Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2020-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0235682 |
| _version_ | 1819147729471799296 |
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| author | Sarah J Vancuren Scott J Dos Santos Janet E Hill Maternal Microbiome Legacy Project Team |
| author_facet | Sarah J Vancuren Scott J Dos Santos Janet E Hill Maternal Microbiome Legacy Project Team |
| author_sort | Sarah J Vancuren |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T13:34:27Z |
| format | Article |
| id | doaj.art-d9b2445363b74cf39471c7638b1e612b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T13:34:27Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-d9b2445363b74cf39471c7638b1e612b2022-12-21T18:24:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-01157e023568210.1371/journal.pone.0235682Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.Sarah J VancurenScott J Dos SantosJanet E HillMaternal Microbiome Legacy Project TeamAmplification 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.https://doi.org/10.1371/journal.pone.0235682 |
| spellingShingle | Sarah J Vancuren Scott J Dos Santos Janet E Hill Maternal Microbiome Legacy Project Team Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. PLoS ONE |
| title | Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. |
| title_full | Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. |
| title_fullStr | Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. |
| title_full_unstemmed | Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. |
| title_short | Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling. |
| title_sort | evaluation of variant calling for cpn60 barcode sequence based microbiome profiling |
| url | https://doi.org/10.1371/journal.pone.0235682 |
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