ArticleMicrobial genomics2020
Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels.
Article in Microbial genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Dye-based qPCR assays for the separate quantification of total bacterial, fungal, arthropod, and plant DNA.PloS one · 2026Article
- Validating digital polymerase chain reaction for 16S rRNA gene amplification from low biomass environmental samples.ISME communications · 2025Article
- Endometrial Cancer: A Pilot Study of the Tissue Microbiota.Microorganisms · 2024Article
- Characterization of bacteria expectorated during forced salivation of the Phlebotomus papatasi: A neglected component of sand fly infectious inoculums.PLoS neglected tropical diseases · 2024Article
- Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia.The Journal of molecular diagnostics : JMD · 2024Article
- Benchmarking DNA isolation methods for marine metagenomics.Scientific reports · 2023Article
- Combining 16S Sequencing and qPCR Quantification RevealsBiomolecules · 2023Article
- [Application of Droplet-Based Microfluidics in Microbial Research].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2023Review
- Foliage of Tropical Trees and Shrubs and Their Secondary Metabolites Modify In Vitro Ruminal Fermentation, Methane and Gas Production without a Tight Correlation with the Microbiota.Animals : an open access journal from MDPI · 2022Article
- ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples.BMC microbiology · 2021Article
- The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.Scientific reports · 2021Article
- Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.PloS one · 2021Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The quantification of the total microbial content in metagenomic samples is critical for investigating the interplay between the microbiome and its host, as well as for assessing the accuracy and precision of the relative microbial composition which can be strongly biased in low microbial biomass samples. In the present study, we demonstrate that digital droplet PCR (ddPCR) can provide accurate quantification of the total copy number of the 16S rRNA gene, the gene usually exploited for assessing total bacterial abundance in metagenomic DNA samples. Notably, using DNA templates with different integrity levels, as measured by the DNA integrity number (DIN), we demonstrated that 16S rRNA copy number quantification is strongly affected by DNA quality and determined a precise correlation between quantification underestimation and DNA degradation levels. Therefore, we propose an input DNA mass correction, according to the observed DIN value, which could prevent inaccurate quantification of 16S copy number in degraded metagenomic DNAs. Our results highlight that a preliminary evaluation of the metagenomic DNA integrity should be considered before performing metagenomic analyses of different samples, both for the assessment of the reliability of observed differential abundances in different conditions and to obtain significant functional insights.
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