Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Nat Methods. 2016 May;13(5):435-8. doi: 10.1038/nmeth.3802. Epub 2016 Mar 21.


Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (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.

MeSH terms

  • Escherichia coli / classification
  • Escherichia coli / genetics
  • Escherichia coli / isolation & purification
  • Escherichia coli / pathogenicity
  • Gene Expression Profiling
  • Genome, Bacterial
  • Germany
  • Humans
  • Intestinal Mucosa / microbiology*
  • Metagenome / genetics*
  • Metagenomics / methods*
  • Microbial Consortia / genetics*
  • Phylogeny*
  • Skin / microbiology*
  • Software
  • Species Specificity