TrIdent

TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.

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Thank you for being a beta-tester!

Some things to know:

• This page contains basic background information on TrIdent. To learn how TrIdent is used and the expected output, visit the tutorial here.
• TrIdent comes preloaded with a small sample dataset so users can follow along with the tutorial in their own R console. The tutorial takes ~5-10 minutes.
• Find TrIdent installation instructions here.
• If you are using your own data, make sure it’s correct! You need an ultrapurified virome and a metagenome from the same sample. Find detailed input data requirements here.
• Please email me at jlmaier@ncsu.edu if you have any questions or issues.
• If you try TrIdent to any extent, please let me know your thoughts here so I can improve!
• If read coverage pattern-matching is of interest to you, check out my other R package- ProActive.

Background on Transductomics and TrIdent

TrIdent is a reference-independent bioinformatics tool that automates the transductomics data analysis by automatically detecting, classifying and characterizing potential transducing events. Transductomics is a DNA-sequencing based method for the detection and characterization of transduction events. Developed by Kleiner et al. (2020), transductomics relies on mapping reads from a virome (VLP-fraction) of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by viruses and other VLPs (Virus-like particles) will map back to the bacterial contigs of origin creating read coverage patterns indicative of potential ongoing transduction.

To obtain the data needed for transductomics, a microbiome sample of interest is split to prepare two sub-sample types:

• Whole-community: Represents the ‘whole-community’ (all bacteria, fungi, virus, etc) in the microbiome of interest
• VLP-fraction: Represents only the virus and ‘viral-like particles’ associated with the microbiome of interest
  • The VLP-fraction must be obtained by an appropriate ultra-purification protocol for your sample type to remove bacterial cells and contaminating free bacterial DNA.

Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities. Microbiome 8, 158 (2020). [https://doi.org/10.1186/s40168-020-00935-5]

With transductomics and TrIdent, a researcher can obtain information about the phage-host pairs involved in transduction, the types of transduction occuring, and the region of the host genome that is potentially transduced, which allows exploration of transferred genes.