Case study

METAGENOMICS

Develop a ready-to-use and robust toolbox for Metagenomic applications and evaluate microbiome-based biomarkers of added medical value

Cloud tag

Background

In collaboration with BIOASTER, the industrial partner wanted to better understand the potential of Metagenomics analysis for diagnostic purpose.

Challenges

Gut microbiota is emerging as new diagnostic and prognostic marker and/or therapeutic target to improve the management of cancer and infectious diseases.

However, methods of sample collection and preparation are not standardized yet. In addition, reliable and ready to use bioinformatics analysis pipeline and advanced softwares are needed for results interpretation by physician end users.

Solution

The project aimed at developing and evaluating sample preparation methods and 16S-metagenomic pipeline of analysis and softwares useful for assessing – by NGS – microbiome markers derived from human clinical specimens like stools, blood, urine and broncho-alveolar lavage (BAL).

Another objective of this multifaceted project was to evaluate the diagnostic added value of microbiome biomarkers in some clinical applications.

Results

The outcome of this ambitious project was multiple:

  • We have performed a head-to-head comparison of proprietary and commercial sample preparation methods from stools samples and have identified the most reliable and robust protocols.
  • We have developed and enriched 16S metagenomic bioinformatics pipelines of analysis for the identification of pathogen antibiotic resistance gene from BAL samples
  • We have developed and validated a software solution for 16S metagenomic profiling interpretation helpful for physicians. This software has been out-licensed to an industrial partner.
  • We have discover and validated viral metagenomic biomarkers associated to disease prognosis in hematological patients under chemotherapy regimen

Outlook

Successful results obtained in this project permitted to the industrial partner to develop a robust and reliable workflow for accurate metagenomics analysis in several diagnostic applications.

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