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Related Experiment Video

Updated: Jun 23, 2026

An Integrated Raman Spectroscopy and Mass Spectrometry Platform to Study Single-Cell Drug Uptake, Metabolism, and Effects
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An Integrated Raman Spectroscopy and Mass Spectrometry Platform to Study Single-Cell Drug Uptake, Metabolism, and Effects

Published on: January 9, 2020

Precision culturomics enabled by unlabeled single-cell morphology and Raman spectra.

Qiaoxing Liang1,2,3,4, Xihong Lan1,2,3,5, Jiayi Wu2

  • 1School of Life Sciences, Fudan University, Shanghai, China.

Nature Communications
|June 20, 2026
PubMed
Summary

Precision single-cell culturomics uses machine learning and Raman spectrometry to identify and culture specific bacteria from the human microbiome. This method aids in understanding microbial evolution and antibiotic resistance.

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Area of Science:

  • Microbiology
  • Genomics
  • Biotechnology

Background:

  • Selective bacterial enrichment from complex microbiomes is difficult.
  • Current methods often fail to analyze single cells before colony formation.

Purpose of the Study:

  • To develop a precision single-cell culturomics method for microbiome analysis.
  • To enable species-level identification and selective culturing of bacteria.
  • To investigate microbial evolution and antibiotic resistance at the single-cell level.

Main Methods:

  • Label-free morphology and Raman spectrometry for single-cell analysis.
  • Laser-Induced Forward Transfer (LIFT) technology for precise cell isolation.
  • Machine learning framework for species identification and spectral quantification.
  • Genomic analysis of single-cell cultures.

Main Results:

  • Achieved species-level identification of single cells in complex microbiomes.
  • Enabled selective culturing of specific bacteria from fecal and vaginal samples.
  • Quantified cellular components using Raman spectra.
  • Genomic analysis revealed antibiotic-induced resistance and convergent evolution in gut commensals.

Conclusions:

  • Precision single-cell culturomics is a powerful tool for microbiome research.
  • The method allows detailed analysis of microbial phenotypic variations.
  • Provides insights into the impact of antibiotics on microbial communities.