ArticlemBio2021
Metagenomic Quantification of Genes with Internal Standards.
Article in mBio, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
What it found
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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.
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.
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Who cites it
23 citing papers in PubMed, 51 citations in OpenAlex.
- Article
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- Standardized and batch effect-independent technologies enable global collaboration in microbiome research.The ISME journal · 2026Article
- A Practical Framework for Environmental Antibiotic Resistance Monitoring in Freshwater Ecosystems.Antibiotics (Basel, Switzerland) · 2025Review
- Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits.Environmental science & technology · 2025Article
- Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.Nucleic acids research · 2025Article
- The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.Microbiome · 2025Review
- Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.ISME communications · 2025Article
- Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725-920 CE.PloS one · 2025Article
- Source-to-tap investigation of the occurrence of nontuberculous mycobacteria in a full-scale chloraminated drinking water system.Applied and environmental microbiology · 2024Article
- Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.Food and environmental virology · 2024Article
- A novel synthetic nucleic acid mixture for quantification of microbes by mNGS.Microbial genomics · 2024Article
- Synechococcus nitrogen gene loss in iron-limited ocean regions.ISME communications · 2023Article
- Assessment of the stability of antimicrobials and resistance genes during short- and long-term storage condition: accounting for uncertainties in bioanalytical workflows.Analytical and bioanalytical chemistry · 2023Article
- A standardized quantitative analysis strategy for stable isotope probing metagenomics.mSystems · 2023Article
- Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp.BMC genomics · 2023Article
- Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control.Environmental science & technology · 2022Review
- Diel investments in metabolite production and consumption in a model microbial system.The ISME journal · 2022Article
- A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure.Applied and environmental microbiology · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families.
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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.