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Related Experiment Video

Updated: Oct 21, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

863

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.

Subina Mehta1, Marie Crane1, Emma Leith1

  • 1University of Minnesota, Twin Cities, MN, 55455, USA.

F1000Research
|September 7, 2021
PubMed
Summary
This summary is machine-generated.

The ASaiM analysis framework was optimized for metatranscriptomics, enabling researchers to study microbial RNA expression. This validated workflow, ASaiM-MT, aids in understanding microbiome functional responses in diverse studies.

Keywords:
Galaxyfunctional analysismetatranscriptomicsmicrobiome

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • The Earth Microbiome Project (EMP) advanced understanding of microbial communities and their environmental/health impacts.
  • Next-generation sequencing (NGS) and bioinformatics have deepened insights into microbial taxonomic and genetic composition.
  • Metagenomics reveals genetic potential but lacks gene product quantification, unlike metatranscriptomics which studies RNA expression and active pathways.

Purpose of the Study:

  • To validate and optimize the ASaiM analysis framework specifically for metatranscriptomics data.
  • To develop a robust workflow for analyzing dynamic gene expression in microbial communities.
  • To enhance the interrogation and characterization of metatranscriptomic data within broader meta-omic studies.

Main Methods:

  • Focused on validating and optimizing existing tools within the ASaiM framework for metatranscriptomics.
  • Developed and tested a specific workflow for metatranscriptomics data analysis.
  • Ensured the workflow is publicly available, documented, and supported with training materials.

Main Results:

  • Successfully validated and optimized ASaiM for metatranscriptomics data analysis.
  • Delivered a robust and improved ASaiM-metatranscriptomics (ASaiM-MT) workflow.
  • Demonstrated the workflow's capability to analyze dynamic functional responses of microbiomes.

Conclusions:

  • The optimized ASaiM-MT workflow provides a reliable tool for metatranscriptomics research.
  • Enables researchers to gain deeper insights into the functional dynamics of microbial communities.
  • Facilitates the integration of metatranscriptomic data into comprehensive microbiome studies.