title: Strain-level microbial epidemiology and population genomics from shotgun metagenomics.
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.
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Matthias
authors.initials: M
authors.lastname: Scholz
authors.affiliation: Center for Microbiome Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
authors.forename: Doyle V
authors.initials: DV
authors.lastname: Ward
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Edoardo
authors.initials: E
authors.lastname: Pasolli
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Thomas
authors.initials: T
authors.lastname: Tolio
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Moreno
authors.initials: M
authors.lastname: Zolfo
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Asnicar
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Duy Tin
authors.identifier: 0000-0002-4169-7727
authors.initials: DT
authors.lastname: Truong
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Adrian
authors.initials: A
authors.lastname: Tett
authors.affiliation: Department of Pediatrics, Perinatal Institute, Cincinnati, Ohio, USA.
authors.forename: Ardythe L
authors.initials: AL
authors.lastname: Morrow
authors.affiliation: Centre for Integrative Biology, University of Trento, Trento, Italy.
authors.forename: Nicola
authors.identifier: 0000-0002-1583-5794
authors.initials: N
authors.lastname: Segata
mesh_terms: D004926:Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D005858:Germany; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology*; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D059013:Microbial Consortia / Q000235:genetics*; D010802:Phylogeny; D012867:Skin / Q000382:microbiology*; D012984:Software; D013045:Species Specificity