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Related Experiment Video

Updated: Dec 16, 2025

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High-Throughput Stool Metaproteomics: Method and Application to Human Specimens.

Carlos G Gonzalez1, Hannah C Wastyk2, Madeline Topf3

  • 1Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, California, USA.

Msystems
|July 2, 2020
PubMed
Summary
This summary is machine-generated.

A new high-throughput stool proteomic processing pipeline (SHT-Pro) enables rapid, reproducible analysis of host-gut microbe interactions. This method significantly accelerates sample processing, facilitating large-scale clinical studies and advancing microbiome research.

Keywords:
dietfermentedfiberhigh-throughputmass spectrometrymetaproteomicsmicrobiomeproteomicsstool

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Area of Science:

  • Microbiome research
  • Proteomics
  • Host-microbe interactions

Background:

  • Stool proteomics offers insights into host-gut microbe interactions but is underutilized due to low throughput and contamination issues.
  • Existing DNA sequencing methods provide microbial composition but lack mechanistic insights into host-microbe protein dynamics.
  • Mass spectrometry-based proteomics is powerful but hampered by laborious, low-throughput pipelines for clinical stool samples.

Purpose of the Study:

  • To develop a high-throughput, reproducible, and quantitative stool proteomic processing pipeline.
  • To address the limitations of existing methods for large-scale stool sample analysis.
  • To enable advanced profiling of host-gut microbiome interactions in clinical settings.

Main Methods:

  • Development of a novel stool proteomic processing pipeline (SHT-Pro).
  • Processing of 290 stool samples from a dietary intervention study.
  • Quantitative mass spectrometry analysis for protein profiling.

Main Results:

  • The SHT-Pro pipeline processed 290 samples in ~1.5 weeks, significantly increasing throughput.
  • Identified a monotonic increase in altered proteins in participants on fiber- or fermented food-enriched diets.
  • Achieved up to 89% accuracy in classifying participants based on diet-altered proteomic profiles.

Conclusions:

  • This study presents the first high-throughput, technically reproducible method for stool proteomics.
  • SHT-Pro has the potential to establish stool proteomics as a key tool for clinical microbiome research.
  • The developed pipeline is adaptable for large-scale clinical studies, accelerating discovery in host-gut interactions.