1. Strain-level microbial epidemiology and population genomics from shotgun metagenomics.
- Author
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Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, Truong DT, Tett A, Morrow AL, and Segata N
- Subjects
- Escherichia coli classification, Escherichia coli genetics, Escherichia coli isolation & purification, Escherichia coli pathogenicity, Gene Expression Profiling, Genome, Bacterial, Germany, Humans, Software, Species Specificity, Intestinal Mucosa microbiology, Metagenome genetics, Metagenomics methods, Microbial Consortia genetics, Phylogeny, Skin microbiology
- 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.
- Published
- 2016
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