Advancing Long-Read Metagenomics: Computational Tools for Real-Time Monitoring and Biotechnological Applications

Abstract

Metagenomics has expanded our ability to study complex microbial communities, yet its practical application faces barriers including the requirement of programming expertise, and complex command-line workflows that hinder rapid analysis and interpretation. These challenges can affect collaborative research between wet-lab scientists and bioinformaticians, often creating bottlenecks in time-sensitive studies.

This dissertation addresses these challenges by describing accessible computational tools specifically optimized for long-read sequencing data and real-time monitoring of microbial communities. The research includes an investigation of chain-elongating microbiomes in bioreactors, revealing key microbial players and metabolic pathways involved in medium-chain carboxylate production. Through metagenomic analyses, the collaborative work identifies the role of oxygen in n-caprylate production and the complex interactions between aerobic and anaerobic species.

The dissertation introduces MMonitor, a novel software platform that combines compu- tational pipelines with interactive visualization for real-time analysis of metagenomic data from Oxford Nanopore Technologies sequencing. MMonitor’s capabilities are demonstrated through applications in tracking bioreactor microbiomes, as well as in contamination control for artificial intelligence training data. Additional methodological contributions include QuickBinDM, which accelerates long-read metagenomic binning through pre-screening approaches, and GeneGone, a web application for the validation of gene deletion experiments.

Together, these tools and analyses advance our understanding of complex microbial communities while making metagenomic analysis more accessible to researchers. The work has implications for bioinformaticians, biologists and researchers from related fields interested in metagenomics and the tracking of microbial communities.