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Strain-level microbial epidemiology and population genomics from shotgun metagenomics.
Scholz, Matthias; Ward, Doyle V; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian; Morrow, Ardythe L; Segata, Nicola.
Affiliation
  • Scholz M; Centre for Integrative Biology, University of Trento, Trento, Italy.
  • Ward DV; Center for Microbiome Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
  • Pasolli E; Centre for Integrative Biology, University of Trento, Trento, Italy.
  • Tolio T; Centre for Integrative Biology, University of Trento, Trento, Italy.
  • Zolfo M; Centre for Integrative Biology, University of Trento, Trento, Italy.
  • Asnicar F; Centre for Integrative Biology, University of Trento, Trento, Italy.
  • Truong DT; Centre for Integrative Biology, University of Trento, Trento, Italy.
  • Tett A; Centre for Integrative Biology, University of Trento, Trento, Italy.
  • Morrow AL; Department of Pediatrics, Perinatal Institute, Cincinnati, Ohio, USA.
  • Segata N; Centre for Integrative Biology, University of Trento, Trento, Italy.
Nat Methods ; 13(5): 435-8, 2016 05.
Article in En | MEDLINE | ID: mdl-26999001
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phylogeny / Skin / Metagenome / Metagenomics / Microbial Consortia / Intestinal Mucosa Type of study: Screening_studies Limits: Humans Country/Region as subject: Europa Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2016 Type: Article Affiliation country: Italy
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phylogeny / Skin / Metagenome / Metagenomics / Microbial Consortia / Intestinal Mucosa Type of study: Screening_studies Limits: Humans Country/Region as subject: Europa Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2016 Type: Article Affiliation country: Italy