Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

被引：526

作者：

Asnicar, Francesco ^{[1
]}

Thomas, Andrew Maltez ^{[1
]}

Beghini, Francesco ^{[1
]}

Mengoni, Claudia ^{[1
]}

Manara, Serena ^{[1
]}

Manghi, Paolo ^{[1
]}

Zhu, Qiyun ^{[2
]}

Bolzan, Mattia ^{[1
,9
]}

Cumbo, Fabio ^{[1
]}

May, Uyen ^{[3
]}

Sanders, Jon G. ^{[2
,12
]}

Zolfo, Moreno ^{[1
]}

Kopylova, Evguenia ^{[2
,11
]}

Pasolli, Edoardo ^{[1
,10
]}

Knight, Rob ^{[2
,4
,5
,6
]}

Mirarab, Siavash ^{[3
]}

Huttenhower, Curtis ^{[7
,8
]}

Segata, Nicola ^{[1
]}

机构：

[1] Univ Trento, Dept CIBIO, Trento, Italy

[2] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Dept Elect & Comp Engn, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[5] Univ Calif San Diego, Ctr Microbiome Innovat, La Jolla, CA 92093 USA

[6] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[7] Harvard TH Chan Sch Publ Hlth, Dept Biostat, Boston, MA USA

[8] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[9] PreBiomics Srl, Trento, Italy

[10] Univ Naples Federico II, Dept Agr Sci, Portici, Italy

[11] Clar Genom BVBA, Sint Michielskaai 34, B-2000 Antwerp, Belgium

[12] Cornell Univ, Cornell Inst Host Microbe Interact & Dis, Ithaca, NY USA

来源：

NATURE COMMUNICATIONS | 2020年 / 11卷 / 01期

基金：

欧洲研究理事会; 美国国家卫生研究院;

关键词：

MULTIPLE SEQUENCE ALIGNMENT; TREE; INFORMATION; ACCURACY; BACTERIA; BLOCKS; SEARCH; TOOL;

D O I：

10.1038/s41467-020-16366-7

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.0, an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences. For individual clades of interest, it reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers. At the other extreme of resolution, it scales to large phylogenies comprising >17,000 microbial species. Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 to support genomic and metagenomic analyses.

引用

页数：10

共 73 条

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