) and the hologenome (the ensemble of genomes of host-associated micro-organisms, the nuclear and the organellar genome of the host). Studying and understanding the processes guiding these associations can be paramount both from an ecological and an evolutionary point of view as variations in the environment can have many different impacts on the holobiont and the hologenome, with feedbacks on organism fitness, including its capacity to respond to stresses and disturbances.

Since the majority of the organisms comprising an holobiont cannot be cultured nor studied outside their host, integrated culture-independent approaches are necessary, such as metagenomic and metabarcoding approaches. These allow, after the isolation of the nucleic acids composing the fraction of holobiont/hologenome, their sequencing to obtain a wider, clearer view of the identity and function of the components of the holobiont and the relationships they have with their hosts.