Figure 2.

Temporal Shifts in the Pathobiome Relating to Host Health and Disease Status over Time.

The healthy symbiome (top left of figure, and associated with a particular body compartment; see Figure 1) is altered (to a pathobiome) when the host enters a progressive disease state. During early (‘subclinical’) stages of disease, the altered symbiome may precede detection of specific symptoms (in humans) and signs (in humans, animals, and plants). During later stages of disease, where symptoms and clinical signs are apparent, the pathobiome may be further altered in specific host compartments, although not necessarily as a direct cause or effect of those symptoms and signs detected. Where recovery of the host occurs (e.g., where infection by a specific agent is cleared, a treatment is provided, or an immune response occurs), reversion to a healthy symbiome may occur. In other cases, where disease progression leads to death, the disease-associated pathobiome gives way to microbial decay of host tissues. In the latter, the consortium of microbes associated with the decaying host and its compartments should not be classified as a ‘pathobiome’.