Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform
High-throughput sequencing of 16S rRNA gene amplicons has revolutionized the capacity and depth of microbial community profiling. Several sequencing platforms are available, but most phylogenetic studies are performed on the 454-pyrosequencing platform because its longer reads can give finer phyloge...
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| Format: | Online |
| Language: | English |
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BioMed Central
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971627/ |
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pubmed-3971627 |
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pubmed-39716272014-04-02 Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform Fichot, Erin B Norman, R Sean Commentary High-throughput sequencing of 16S rRNA gene amplicons has revolutionized the capacity and depth of microbial community profiling. Several sequencing platforms are available, but most phylogenetic studies are performed on the 454-pyrosequencing platform because its longer reads can give finer phylogenetic resolution. The Pacific Biosciences (PacBio) sequencing platform is significantly less expensive per run, does not rely on amplification for library generation, and generates reads that are, on average, four times longer than those from 454 (C2 chemistry), but the resulting high error rates appear to preclude its use in phylogenetic profiling. Recently, however, the PacBio platform was used to characterize four electrosynthetic microbiomes to the genus-level for less than USD 1,000 through the use of PacBio’s circular consensus sequence technology. Here, we describe in greater detail: 1) the output from successful 16S rRNA gene amplicon profiling with PacBio, 2) how the analysis was contingent upon several alterations to standard bioinformatic quality control workflows, and 3) the advantages and disadvantages of using the PacBio platform for community profiling. BioMed Central 2013-03-04 /pmc/articles/PMC3971627/ /pubmed/24450498 http://dx.doi.org/10.1186/2049-2618-1-10 Text en Copyright © 2013 Fichot and Norman; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Fichot, Erin B Norman, R Sean |
| spellingShingle |
Fichot, Erin B Norman, R Sean Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform |
| author_facet |
Fichot, Erin B Norman, R Sean |
| author_sort |
Fichot, Erin B |
| title |
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform |
| title_short |
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform |
| title_full |
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform |
| title_fullStr |
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform |
| title_full_unstemmed |
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform |
| title_sort |
microbial phylogenetic profiling with the pacific biosciences sequencing platform |
| description |
High-throughput sequencing of 16S rRNA gene amplicons has revolutionized the capacity and depth of microbial community profiling. Several sequencing platforms are available, but most phylogenetic studies are performed on the 454-pyrosequencing platform because its longer reads can give finer phylogenetic resolution. The Pacific Biosciences (PacBio) sequencing platform is significantly less expensive per run, does not rely on amplification for library generation, and generates reads that are, on average, four times longer than those from 454 (C2 chemistry), but the resulting high error rates appear to preclude its use in phylogenetic profiling. Recently, however, the PacBio platform was used to characterize four electrosynthetic microbiomes to the genus-level for less than USD 1,000 through the use of PacBio’s circular consensus sequence technology. Here, we describe in greater detail: 1) the output from successful 16S rRNA gene amplicon profiling with PacBio, 2) how the analysis was contingent upon several alterations to standard bioinformatic quality control workflows, and 3) the advantages and disadvantages of using the PacBio platform for community profiling. |
| publisher |
BioMed Central |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971627/ |
| _version_ |
1612072912861265920 |