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Related Concept Videos

iChip01:24

iChip

The cultivation of environmental microorganisms has long been hindered by the inability to replicate complex native conditions in vitro. The isolation chip (iChip) addresses this limitation by facilitating the growth of previously uncultivable microorganisms through in situ incubation. Designed for high-throughput microbial cultivation, the iChip comprises hundreds of microchambers, each capable of housing a single microbial cell. These microchambers are loaded with a mixture of molten agar and...

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Related Experiment Video

Updated: Jun 23, 2026

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms
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ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia.

Ranjith Kumar Ravi Kumar1, Massamba Mbacke Ndiaye1, Iman Haddad1

  • 1Spectrométrie de Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France.

Journal of Proteome Research
|February 14, 2024
PubMed
Summary
This summary is machine-generated.

A novel microfluidic ChipFilter device enables direct cell lysis and protein digestion for metaproteomics. This method enhances microbial protein identification, even from low-density samples, improving microbiome functional analysis.

Keywords:
metaproteomicproteomicsample preparation

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Area of Science:

  • Microbiology
  • Proteomics
  • Analytical Chemistry

Background:

  • Metaproteomics offers functional insights into microbiomes but faces challenges in protein extraction from complex samples.
  • Current methods struggle with low cell densities and heterogeneous microbial communities.

Purpose of the Study:

  • To evaluate a ChipFilter microfluidic device for direct microbial cell lysis and protein digestion in metaproteomic workflows.
  • To assess the efficiency of the ChipFilter coupled with LC-MS/MS for identifying microbial proteins.

Main Methods:

  • Utilized a ChipFilter microfluidic device for direct cell lysis and in-situ protein digestion.
  • Employed liquid chromatography tandem mass spectrometry (LC-MS/MS) for peptide identification and quantification.
  • Tested the system with pure cultures (E. coli, B. subtilis, S. cerevisiae) and a complex 17-species gut microbiome mixture.

Main Results:

  • The ChipFilter system successfully identified microbial proteins directly from lysed cells.
  • Higher numbers of proteins and peptides were identified compared to standard protocols, particularly at low cell densities.
  • The ChipFilter preparation identified and quantified 16 out of 17 species in a complex gut microbiome sample.

Conclusions:

  • The ChipFilter microfluidic device is an effective tool for metaproteomic analysis of microbiomes.
  • This approach overcomes technical challenges in protein extraction, especially for low-volume or low-cell-density samples.
  • The method facilitates improved functional characterization of microbial communities.