Meta-Analysis

. 2018 Oct;15(10):796-798.

doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 1.

Qiita: rapid, web-enabled microbiome meta-analysis

Antonio Gonzalez¹, Jose A Navas-Molina^{1

2

3}, Tomasz Kosciolek¹, Daniel McDonald¹, Yoshiki Vázquez-Baeza¹, Gail Ackermann¹, Jeff DeReus¹, Stefan Janssen¹, Austin D Swafford⁴, Stephanie B Orchanian⁴, Jon G Sanders¹, Joshua Shorenstein^{1

5}, Hannes Holste^{1

2}, Semar Petrus⁶, Adam Robbins-Pianka⁷, Colin J Brislawn⁸, Mingxun Wang⁹, Jai Ram Rideout¹⁰, Evan Bolyen¹⁰, Matthew Dillon¹⁰, J Gregory Caporaso^{10

11}, Pieter C Dorrestein^{1

4

9}, Rob Knight^{12

13

14}

Affiliations

¹ Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
² Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
³ Google LLC, Mountain View, CA, USA.
⁴ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁵ Inscripta, Inc., Boulder, CO, USA.
⁶ Department of Biology, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Computer Science, University of Colorado, Boulder, Boulder, CO, USA.
⁸ Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
⁹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
¹¹ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
¹² Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. robknight@qiuluzeuv.cn.
¹³ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. robknight@qiuluzeuv.cn.
¹⁴ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. robknight@qiuluzeuv.cn.

PMID: 30275573
PMCID: "VSports手机版" PMC6235622
DOI: "VSports手机版" 10.1038/s41592-018-0141-9

Meta-Analysis

Qiita: rapid, web-enabled microbiome meta-analysis

Antonio Gonzalez et al. Nat Methods. 2018 Oct.

. 2018 Oct;15(10):796-798.

doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 1.

Authors (V体育平台登录)

Affiliations (V体育平台登录)

¹ Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
² Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
³ Google LLC, Mountain View, CA, USA.
⁴ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁵ Inscripta, Inc., Boulder, CO, USA.
⁶ Department of Biology, University of California, San Diego, La Jolla, CA, USA.
⁷ Department of Computer Science, University of Colorado, Boulder, Boulder, CO, USA.
⁸ Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
⁹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
¹¹ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
¹² Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. robknight@qiuluzeuv.cn.
¹³ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. robknight@qiuluzeuv.cn.
¹⁴ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. robknight@qiuluzeuv.cn.

PMID: 30275573
PMCID: PMC6235622
DOI: 10.1038/s41592-018-0141-9

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. VSports手机版.

PubMed Disclaimer

Conflict of interest statement

Competing Financial Interests Statement

The authors declare no competing financial interests.

VSports最新版本 - Figures

**Figure 1.**
Example meta-analysis in Qiita. A. Unweighted UniFrac PCoA meta-analysis of three studies examining different IBD subtypes, *C. difficile* patients who underwent FMT, and the HMP1 and iHMP data. B. Only fecal samples from the same studies as in A. C. Fecal samples only from studies that used the same data-generation methods. D. Calculated distances from a healthy plane as described in Ref. 3. Box plots show the median value (center line), the upper and lower quartiles of the data (box edges), maxima and minima (whiskers), and outliers (individual data points). CD, Crohn’s disease; IC, ileal Crohn’s disease; UC, ulcerative colitis; HC, healthy cohort; CCD, colonic Crohn’s disease; ICD_r, ileal Crohn’s disease patients with previous ileocecal resection; ICD_nr, ileal Crohn’s disease patients with no previous ileocaecal resection; post-FMT, patients with *C. difficile* infection pre-FMT; pre-FMT, patients with *C. difficile* infection post-FMT.

See this image and copyright information in PMC

"VSports app下载" References

1. Caporaso JG et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6, 1621–1624, doi:"VSports注册入口" 10.1038/ismej.2012.8 (2012). - DOI - PMC - PubMed
1. Thompson LR et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463, doi:VSports - 10.1038/nature24621 (2017). - DOI - PMC - PubMed
1. Halfvarson J et al. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol 2, 17004, doi:10.1038/nmicrobiol.2017.4 (2017). - DOI - PMC - PubMed
1. Lozupone CA & Knight R Global patterns in bacterial diversity. Proc Natl Acad Sci U S A 104, 11436–11440, doi:10.1073/pnas.0611525104 (2007). - DOI - PMC - PubMed
1. Ley RE, Lozupone CA, Hamady M, Knight R & Gordon JI Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6, 776–788, doi:10.1038/nrmicro1978 (2008). - DOI - PMC - PubMed

Methods Only References

1. Vazquez-Baeza Y, Pirrung M, Gonzalez A & Knight R EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2, 16, doi:"V体育官网入口" 10.1186/2047-217X-2-16 (2013). - DOI - PMC - PubMed
1. Waskom, M. Seaborn: statistical data visualization. (2012).

Publication types

"V体育ios版" Actions
V体育安卓版 - Actions
"VSports最新版本" Actions

"VSports最新版本" MeSH terms

Actions (V体育官网入口)
Actions
"VSports手机版" Actions
Actions
Actions
Actions
Actions (VSports最新版本)

Grants and funding

LinkOut - more resources

Full Text Sources
Other Literature Sources
- "VSports" The Lens - Patent Citations Database
Medical
- ClinicalTrials.gov

Save citation to file

V体育ios版 - Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

VSports在线直播 - Your RSS Feed

Qiita: rapid, web-enabled microbiome meta-analysis

Affiliations

Qiita: rapid, web-enabled microbiome meta-analysis

Authors (V体育平台登录)

Affiliations (V体育平台登录)

Abstract

Conflict of interest statement

VSports最新版本 - Figures

"VSports app下载" References

Methods Only References

Publication types

"VSports最新版本" MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical