The human microbiome: ecosystem resilience and health

Abstract

Given the importance of the microbiome for human health, both the stability and the response to disturbance of this microbial ecosystem are crucial issues. Yet, the current understanding of these factors is insufficient. Early data suggest there is relative stability in the microbiome of adults in the absence of gross perturbation, and that long-term stability of the human indigenous microbial communities is maintained not by inertia but by the action of restorative forces within a dynamic system. After brief exposures to some antibiotics, there is an immediate and substantial perturbation and at least a partial recovery of taxonomic composition. Responses to antibiotics are individualized and are influenced by prior experience with the same antibiotic. These findings suggest that the human microbiome has properties of resilience. Besides serving to reveal critical underlying functional attributes, microbial interactions, and keystone species within the indigenous microbiota, the response to disturbance may have value in predicting future instability and disease and in managing the human microbial ecosystem.

Figure 1

‘Basins of attraction’, or alternative stable states or regimes, in a stability landscape. External forces and internal change can alter the landscape (from scheme 1 to 4) such that an ecosystem (represented as the ball) becomes less resilient and attracted to a new stable state (or regime). Because the landscape topography predicts the near future state of the ecosystem, the topography for a specific human habitat may have clinical utility in patient management. (From ref )

Figure 2

Ecological distance (Bray-Curtis metric) between last pre-ciprofloxacin sample and all others from the same subject over time. There is relative stability before each of the two 5-day courses of ciprofloxacin (arrows) and variable bacterial community recovery, but there is a compounded effect of the two antibiotic courses in each of the subjects, D, E and F. (Modified from ref )