| Chapter title |
Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package
|
|---|---|
| Chapter number | 9 |
| Book title |
Oral Biology
|
| Published in |
Methods in molecular biology, January 2017
|
| DOI | 10.1007/978-1-4939-6685-1_9 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6683-7, 978-1-4939-6685-1
|
| Authors |
Blair Lawley, Gerald W. Tannock, Lawley, Blair, Tannock, Gerald W |
| Editors |
Gregory J. Seymour, Mary P. Cullinan, Nicholas C.K. Heng |
| Abstract |
The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures. The workflow can be adapted to input from major sequence platforms and uses freely available open source software that can be implemented on a range of operating systems. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 3 | 13% |
| Canada | 2 | 8% |
| United Kingdom | 2 | 8% |
| Australia | 1 | 4% |
| Germany | 1 | 4% |
| China | 1 | 4% |
| Spain | 1 | 4% |
| India | 1 | 4% |
| France | 1 | 4% |
| Other | 1 | 4% |
| Unknown | 10 | 42% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 14 | 58% |
| Members of the public | 10 | 42% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 1% |
| Unknown | 77 | 99% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 13 | 17% |
| Researcher | 13 | 17% |
| Student > Bachelor | 11 | 14% |
| Student > Doctoral Student | 6 | 8% |
| Student > Master | 5 | 6% |
| Other | 14 | 18% |
| Unknown | 16 | 21% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 15 | 19% |
| Biochemistry, Genetics and Molecular Biology | 15 | 19% |
| Immunology and Microbiology | 7 | 9% |
| Environmental Science | 6 | 8% |
| Engineering | 4 | 5% |
| Other | 14 | 18% |
| Unknown | 17 | 22% |