Figure 1.

Different Pathobiomes in Discrete Compartments of the Host.

Defining the pathobiome necessitates the contextualisation of data pertaining to the symbiont profile with observations consistent with definition of a disease state (e.g., clinical signs). Since disease is often associated with specific host compartments (e.g., gut lumen, skin, epithelia of internal organs, etc.) it is relevant to consider the pathobiome also operating within these compartments. Furthermore, given that many diseases involve a progressive departure from the healthy state, the pathobiome associated with this progression may also be expected to change, leading to specific symbiont profiles (pathobiomes) in early, established, and late stages of disease (see Figure 2). The recognition of such spatial and temporal changes in the symbiont profile of a given host (and its compartments) has the potential to complicate definition of a single ‘pathobiome’ associated with a specific disease state. In the model shown here, the composition of a simple microbiome (containing four taxa, defined by dots of different colours) may differ spatially in one or more compartments and, in time, in a host undergoing progression from healthy to diseased states (diseased tissue in grey). We propose that changes in profile occurring within specific compartments may also differ (i.e., the pathobiome associated with the skin will not necessarily be the same as that observed in the blood or gut). We do not predict whether changes in profile drive the appearance of disease within specific compartments or, conversely, that diseased tissue precedes changes in the profile. Furthermore, it is not assumed that a pathobiome is less diverse than that observed during health. As such, the pathobiome associated with diseased tissue should be defined relative to the symbiont profile occurring in the healthy state.