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Related Experiment Video

Updated: Jun 1, 2025

A Microfluidic Platform for Precision Small-volume Sample Processing and Its Use to Size Separate Biological Particles with an Acoustic Microdevice
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A single microfluidic device for multi-omics analysis sample preparation.

Ranjith Kumar Ravi Kumar1, Iman Haddad1, Massamba Mbacké Ndiaye1

  • 1Spectrométrie de Masse Biologique et Protéomique SMBP, ESPCI Paris, LPC CNRS UMR 8249, PSL University, 10 Rue Vauquelin, F-75005 Paris, France. yann.verdier@espci.fr.

Lab on a Chip
|January 17, 2025
PubMed
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This study introduces a new workflow using the ChipFilter device for simultaneous proteomic and genomic analysis of microbial samples. This method enhances microbiome comprehension by enabling parallel analysis of proteins and nucleic acids from a single sample, reducing bias.

Area of Science:

  • Microbiology
  • Biotechnology
  • Analytical Chemistry

Background:

  • Comprehensive microbiome analysis requires integrating multi-omics data, such as genomics and proteomics.
  • Accurate sample processing and analytical methods are essential for reliable microbiome data.
  • The ChipFilter device was previously validated for microbial proteomic analysis.

Purpose of the Study:

  • To develop and validate a workflow for concurrent proteomic and genomic analysis from the same microbial sample.
  • To assess the efficacy of the ChipFilter device in preparing samples for parallel omics analyses.
  • To evaluate the impact of the workflow on sample bias, especially for low-abundant samples.

Main Methods:

  • Utilized the ChipFilter device for simultaneous lysis and proteolysis of microbial cultures (E. coli, B. subtilis, S. cerevisiae).

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Last Updated: Jun 1, 2025

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  • Performed peptide recovery for Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) based proteomic analysis.
  • Recovered and amplified DNA using Polymerase Chain Reaction (PCR) for subsequent genomic analysis.
  • Applied the workflow to a complex microbial mixture and compared DNA sequencing results with a commercial kit.

    • Main Results:

    • Successfully identified microbial proteins using LC-MS/MS after ChipFilter processing.
    • Achieved successful DNA amplification and sequencing from the same samples used for proteomic analysis.
    • Identified over 5000 proteins in a complex microbial mixture.
    • DNA sequencing performance was comparable to DNA extracted using a commercial kit, even with prior proteolysis.

    Conclusions:

    • The ChipFilter device is suitable for preparing samples for parallel proteomic and genomic analyses.
    • This integrated workflow is particularly beneficial for analyzing low-abundant microbial samples.
    • The method significantly reduces sampling bias in multi-omics microbiome studies.