TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Transduction is a key mechanism of horizontal gene transfer in bacteria, mediated by virus-like particles (VLPs).
• Transductomics, a sequencing-based approach, identifies DNA within VLPs but requires laborious manual analysis of VLP-derived DNA.
• Current manual methods are time-consuming and limit the scalability of transductomics for large datasets.

Purpose of the Study:

• To develop an automated computational tool for transductomics data analysis.
• To improve the efficiency, accessibility, and reproducibility of transductomics research.
• To investigate bacterial DNA packaging by VLPs in the murine gut microbiota.

Main Methods:

• Development of a novel pattern-matching algorithm named TrIdent (Transduction Identification).
• Implementation of TrIdent as an R package for public use.
• Validation of TrIdent by comparing its classifications against manual classifications on existing and newly generated transductomics datasets.

Main Results:

• TrIdent provides classifications comparable to manual analysis, demonstrating high agreement with human experts.
• The software drastically reduces analysis time, making transductomics feasible for large-scale studies.
• Analysis of murine gut transductomes using TrIdent revealed significant enrichment of Oscillospiraceae and Turicibacteraceae DNA within VLPs.

Conclusions:

• TrIdent offers a significant advancement in transductomics, providing a faster, more reproducible, and accessible alternative to manual data processing.
• The automated analysis facilitated the discovery of specific bacterial families heavily involved in transduction within the murine gut.
• This tool empowers broader application of transductomics for understanding microbial gene transfer dynamics.