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Nat Methods. 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.

Author information

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.

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.

PMID:
26999001
DOI:
10.1038/nmeth.3802
[Indexed for MEDLINE]

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