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.

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... equence data from the 5' region of the cpn60 barcode amplified from the human vaginal microbiome (n=25), infant stool (n=47), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database. Results were compared in terms of number of OTU formed, resolution of OTU sequences, and overall community composition. Variant calling resulted in high resolution profiles that were consistent in composition to those generated with previous 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.