Work

MMonitor for real-time monitoring of microbial communities using long reads

Year: 2025

Type: article

Abstract: Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source software platform for real-time analysis and visualization of metagenomic Oxford Nanopore Technologies (ONT) sequencing data. MMonitor includes two components: a desktop application for running bioinformatics pipelines through a graphical user interface (GUI) or command-line interface (CLI) and a web-based dashboard for interactive result inspection. The dashboard provides taxonomic composition over time, quality scores, diversity indices, and taxonomy-metadata correlations. Integrated pipelines enable automated de novo assembly and reconstruction of metagenome-assembled genomes (MAGs). To validate MMonitor, we tracked human gut microbial populations in three bioreactors using 16S rRNA gene sequencing and applied it to whole-genome sequencing (WGS) data to generate high-quality annotated MAGs. We compare MMonitor with other real-time metagenomic tools, outlining their strengths and limitations. • Real-time monitoring of microbial communities from nanopore sequencing • Taxonomic, functional, and time-series analyses with automated database updates • Enables high-quality assembly and annotation of metagenome-assembled genomes • Open-source platform combining GUI, CLI, and web dashboard for accessible tracking Metagenome monitoring is essential for understanding and managing microbial communities in dynamic environments. However, existing tools for metagenome analysis often lack key features needed for effective real-time monitoring—including immediate processing of nanopore data, intuitive user interfaces, simple deployment, and clear visual summaries. Many workflows require advanced computational skills, manual integration of multiple software packages, or substantial hardware resources, which can delay responses in biologically active systems such as clinical diagnostics, industrial bioprocesses, and environmental surveillance. MMonitor addresses these limitations by providing real-time analysis of nanopore sequencing data within an accessible, easy-to-configure platform. Lucas et al. present MMonitor, an open-source software enabling real-time monitoring of microbial communities using nanopore sequencing. The tool integrates taxonomic and functional analyses with automated visualization and metagenome assembly, allowing researchers to track microbiome dynamics and identify community changes during ongoing sequencing runs.

Source: Cell Reports Methods

DOI: 10.1016/j.crmeth.2025.101266