skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Qiita: rapid, web-enabled microbiome meta-analysis

Abstract

Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.

Authors:
; ORCiD logo; ; ; ; ; ; ; ; ; ; ; ORCiD logo; ; ; ; ; ORCiD logo; ; more »; ORCiD logo; ORCiD logo; ORCiD logo « less
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1507757
Report Number(s):
PNNL-SA-138026
Journal ID: ISSN 1548-7091
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Nature Methods
Additional Journal Information:
Journal Volume: 15; Journal Issue: 10; Journal ID: ISSN 1548-7091
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
microbiome, bioinformatics software, open source software

Citation Formats

Gonzalez, Antonio, Navas-Molina, Jose A., Kosciolek, Tomasz, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Ackermann, Gail, DeReus, Jeff, Janssen, Stefan, Swafford, Austin D., Orchanian, Stephanie B., Sanders, Jon G., Shorenstein, Joshua, Holste, Hannes, Petrus, Semar, Robbins-Pianka, Adam, Brislawn, Colin J., Wang, Mingxun, Rideout, Jai Ram, Bolyen, Evan, Dillon, Matthew, Caporaso, J. Gregory, Dorrestein, Pieter C., and Knight, Rob. Qiita: rapid, web-enabled microbiome meta-analysis. United States: N. p., 2018. Web. doi:10.1038/s41592-018-0141-9.
Gonzalez, Antonio, Navas-Molina, Jose A., Kosciolek, Tomasz, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Ackermann, Gail, DeReus, Jeff, Janssen, Stefan, Swafford, Austin D., Orchanian, Stephanie B., Sanders, Jon G., Shorenstein, Joshua, Holste, Hannes, Petrus, Semar, Robbins-Pianka, Adam, Brislawn, Colin J., Wang, Mingxun, Rideout, Jai Ram, Bolyen, Evan, Dillon, Matthew, Caporaso, J. Gregory, Dorrestein, Pieter C., & Knight, Rob. Qiita: rapid, web-enabled microbiome meta-analysis. United States. doi:10.1038/s41592-018-0141-9.
Gonzalez, Antonio, Navas-Molina, Jose A., Kosciolek, Tomasz, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Ackermann, Gail, DeReus, Jeff, Janssen, Stefan, Swafford, Austin D., Orchanian, Stephanie B., Sanders, Jon G., Shorenstein, Joshua, Holste, Hannes, Petrus, Semar, Robbins-Pianka, Adam, Brislawn, Colin J., Wang, Mingxun, Rideout, Jai Ram, Bolyen, Evan, Dillon, Matthew, Caporaso, J. Gregory, Dorrestein, Pieter C., and Knight, Rob. Mon . "Qiita: rapid, web-enabled microbiome meta-analysis". United States. doi:10.1038/s41592-018-0141-9.
@article{osti_1507757,
title = {Qiita: rapid, web-enabled microbiome meta-analysis},
author = {Gonzalez, Antonio and Navas-Molina, Jose A. and Kosciolek, Tomasz and McDonald, Daniel and Vázquez-Baeza, Yoshiki and Ackermann, Gail and DeReus, Jeff and Janssen, Stefan and Swafford, Austin D. and Orchanian, Stephanie B. and Sanders, Jon G. and Shorenstein, Joshua and Holste, Hannes and Petrus, Semar and Robbins-Pianka, Adam and Brislawn, Colin J. and Wang, Mingxun and Rideout, Jai Ram and Bolyen, Evan and Dillon, Matthew and Caporaso, J. Gregory and Dorrestein, Pieter C. and Knight, Rob},
abstractNote = {Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.},
doi = {10.1038/s41592-018-0141-9},
journal = {Nature Methods},
issn = {1548-7091},
number = 10,
volume = 15,
place = {United States},
year = {2018},
month = {10}
}

Works referenced in this record:

Global patterns in bacterial diversity
journal, June 2007

  • Lozupone, C. A.; Knight, R.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 27
  • DOI: 10.1073/pnas.0611525104

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection
journal, March 2015


Meta-analyses of studies of the human microbiota
journal, July 2013

  • Lozupone, C. A.; Stombaugh, J.; Gonzalez, A.
  • Genome Research, Vol. 23, Issue 10
  • DOI: 10.1101/gr.151803.112

Collect reliable data on embryo selection
journal, November 2017


Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
journal, August 2016

  • Wang, Mingxun; Carver, Jeremy J.; Phelan, Vanessa V.
  • Nature Biotechnology, Vol. 34, Issue 8
  • DOI: 10.1038/nbt.3597

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012

  • Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
  • The ISME Journal, Vol. 6, Issue 8
  • DOI: 10.1038/ismej.2012.8

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease
journal, March 2014


EMPeror: a tool for visualizing high-throughput microbial community data
journal, November 2013

  • Vázquez-Baeza, Yoshiki; Pirrung, Meg; Gonzalez, Antonio
  • GigaScience, Vol. 2, Issue 1
  • DOI: 10.1186/2047-217X-2-16

Tiny microbes, enormous impacts: what matters in gut microbiome studies?
journal, October 2016


Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
journal, May 2011

  • Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn
  • Nature Biotechnology, Vol. 29, Issue 5
  • DOI: 10.1038/nbt.1823

Dynamics of the human gut microbiome in inflammatory bowel disease
journal, February 2017

  • Halfvarson, Jonas; Brislawn, Colin J.; Lamendella, Regina
  • Nature Microbiology, Vol. 2, Issue 5
  • DOI: 10.1038/nmicrobiol.2017.4

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
journal, December 2012

  • Bokulich, Nicholas A.; Subramanian, Sathish; Faith, Jeremiah J.
  • Nature Methods, Vol. 10, Issue 1
  • DOI: 10.1038/nmeth.2276

Worlds within worlds: evolution of the vertebrate gut microbiota
journal, October 2008

  • Ley, Ruth E.; Lozupone, Catherine A.; Hamady, Micah
  • Nature Reviews Microbiology, Vol. 6, Issue 10
  • DOI: 10.1038/nrmicro1978

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
journal, December 2005


QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303