Strain-level microbial epidemiology and population genomics from shotgun metagenomics

被引：1

作者：

Scholz, Matthias ^{[1
]}

Ward, Doyle V. ^{[2
]}

Pasolli, Edoardo ^{[1
]}

Tolio, Thomas ^{[1
]}

Zolfo, Moreno ^{[1
]}

Asnicar, Francesco ^{[1
]}

Duy Tin Truong ^{[1
]}

Tett, Adrian ^{[1
]}

Morrow, Ardythe L. ^{[3
]}

Segata, Nicola ^{[1
]}

机构：

[1] Univ Trento, Ctr Integrat Biol, Trento, Italy

[2] Univ Massachusetts, Sch Med, Ctr Microbiome Res, Worcester, MA USA

[3] Perinatal Inst, Dept Pediat, Cincinnati, OH USA

来源：

NATURE METHODS | 2016年 / 13卷 / 05期

基金：

美国国家卫生研究院;

关键词：

HUMAN GUT MICROBIOME; NECROTIZING ENTEROCOLITIS; ESCHERICHIA-COLI; IDENTIFICATION; ALIGNMENT; OUTBREAK; SAMPLES; SEARCH;

D O I：

10.1038/NMETH.3802

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.

引用

页码：435 / +

页数：8

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Ward D.V.
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Zolfo M.
Asnicar F.
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Tett A.
Morrow A.L.
Segata N.
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