Proximity ligation sequencing of mixed bacterial communities

Full Project Title

Proximity ligation with shotgun sequencing to link antibiotic resistance genes with their bacterial hosts in mixed bacterial communities

Project Summary

Metagenomics provides in-depth information about the microbiome in a specific sample, including bacterial composition, metabolic capacity, carriage of antibiotic resistance genes, plasmids, phage, and other mobile genetic elements. However, linking the possession of mobile genetic elements and their associated antibiotic resistance genes to a specific strain in the mixed bacterial community is often lost due to the fragmentation of genomic DNA during normal metagenomic sequencing protocols. A proximity ligation sequencing assay for metagenomic samples has been developed to obtain complete microbiome assemblies by associating mobile genetic elements with their hosts, and has been successfully used to study microbiomes in environments such as wastewater and animal infection samples. This project seeks to establish this protocol at UQ to enable high-resolution analysis of mixed bacterial communities.

We aim to optimise the proximity ligation with shotgun sequencing protocol for the purpose of linking antibiotic resistance genes and plasmids with their bacterial hosts within mixed population communities.

Potential Outcomes

This project will establish in-house detailed molecular and bioinformatic protocols for the deployment of proximity ligation sequencing methodology in metagenomic samples, including determination of its accuracy and limit of detection. Our protocols and validation results will provide a valuable benchmark and guide for future users at UQ to design experiments on their bacterial communities of interest.