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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes.

Javier Macho Rendón1, Benjamin Lang2,3, Marc Ramos Llorens1

  • 1Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.

Nucleic Acids Research
|October 21, 2020
PubMed
Summary

DualSeqDB is a new database that analyzes gene expression changes in bacteria and hosts during infection. This resource aids in understanding bacterial pathogenesis and developing new antimicrobial therapies.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Antibiotic resistance is a global health threat, yet bacterial pathogenesis mechanisms are poorly understood.
  • High-throughput sequencing generates vast transcriptomic data crucial for infection mechanism research.

Purpose of the Study:

  • To introduce DualSeqDB, a database for identifying gene transcriptional changes in pathogenic bacteria and their hosts during infection.
  • To provide a standardized resource for analyzing differential gene expression data.

Main Methods:

  • Compiled data from eight studies, including nearly 300,000 entries.
  • Analyzed raw transcriptomic data using a standardized bioinformatics pipeline.
  • Included data from seven pathogenic bacterial strains and various host cell types/tissues (human, mouse, non-human primate).

Main Results:

  • DualSeqDB contains comprehensive differential gene expression data for bacteria and hosts under various infection conditions (in vivo and in vitro).
  • Ensured data consistency through a uniform analysis pipeline across diverse studies.
  • Covers multiple host species and bacterial pathogens at different infection time points.

Conclusions:

  • DualSeqDB facilitates the systematic characterization of genes involved in host-pathogen interactions.
  • The database supports the development of novel antimicrobial strategies and targeted therapies against infectious diseases.