Microbes surround us—from inside our belly to the soil and oceans—and they do work essential for health, agriculture, and the world. And yet they are notoriously difficult to study because microbiomes are so complex and most microbes can’t be cultured in a lab. Conventional analytical methods show what microbes are doing at one moment, but not necessarily what they are doing in the next one.
This article explains how new chemical biology reagents are transforming what microbiome scientists do. These reagents cover:
- Bioorthogonal chemistry (BONCAT): tagging active microbes by adding labels to proteins that are being newly made.
- Stable isotope probing (SIP): monitoring how microbes break down nutrients by tracing “heavy” isotopes of elements such as carbon and nitrogen.
- Raman-based single-cell phenotyping: scanning chemical tags of living cell.
Together, these methods enable researchers to “see” what microbes are alive, what nutrients they are consuming, and how they are interacting with one another. By linking identity (who the microbes are) with activity (what they’re doing), scientists can at last close the gap between genetic potential and actual function.
The review also mentions thrilling innovations like BONCAT together with cell sorting (BONCAT-FACS), SIP workflows on an automated platform, and microfluidic Raman-activated cell sorting (RACS). Such methods speed up, make precise, and enable scalability. Most importantly, by combining these chemical biology tools with “multi-omics” (genomics, transcriptomics, proteomics, and metabolomics), a significantly more detailed view of microbial ecosystems is built.
Why is that the case? Because improved tools for tracking microbiomes can speed up discoveries in ecology (carbon cycling, nitrogen fixation), health (gut microbiome diagnosis), and biotechnology (wastewater treatment, bioremediation, novel therapeutics). Such tools can even aid us in designing how to control microbiomes to benefit humans and the planet.
In brief, the article contends that chemical biology is revealing a new era in the science of microbiome—through which we can move from annotating communities to engineering and controlling them.
Full text: Yumechris Amekan, Kelly R. Redeker, James P.J. Chong, Innovative chemical biology tools for monitoring activity in complex microbiomes, Current Research in Biotechnology, Volume 10, 2025, 100334, https://doi.org/10.1016/j.crbiot.2025.100334.