Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

被引：117

作者：

Flygare, Steven ^{[1
]}

Simmon, Keith ^{[3
]}

Miller, Chase ^{[1
]}

Qiao, Yi ^{[1
]}

Kennedy, Brett ^{[1
]}

Di Sera, Tonya ^{[1
]}

Graf, Erin H. ^{[2
]}

Tardif, Keith D. ^{[4
]}

Kapusta, Aurelie ^{[1
]}

Rynearson, Shawn ^{[1
]}

Stockmann, Chris ^{[5
]}

Queen, Krista ^{[6
]}

Tong, Suxiang ^{[6
]}

Voelkerding, Karl V. ^{[2
,4
]}

Blaschke, Anne ^{[5
]}

Byington, Carrie L. ^{[5
]}

Jain, Seema ^{[6
]}

Pavia, Andrew ^{[5
]}

Ampofo, Krow ^{[5
]}

Eilbeck, Karen ^{[3
,7
]}

Marth, Gabor ^{[1
,7
]}

Yandell, Mark ^{[1
,7
]}

Schlaberg, Robert ^{[2
,4
]}

机构：

[1] Univ Utah, Dept Human Genet, Salt Lake City, UT USA

[2] Univ Utah, Dept Pathol, Salt Lake City, UT USA

[3] Univ Utah, Dept Biomed Informat, Salt Lake City, UT USA

[4] ARUP Inst Clin & Expt Pathol, Salt Lake City, UT USA

[5] Univ Utah, Dept Pediat, Salt Lake City, UT USA

[6] Ctr Dis Control & Prevent, Atlanta, GA USA

[7] USTAR Ctr Genet Discovery, Salt Lake City, UT USA

来源：

GENOME BIOLOGY | 2016年 / 17卷

基金：

美国国家卫生研究院;

关键词：

Metagenomics; Microbiome; Pathogen detection; Infectious disease diagnostics; GUT MICROBIOTA; CONTAMINATION; CLASSIFICATION; CANCER; VIRUS; QUANTIFICATION; IDENTIFICATION; GREENGENES; DISCOVERY; DATABASE;

D O I：

10.1186/s13059-016-0969-1

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption. Results: We present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface. Conclusions: Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.

引用

页数：18

共 70 条

[21] The Earth Microbiome project: successes and aspirations [J].

Gilbert, Jack A. ;

Jansson, Janet K. ;

Knight, Rob .

BMC BIOLOGY, 2014, 12

[22] Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak [J].

Gire, Stephen K. ;

Goba, Augustine ;

Andersen, Kristian G. ;

Sealfon, Rachel S. G. ;

Park, Daniel J. ;

Kanneh, Lansana ;

Jalloh, Simbirie ;

Momoh, Mambu ;

Fullah, Mohamed ;

Dudas, Gytis ;

Wohl, Shirlee ;

Moses, Lina M. ;

Yozwiak, Nathan L. ;

Winnicki, Sarah ;

Matranga, Christian B. ;

Malboeuf, Christine M. ;

Qu, James ;

Gladden, Adrianne D. ;

Schaffner, Stephen F. ;

Yang, Xiao ;

Jiang, Pan-Pan ;

Nekoui, Mahan ;

Colubri, Andres ;

Coomber, Moinya Ruth ;

Fonnie, Mbalu ;

Moigboi, Alex ;

Gbakie, Michael ;

Kamara, Fatima K. ;

Tucker, Veronica ;

Konuwa, Edwin ;

Saffa, Sidiki ;

Sellu, Josephine ;

Jalloh, Abdul Azziz ;

Kovoma, Alice ;

Koninga, James ;

Mustapha, Ibrahim ;

Kargbo, Kandeh ;

Foday, Momoh ;

Yillah, Mohamed ;

Kanneh, Franklyn ;

Robert, Willie ;

Massally, James L. B. ;

Chapman, Sinead B. ;

Bochicchio, James ;

Murphy, Cheryl ;

Nusbaum, Chad ;

Young, Sarah ;

Birren, BruceW. ;

Grant, Donald S. ;

Scheiffelin, John S. .

SCIENCE, 2014, 345 (6202) :1369-1372

[23] Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel [J].

Graf, Erin H. ;

Simmon, Keith E. ;

Tardif, Keith D. ;

Hymas, Weston ;

Flygare, Steven ;

Eilbeck, Karen ;

Yandell, Mark ;

Schlaberg, Robert .

JOURNAL OF CLINICAL MICROBIOLOGY, 2016, 54 (04) :1000-1007

[24] A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa [J].

Grard, Gilda ;

Fair, Joseph N. ;

Lee, Deanna ;

Slikas, Elizabeth ;

Steffen, Imke ;

Muyembe, Jean-Jacques ;

Sittler, Taylor ;

Veeraraghavan, Narayanan ;

Ruby, J. Graham ;

Wang, Chunlin ;

Makuwa, Maria ;

Mulembakani, Prime ;

Tesh, Robert B. ;

Mazet, Jonna ;

Rimoin, Anne W. ;

Taylor, Travis ;

Schneider, Bradley S. ;

Simmons, Graham ;

Delwart, Eric ;

Wolfe, Nathan D. ;

Chiu, Charles Y. ;

Leroy, Eric M. .

PLOS PATHOGENS, 2012, 8 (09)

[25] Modelling and simulating generic RNA-Seq experiments with the flux simulator [J].

Griebel, Thasso ;

Zacher, Benedikt ;

Ribeca, Paolo ;

Raineri, Emanuele ;

Lacroix, Vincent ;

Guigo, Roderic ;

Sammeth, Michael .

NUCLEIC ACIDS RESEARCH, 2012, 40 (20) :10073-10083

[26] Gene expression profiles in febrile children with defined viral and bacterial infection [J].

Hu, Xinran ;

Yu, Jinsheng ;

Crosby, Seth D. ;

Storch, Gregory A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (31) :12792-12797

[27] Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance [J].

Hu, Yunwen ;

Lu, Shuihua ;

Song, Zhigang ;

Wang, Wei ;

Hao, Pei ;

Li, Jianhua ;

Zhang, Xiaonan ;

Yen, Hui-Ling ;

Shi, Bisheng ;

Li, Tao ;

Guan, Wencai ;

Xu, Lei ;

Liu, Yi ;

Wang, Sen ;

Zhang, Xiaoling ;

Tian, Di ;

Zhu, Zhaoqin ;

He, Jing ;

Huang, Kai ;

Chen, Huijie ;

Zheng, Lulu ;

Li, Xuan ;

Ping, Jie ;

Kang, Bin ;

Xi, Xiuhong ;

Zha, Lijun ;

Li, Yixue ;

Zhang, Zhiyong ;

Peiris, Malik ;

Yuan, Zhenghong .

LANCET, 2013, 381 (9885) :2273-2279

[28] A novel diagnostic approach may reduce inappropriate antibiotic use for acute respiratory infections [J].

Hudson, Lori L. ;

Woods, Christopher W. ;

Ginsburg, Geoffrey S. .

EXPERT REVIEW OF ANTI-INFECTIVE THERAPY, 2014, 12 (03) :279-282

[29] The secret garden's gardeners Research increasingly appreciates the crucial role of gut viruses for human health and disease [J].

Hunter, Philip .

EMBO REPORTS, 2013, 14 (08) :683-685

[30] Community-Acquired Pneumonia Requiring Hospitalization among US Children [J].

Jain, Seema ;

Williams, Derek J. ;

Arnold, Sandra R. ;

Ampofo, Krow ;

Bramley, Anna M. ;

Reed, Carrie ;

Stockmann, Chris ;

Anderson, Evan J. ;

Grijalva, Carlos G. ;

Self, Wesley H. ;

Zhu, Yuwei ;

Patel, Anami ;

Hymas, Weston ;

Chappell, James D. ;

Kaufman, Robert A. ;

Kan, J. Herman ;

Dansie, David ;

Lenny, Noel ;

Hillyard, David R. ;

Haynes, Lia M. ;

Levine, Min ;

Lindstrom, Stephen ;

Winchell, Jonas M. ;

Katz, Jacqueline M. ;

Erdman, Dean ;

Schneider, Eileen ;

Hicks, Lauri A. ;

Wunderink, Richard G. ;

Edwards, Kathryn M. ;

Pavia, Andrew T. ;

McCullers, Jonathan A. ;

Finelli, Lyn .

NEW ENGLAND JOURNAL OF MEDICINE, 2015, 372 (09) :835-845

← 1 2 3 4 5 6 7 →