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
Summary
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).
- 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.
