Title |
Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform
|
---|---|
Published in |
Microbiome, March 2013
|
DOI | 10.1186/2049-2618-1-10 |
Pubmed ID | |
Authors |
Erin B Fichot, R Sean Norman |
Abstract |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 10 | 40% |
United Kingdom | 2 | 8% |
France | 1 | 4% |
Canada | 1 | 4% |
Montenegro | 1 | 4% |
Norway | 1 | 4% |
Grenada | 1 | 4% |
Unknown | 8 | 32% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 16 | 64% |
Members of the public | 7 | 28% |
Science communicators (journalists, bloggers, editors) | 1 | 4% |
Practitioners (doctors, other healthcare professionals) | 1 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 10 | 3% |
Netherlands | 3 | <1% |
Spain | 2 | <1% |
Sweden | 2 | <1% |
Brazil | 2 | <1% |
United Kingdom | 2 | <1% |
Japan | 2 | <1% |
India | 1 | <1% |
Korea, Republic of | 1 | <1% |
Other | 8 | 2% |
Unknown | 309 | 90% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 89 | 26% |
Student > Ph. D. Student | 78 | 23% |
Student > Master | 40 | 12% |
Student > Bachelor | 25 | 7% |
Student > Doctoral Student | 21 | 6% |
Other | 59 | 17% |
Unknown | 30 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 182 | 53% |
Biochemistry, Genetics and Molecular Biology | 57 | 17% |
Immunology and Microbiology | 17 | 5% |
Computer Science | 12 | 4% |
Medicine and Dentistry | 10 | 3% |
Other | 27 | 8% |
Unknown | 37 | 11% |