Advancing our understanding of the human microbiome using QIIME

José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann, Donna Berg-Lyons, Susan Holmes, James G Caporaso, Rob Knight

Research output: Chapter in Book/Report/Conference proceedingChapter

218 Citations (Scopus)

Abstract

High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.

Original languageEnglish (US)
Title of host publicationMethods in Enzymology
Pages371-444
Number of pages74
Volume531
DOIs
StatePublished - 2013

Publication series

NameMethods in Enzymology
Volume531
ISSN (Print)00766879
ISSN (Electronic)15577988

Fingerprint

Microbiota
Ecology
Bioinformatics
Computational Biology
Pipelines
High-Throughput Nucleotide Sequencing
DNA sequences
rRNA Genes
Software packages
Transgenic Mice
Sequence Analysis
Publications
Software
Visualization
Genes
Throughput
Guidelines
Technology
DNA

Keywords

  • Highthroughput sequencing
  • Microbial community analyses
  • Microbial ecology
  • Microbiome
  • QIIME

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Navas-Molina, J. A., Peralta-Sánchez, J. M., González, A., McMurdie, P. J., Vázquez-Baeza, Y., Xu, Z., ... Knight, R. (2013). Advancing our understanding of the human microbiome using QIIME. In Methods in Enzymology (Vol. 531, pp. 371-444). (Methods in Enzymology; Vol. 531). https://doi.org/10.1016/B978-0-12-407863-5.00019-8

Advancing our understanding of the human microbiome using QIIME. / Navas-Molina, José A.; Peralta-Sánchez, Juan M.; González, Antonio; McMurdie, Paul J.; Vázquez-Baeza, Yoshiki; Xu, Zhenjiang; Ursell, Luke K.; Lauber, Christian; Zhou, Hongwei; Song, Se Jin; Huntley, James; Ackermann, Gail L.; Berg-Lyons, Donna; Holmes, Susan; Caporaso, James G; Knight, Rob.

Methods in Enzymology. Vol. 531 2013. p. 371-444 (Methods in Enzymology; Vol. 531).

Research output: Chapter in Book/Report/Conference proceedingChapter

Navas-Molina, JA, Peralta-Sánchez, JM, González, A, McMurdie, PJ, Vázquez-Baeza, Y, Xu, Z, Ursell, LK, Lauber, C, Zhou, H, Song, SJ, Huntley, J, Ackermann, GL, Berg-Lyons, D, Holmes, S, Caporaso, JG & Knight, R 2013, Advancing our understanding of the human microbiome using QIIME. in Methods in Enzymology. vol. 531, Methods in Enzymology, vol. 531, pp. 371-444. https://doi.org/10.1016/B978-0-12-407863-5.00019-8
Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z et al. Advancing our understanding of the human microbiome using QIIME. In Methods in Enzymology. Vol. 531. 2013. p. 371-444. (Methods in Enzymology). https://doi.org/10.1016/B978-0-12-407863-5.00019-8
Navas-Molina, José A. ; Peralta-Sánchez, Juan M. ; González, Antonio ; McMurdie, Paul J. ; Vázquez-Baeza, Yoshiki ; Xu, Zhenjiang ; Ursell, Luke K. ; Lauber, Christian ; Zhou, Hongwei ; Song, Se Jin ; Huntley, James ; Ackermann, Gail L. ; Berg-Lyons, Donna ; Holmes, Susan ; Caporaso, James G ; Knight, Rob. / Advancing our understanding of the human microbiome using QIIME. Methods in Enzymology. Vol. 531 2013. pp. 371-444 (Methods in Enzymology).
@inbook{cc6d86c7956740678b554bc806934eec,
title = "Advancing our understanding of the human microbiome using QIIME",
abstract = "High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.",
keywords = "Highthroughput sequencing, Microbial community analyses, Microbial ecology, Microbiome, QIIME",
author = "Navas-Molina, {Jos{\'e} A.} and Peralta-S{\'a}nchez, {Juan M.} and Antonio Gonz{\'a}lez and McMurdie, {Paul J.} and Yoshiki V{\'a}zquez-Baeza and Zhenjiang Xu and Ursell, {Luke K.} and Christian Lauber and Hongwei Zhou and Song, {Se Jin} and James Huntley and Ackermann, {Gail L.} and Donna Berg-Lyons and Susan Holmes and Caporaso, {James G} and Rob Knight",
year = "2013",
doi = "10.1016/B978-0-12-407863-5.00019-8",
language = "English (US)",
isbn = "9780124078635",
volume = "531",
series = "Methods in Enzymology",
pages = "371--444",
booktitle = "Methods in Enzymology",

}

TY - CHAP

T1 - Advancing our understanding of the human microbiome using QIIME

AU - Navas-Molina, José A.

AU - Peralta-Sánchez, Juan M.

AU - González, Antonio

AU - McMurdie, Paul J.

AU - Vázquez-Baeza, Yoshiki

AU - Xu, Zhenjiang

AU - Ursell, Luke K.

AU - Lauber, Christian

AU - Zhou, Hongwei

AU - Song, Se Jin

AU - Huntley, James

AU - Ackermann, Gail L.

AU - Berg-Lyons, Donna

AU - Holmes, Susan

AU - Caporaso, James G

AU - Knight, Rob

PY - 2013

Y1 - 2013

N2 - High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.

AB - High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.

KW - Highthroughput sequencing

KW - Microbial community analyses

KW - Microbial ecology

KW - Microbiome

KW - QIIME

UR - http://www.scopus.com/inward/record.url?scp=84884577945&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84884577945&partnerID=8YFLogxK

U2 - 10.1016/B978-0-12-407863-5.00019-8

DO - 10.1016/B978-0-12-407863-5.00019-8

M3 - Chapter

SN - 9780124078635

VL - 531

T3 - Methods in Enzymology

SP - 371

EP - 444

BT - Methods in Enzymology

ER -