ArticleNature protocols2021
Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
32 citing papers in PubMed, 69 citations in OpenAlex.
- From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.Microbiology and molecular biology reviews : MMBR · 2026Review
- In situ deep-sea surface-enhanced Raman scattering sensor reveals cyanide as a key factor in cold seep nitrogen cycling.Science advances · 2026Article
- The ecology of bacterial attachment to phytoplankton.Nature microbiology · 2026Review
- Unlocking Microbial Dark Matter: A Comprehensive Review of Isolation Technologies from Traditional Culturing to Single-Cell Technologies.Microorganisms · 2026Review
- Lactulose selectively stimulates members of the gut microbiota, as determined by multi-modal activity-based sorting.Gut microbes · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-seq.Innovation (Cambridge (Mass.)) · 2025Article
- Optical sorting: past, present and future.Light, science & applications · 2025Review
- Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting.Microbiome research reports · 2025Article
- Microbial single-cell applications under anoxic conditions.Applied and environmental microbiology · 2024Review
- Diagnosing and engineering gut microbiomes.EMBO molecular medicine · 2024Review
- Raman-Activated, Interactive Sorting of Isotope-Labeled Bacteria.Sensors (Basel, Switzerland) · 2024Article
- Raman Spectroscopy as a Research and Diagnostic Tool in Clinical Hematology and Hematooncology.International journal of molecular sciences · 2024Review
- Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms.Molecules (Basel, Switzerland) · 2024Review
- scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling.mSystems · 2023Article
- Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting.Nature communications · 2023Article
- Isolation and Cultivation of Human Gut Microorganisms: A Review.Microorganisms · 2023Review
- Mid-Infrared Photothermal-Fluorescence In Situ Hybridization for Functional Analysis and Genetic Identification of Single Cells.Analytical chemistry · 2023Article
- Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles.Frontiers in microbiology · 2023Review
- Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 5 countries.
Funding
Abstract
Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.
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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.