Fig. 4

The proposed five-step framework of research and innovation to move from descriptive to predictive reef microbial monitoring, and from reactive to proactive reef management. Functional meta-omics datasets are critical to discover microbial indicators of poor reef health in the field (Phase 1), however high costs (see ‘Assay price’) and long bioinformatics processing times (see ‘Timeframes’) of microbial meta-omics datasets suggest their limited utility for rapid decision-making in reef management. We highlight that this milestone has been largely achieved through various localised studies, though in the years to come, the integration of recently generated datasets obtained in large-scale surveys (most notably the Tara Pacific Expedition) will be crucial to understand the ubiquity of identified microbial indicators at global scales. Once microbial indicators of poor ecosystem health are identified based on functional meta-omics datasets, experimental validation (Phase 2) is needed to confirm the same patterns occur in laboratory conditions, as well as to identify the causality of microbiome-environment associations from the field, which we predict still remains a distant goal and will require years of research. Once experimentally validated, microbial indices can be formulated (Phase 3) and applied research can commence to develop rapid (within weeks, days or minutes, see ‘Timeframes’) and cost-effective (see ‘Assay price’) assays to quickly assess reef health in the field (Phase 4), which can be used in proactive reef management and rapid decision-making (Phase 5)