ArticleProceedings of the National Academy of Sciences of the United States of America2022
SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 49 citations in OpenAlex.
- Social lives of bacteria as revealed through CLASI-FISH.Essays in biochemistry · 2026Review
- Animal gut microbes and microbiomes in the 21st century and beyond.Science China. Life sciences · 2026Review
- Illuminating aging with multimodal optical metabolic imaging.Science advances · 2026Review
- Stimulated Raman photothermal microscopy: theory and implementation.Advances in optics and photonics · 2026Article
- Review
- The Next Frontier in Vibrational Imaging: Chemically Designed Raman Probes Pass the Spectral Barrier.JACS Au · 2026Review
- Simultaneous dual-Raman-shift scanning-free stimulated Raman scattering microscopy for label-free biomolecular imaging.Nature communications · 2026Article
- BactoRamanBioNet: A Multimodal Neural Network for Bacterial Species Identification Using Raman Spectroscopy and Biological Knowledge.Sensors (Basel, Switzerland) · 2026Article
- A Systems Approach to Endophyte-Mediated Plant Holobiont and Microbiome Dynamics.Plants (Basel, Switzerland) · 2026Review
- Recent advances in Raman probes for multiplexed bioimaging.Inflammation and regeneration · 2025Review
- SIP-SRS Imaging of Cell Wall Synthesis Identifies a Synergy between Micafungin and Amphotericin B.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Deuterium-oxide-assisted stimulated Raman scattering microscopy: metabolic imaging for precision medicine.Biophotonics discovery · 2025Review
- Light and metabolism: label-free optical imaging of metabolic activities in biological systems [Invited].Biomedical optics express · 2025Review
- Illuminating life processes by vibrational probes.Nature methods · 2025Review
- Advanced vibrational microscopes for life science.Nature methods · 2025Review
- Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-seq.Innovation (Cambridge (Mass.)) · 2025Article
- SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.Nature microbiology · 2025Article
- GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities.The ISME journal · 2025Article
- Fiber laser based stimulated Raman photothermal microscopy towards a high-performance and user-friendly chemical imaging platform.PhotoniX · 2025Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.