Evidence map›Paper›PMID 41443199›Full record

ArticleCell reports methods2026

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

Timo N Lucas, Ulrike Biehain, Anupam Gautam, Kurt Gemeinhardt, Tobias Lass, Simon Konzalla, Ruth E Ley, Largus T Angenent, Daniel H Huson

Abstract read
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In one paragraph

Article in Cell reports methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Timo N LucasInstitute for Biomedical Informatics (IBMI), University of Tübingen, Sand 14, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany.
Ulrike BiehainCluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany; Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany; Department of Microbiome Science, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany.
Anupam GautamInstitute for Biomedical Informatics (IBMI), University of Tübingen, Sand 14, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany; Department of Microbiome Science, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany.
Kurt GemeinhardtEnvironmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany.
Tobias LassInstitute for Biomedical Informatics (IBMI), University of Tübingen, Sand 14, 72076 Tübingen, Germany.
Simon KonzallaInstitute for Biomedical Informatics (IBMI), University of Tübingen, Sand 14, 72076 Tübingen, Germany.
Ruth E LeyCluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany; Department of Microbiome Science, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany.
Largus T AngenentCluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany; Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany; Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark; The Novo Nordisk Foundation CO(2) Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark; Ag Angenent, Max Planck Institute for Biology, 72076 Tübingen, Germany.
Daniel H HusonInstitute for Biomedical Informatics (IBMI), University of Tübingen, Sand 14, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany. Electronic address: daniel.huson@uni-tuebingen.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

MetagenomicsMicrobiotaSoftwareComputational BiologyGastrointestinal MicrobiomeHigh-Throughput Nucleotide SequencingHumansMetagenomeRNA, Ribosomal, 16SWhole Genome SequencingRNA, Ribosomal, 16Sbioinformatics softwarebiotechnologyCP: biotechnologyCP: microbiologydata visualizationmicrobiomenanopore sequencingreal-time metagenomics

Identifiers

PMID41443199
PMCPMC12853177

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.