Strain-level microbial epidemiology and population genomics from shotgun metagenomics

doi:10.1038/nmeth.3802

. 2016 May;13(5):435-8.

doi: 10.1038/nmeth.3802. Epub 2016 Mar 21.

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Affiliations

¹ Centre for Integrative Biology, University of Trento, Trento, Italy.
² Center for Microbiome Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
³ Department of Pediatrics, Perinatal Institute, Cincinnati, Ohio, USA.

PMID: 26999001
DOI: 10.1038/nmeth.3802

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Matthias Scholz et al. Nat Methods. 2016 May.

. 2016 May;13(5):435-8.

doi: 10.1038/nmeth.3802. Epub 2016 Mar 21.

Authors

Affiliations

¹ Centre for Integrative Biology, University of Trento, Trento, Italy.
² Center for Microbiome Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
³ Department of Pediatrics, Perinatal Institute, Cincinnati, Ohio, USA.

PMID: 26999001
DOI: 10.1038/nmeth.3802

Abstract

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.

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References

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[1] Mol Syst Biol. 2014 Nov 28;10:766 - PubMed

[2] Mol Syst Biol. 2014 Nov 28;10:766 - PubMed

[3] Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 - PubMed

[4] Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 - PubMed

[5] Bioinformatics. 2015 Nov 15;31(22):3691-3 - PubMed

[6] Bioinformatics. 2015 Nov 15;31(22):3691-3 - PubMed

[7] Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38 - PubMed

[8] Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38 - PubMed

[9] Nat Methods. 2012 Jun 10;9(8):811-4 - PubMed

[10] Nat Methods. 2012 Jun 10;9(8):811-4 - PubMed

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Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Affiliations

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

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