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Strain-level microbial epidemiology and population genomics from shotgun metagenomics

by Asnicar, Francesco , Truong, Duy Tin , Segata, Nicola , Tolio, Thomas , Scholz, Matthias , Pasolli, Edoardo , Tett, Adrian , Ward, Doyle V , Zolfo, Moreno , Morrow, Ardythe L

in 45/23 / 45/91 / 631/114/1386 / 631/1647/514/1948 / 631/1647/514/1949 / 631/326/2565 / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical Engineering/Biotechnology / brief-communication / Epidemiology / Escherichia coli - classification / Escherichia coli - genetics / Escherichia coli - isolation & purification / Escherichia coli - pathogenicity / Gene Expression Profiling / Genetic aspects / Genome, Bacterial / Genomics / Germany / Humans / Identification and classification / Innovations / Intestinal Mucosa - microbiology / Life Sciences / Metagenome - genetics / Metagenomics - methods / Microbial Consortia - genetics / Outbreaks / Pathogenic microorganisms / Pathogens / Phylogeny / Population studies / Proteomics / Skin - microbiology / Software / Species Specificity / Studies / Virulence (Microbiology)

2016

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Strain-level microbial epidemiology and population genomics from shotgun metagenomics

by Asnicar, Francesco , Truong, Duy Tin , Segata, Nicola , Tolio, Thomas , Scholz, Matthias , Pasolli, Edoardo , Tett, Adrian , Ward, Doyle V , Zolfo, Moreno , Morrow, Ardythe L

2016

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Strain-level microbial epidemiology and population genomics from shotgun metagenomics

by Asnicar, Francesco , Truong, Duy Tin , Segata, Nicola , Tolio, Thomas , Scholz, Matthias , Pasolli, Edoardo , Tett, Adrian , Ward, Doyle V , Zolfo, Moreno , Morrow, Ardythe L

2016

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Journal Article

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Asnicar, Francesco,

Truong, Duy Tin,

Segata, Nicola,

Tolio, Thomas,

Scholz, Matthias,

Pasolli, Edoardo,

Tett, Adrian,

Ward, Doyle V,

Zolfo, Moreno,

Morrow, Ardythe L

2016

Overview

PanPhlAn detects strains and characterizes strain-specific gene content and activity within metagenomic and metatranscriptomic samples for microbial population analysis and epidemiology. 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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Nature Publishing Group US,Nature Publishing Group

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/ 45/91