Seeing the Metabolic State of a Single Cell: How Many Steps Does It Take?
1. From “Who is there” to “What are they doing”
For decades, microbiome research has been largely driven by sequencing technologies.
Today, we can easily answer:
- Who is present in a microbial community
- What genes are encoded
- How abundant each species is
However, a more fundamental question remains largely unanswered:
What are these cells actually doing at this moment?
Which cells are actively degrading substrates? Which are synthesizing metabolites? Which are accumulating lipids or responding to stress?
This gap reflects a fundamental limitation in current microbiome analysis: we can read the genetic potential, but not directly observe the functional state of individual cells in situ.
2. The iMAPS approach: observing metabolism at single-cell resolution
The iMAPS (in-situ Metabolic Atlas Projects @ Single-cell) Consortium aims to close this gap by building a global framework for real-time, function-first microbiome analysis.
At the core of this effort is metaramanomics, a label-free, non-destructive single-cell technology based on Raman spectroscopy.
Instead of sequencing or labeling, metaramanomics directly captures intracellular biochemical vibrational signals from living cells.
Each cell generates a unique spectral fingerprint reflecting: Lipids, Proteins, Nucleic acids, Metabolic intermediates
By integrating thousands of single-cell Raman spectra, iMAPS enables a new type of biological readout: Who is there, what they are doing, why they are doing it, when, where, and what value they represent (the “6W” framework).
3. From measurement to action: the iMAPS technology stack
To translate single-cell metabolic signals into actionable biology, iMAPS integrates a suite of enabling technologies:
FlowRACS: High-throughput Raman-activated cell sorting for identifying and isolating metabolically active cells in real time.
RAMS / RACS-Seq: Precise single-cell Raman measurement combined with downstream sequencing and cultivation for functional characterization.
DCP: Bridging single-cell selection and scalable cultivation workflows, enabling efficient recovery of target functional strains.
Together, these technologies form a continuous pipeline: observe → interpret → sort → recover → cultivate / sequence
4. CAS iMAPS Summer School 2026: learning by doing
As a key annual program of the iMAPS Consortium, the CAS iMAPS Summer School 2026 will be held across:
? Qingdao ? Beijing / Xiong’an ? Shanghai
This is not a traditional lecture-based course.
It is a hands-on training program where participants directly engage with the full iMAPS workflow.
Participants will experience:
- Raman spectroscopy fundamentals and single-cell theory
- FlowRACS operation for live-cell sorting
- RAMS and DCP experimental workflows
- AI-assisted Raman data interpretation using RamanAI cloud platform
- End-to-end data generation, processing, and functional analysis
From sample preparation to data-driven interpretation, participants will walk through the complete pipeline of single-cell metabolic analysis.
5. Building the next generation of researchers
The program is designed for early-career researchers and graduate students from global universities and research institutes.
The goal is not only to introduce technologies, but to enable participants to:
- Directly experience function-first microbiome analysis
- Understand single-cell metabolic heterogeneity
- Learn how to connect spectral data with biological function
- Explore applications in Biomanufacturing, Agriculture/Environment, and Biomedicine/Human Microbiome
6. A global effort to make the invisible visible
The iMAPS Consortium is supported by the Chinese Academy of Sciences and partner institutions across multiple disciplines.
Currently, the initiative is expanding across biomanufacturing / SynBio, environment, agriculture, public health & medicine, and nutrition & health sectors, building a global network of microbiome metabolic observatories.
The long-term vision is to enable a new paradigm:
microbial metabolism should be observable, measurable, and actionable at the single-cell level.
7. Closing perspective
What does it take to see the metabolic state inside a cell?
Perhaps the answer is simple:
It takes new tools, and a new generation of researchers willing to use them.
The CAS iMAPS Summer School 2026 is designed to help make that transition possible.
