ArticlePeerJ2018
imGLAD: accurate detection and quantification of target organisms in metagenomes.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement.Science translational medicine · 2023Trial
- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- Microbial Biofilms Dynamics and Functionality in an UrbanEnvironmental science & technology · 2026Article
- An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.ISME communications · 2026Article
- Leveraging strain competition to address antimicrobial resistance with microbiota therapies.Gut microbes · 2025Review
- ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets.Genome biology · 2025Article
- Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review.Food and waterborne parasitology · 2025Review
- The physical biogeography ofmBio · 2025Article
- CoverM: read alignment statistics for metagenomics.Bioinformatics (Oxford, England) · 2025Article
- Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.Nucleic acids research · 2025Article
- Quantifying the contribution of the rare biosphere to natural disturbances.The ISME journal · 2025Article
- Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them.ISME communications · 2025Article
- Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools.BMC microbiology · 2024Article
- Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.The ISME journal · 2024Article
- Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains.The ISME journal · 2024Article
- A genome catalogue of lake bacterial diversity and its drivers at continental scale.Nature microbiology · 2023Article
- Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda.Microbiology spectrum · 2023Article
- Metagenomics indicate that public health risk may be higher from flooding following dry versus rainy periods.Environmental microbiology reports · 2022Article
- Article
- Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations.Applied and environmental microbiology · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen
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Registered trials
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.