ArticleMicrobiome2021
Modified PCR protocol to increase sensitivity for determination of bacterial community composition.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- The Changes of Microbiome Attached on Clear Aligners after Drinking Coca-Cola.Polish journal of microbiology · 2026Article
- Integrated local and global Ki67 profiling for prognostic stratification and therapeutic guidance in high-grade neuroendocrine neoplasms: a multicenter validation study.International journal of surgery (London, England) · 2025Article
- Article
- Tobacco smoke exposure, the lower airways microbiome and outcomes of ventilated children.Pediatric research · 2023Article
- Detection and identification of fungi in the lower airway of children with and without cystic fibrosis.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing. Two PCR protocols (standard and modified) were examined in airway samples where we observed a large range in bacterial load (3.1-6.2 log
resultsPCR product was observed using both protocols in 52 samples and in 24 additional samples only with the modified protocol. TBL, diversity metrics, and prominent taxa were compared for samples in three groups based on success of the two protocols (successful with both, success with modified only, unsuccessful for both). TBL differed significantly across the three groups (p<0.001). Specifically, the modified protocol allowed amplification from samples with intermediate TBL. Shannon diversity was similar between the two protocols, and Morisita-Horn beta diversity index showed high agreement between the two protocols within samples (median value 0.9997, range 0.9947 to 1). We show that both protocols identify similar communities, and the technical variability of both protocols was very low. The use of limited PCR cycles was a key feature to limit impact of background by exclusion of 24% of samples with no evidence of bacterial DNA present in the sample.
conclusionThe modified amplification protocol represents a viable approach that increased sensitivity of bacterial community analysis, which is important for study of the human airway microbiome where bacterial load is highly variable. Video abstract.
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Registered trials
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