Fig. 3
Top-down and bottom-up approaches to engineer microbiomes. A The panel represents the bottom-up design methodology that begins with isolates. Genome editing boosts system functions by recognizing gene editing sites that reroute metabolic flux to the intended secondary metabolites. B The panel represents the top-down design methodology. a Depiction of native endophytic micriobiome hub with interacting partners. Categories of the hub endomicrobiome are exclusively based on network topology information within a microbial network. The possible roles of secondary metabolites (SM) inducing core endomicrobiome (CEM) that are expected to mediate interactions between plants and native microbial species includes (i) Scoring of CEMs based on enrichment of SM inducing microbial species in the rhizosphere through chemoattractants released in the form of root exudates. (ii) Restrainment of deleterious biotic stressors. (iii) Bolstering of SM inducing functional CEMs by applying facilitative microbiomes. b Preparation of endosymbiotic cells derived from plant samples. (i) Surface sterilization of plant tissue for removal of epiphytic microbes. (ii) Sample crushing followed by gradient centrifugation for concentrating endomicrobiome. (iii) Isolation of single cell microbial droplets with CEMs using microdroplet devices (iv) Compartmentalization of single cell CEMs using microfluidic devices to separate cells from microbial mixtures. (v) Cell sorting using vibrational spectroscopy techniques like surface enhanced Raman scattering (SERS)/tip enhanced Raman scattering (TERS) and Fourier transform infrared (FTIR) (vi) Optimization of culture media for isolating CEM/s with varying nutritional requirements and growth conditions. (vii) Library development of all possible CEMs using permutations and combinations (viii) High throughput inoculation of sets of CEMs in seeds/seedlings/plants (ix) Identification of potential SM inducing CEMs by chemical profiling of plant tissue/s (x) Mass multiplication of potential SM inducing CEMs for large scale cultivation with the ultimate aim of increasing microbial heterogeneity. The middle panel represents the key aspects of microbiome engineering with increasing and decreasing complexities in bottom-up and top-down approaches. The various shapes of the microbes indicate different isolates chosen throughout the designing process