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bioRxiv · 10.1101/2025.09.08.674848

MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads

Lucas, T. N.·Biehain, U.·Gautam, A.·Gemeinhardt, K.·Lass, T.·Konzalla, S.·Ley, R. E.·Angenent, L. T.·Huson, D. H.
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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 the 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 and reveal functional insights. We also compare MMonitor to other software for real-time metagenomic analysis, highlighting the strengths and limitations of each tool for this use case. By performing automated time-series analyzes, sample management, and updating of reference databases, MMonitor addresses current limitations and supports dynamic microbiome research in various fields. IMPORTANCEMetagenome monitoring is essential for understanding and managing microbial communities in dynamic environments. Rapid and accurate analysis of these communities allows for timely interventions in biologically active environments, for example, in industrial biotechnology, environmental surveillance, and medical diagnostics. Metagenome monitoring tools should have real-time capabilities, intuitive interfaces, convenient setup and distribution, and suitable visual representations for effective monitoring. MMonitor addresses these challenges by offering a platform that combines real-time analysis of nanopore sequencing data with customizable pipelines and advanced visualization tools. It is designed to be accessible to researchers of all levels of computational skill. It supports efficient taxonomic and functional analyses based on popular metagenome software and automates taxonomic profiling, genome assembly, binning, and annotation. The dashboard helps to interpret data and present results. MMonitor is designed to track metagenomes and we hope that it can impact microbiome research and applications in health, biotechnology, agricultural, and environmental sciences.

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Lucas, T. N., Biehain, U., Gautam, A., Gemeinhardt, K., Lass, T., Konzalla, S., Ley, R. E., Angenent, L. T., Huson, D. H.. 2025-09-08. MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads. https://doi.org/10.1101/2025.09.08.674848

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