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Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling

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  • Sarah J Vancuren
  • Scott J Dos Santos
  • Janet E Hill
  • the Maternal Microbiome Legacy Project Team

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.

Suggested Citation

  • Sarah J Vancuren & Scott J Dos Santos & Janet E Hill & the Maternal Microbiome Legacy Project Team, 2020. "Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling," PLOS ONE, Public Library of Science, vol. 15(7), pages 1-14, July.
    • Handle: RePEc:plo:pone00:0235682
    DOI: 10.1371/journal.pone.0235682
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    References listed on IDEAS

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    1. Tobias Guldberg Frøslev & Rasmus Kjøller & Hans Henrik Bruun & Rasmus Ejrnæs & Ane Kirstine Brunbjerg & Carlotta Pietroni & Anders Johannes Hansen, 2017. "Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    2. Andrew D Fernandes & Jean M Macklaim & Thomas G Linn & Gregor Reid & Gregory B Gloor, 2013. "ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-15, July.
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