• GRUMB: a genome-resolved metag...

Treffer: GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.

Title:
GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.
Authors:
Aminu S; College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco.; Department of Biochemistry, Ahmadu Bello University, Zaria, Kaduna, 1096, Nigeria., Ascandari A; College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco., Benhida R; College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco.; Institut de Chimie de Nice (ICN), UMR CNRS 7272, Université Côte d'Azur, Nice, Provence-Alpes-Côte d'Azur, 06108, France., Daoud R; College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2025 Oct 02; Vol. 41 (10).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Microbiota*/genetics , Metagenomics*/methods , Software* , Metagenome*, Machine Learning ; Humans ; Cities
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Grant Information:
Mohammed VI Polytechnic University; African Supercomputing Center at UM6P
Entry Date(s):
Date Created: 20250926 Date Completed: 20251023 Latest Revision: 20251025
Update Code:
20251025
PubMed Central ID:
PMC12548037
DOI:
10.1093/bioinformatics/btaf548
PMID:
41002268
Database:
MEDLINE

Weitere Informationen

Summary: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments.
Availability and Implementation: GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.
(© The Author(s) 2025. Published by Oxford University Press.)