ArticlePloS one2020
Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 21 citations in OpenAlex.
- Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.PLoS computational biology · 2026Article
- Birth Mode Does Not Determine the Presence of Shared Bacterial Strains between the Maternal Vaginal Microbiome and the Infant Stool Microbiome.Microbiology spectrum · 2023Article
- Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants.ISME communications · 2023Article
- Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants.ISME communications · 2023Article
- Evaluating cpn60 for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis.ISME communications · 2023Article
- Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life.Frontiers in cellular and infection microbiology · 2023Article
- Vaginal microbiota associated with oncogenic HPV in a cohort of HPV-vaccinated women living with HIV.International journal of STD & AIDS · 2022Article
- Article
- Life barcoded by DNA barcodes.Conservation genetics resources · 2022Review
- Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls withMicrobiology spectrum · 2021Article
- CaptureSeq: Hybridization-Based Enrichment ofMicroorganisms · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.
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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.