A single cell is the atomic unit of function and the basic step of evolution for life forms on Earth, thus, rapid and exhaustive profiling of the single-cell “in-situ metabolic phenome” and its matching full “genome” plus “culturome” can address “who, what, why, wealth, where, when” (6W) in a microbiome at the ultimate precision and depth. To support this ambitious mission, we have established a prototypic Microbiome Exploration Facility (MEx), by inventing: (i) a high-throughput Flow-mode Raman-activated Cell Sorter (FlowRACS), (ii) a multi-modal Raman-activated Cell Sorter coupled to one-cell-one-tube sequencing or culture (RACS-Seq/Culture), and (iii) a Digital Colony Picker (DCP) that enables mass-paralleled fully-automated single-cell culture, physiological phenotyping and laser-based export of target mono-cultures. Together, these novel instruments support the “in-situ metabolic phenome directed single-cell genomics and culturomics” workflow in an automated and high-throughput manner. To answer and compare the 6W question for the plethora of ecosystems on Earth, we propose the iMAPS Consortium, in which academic, industrial and governmental partners collaborate to build an international network of MEx facilities, and generate single-cell in-situ metabolic atlases via a unified framework of experimental and data standards at a global scale. The iMAPS may profoundly change the way of monitoring, mining and exploiting the power of microbiome, in either natural or synthetic ecosystems. 

Single-cell Metabolic Phenome,6W Question in Microbiome,Microbiome Exploration Facility (MEx),iMAPS Consortium,Single-cell in-situ Metabolic Atlases