Strain-level microbial epidemiology and population genomics from shotgun metagenomics.
basic_science · Level V
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- Record sourced from PubMed, PMID 26999001.
- Also identified by DOI 10.1038/nmeth.3802.
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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.
Medical subject headings
- Intestinal Mucosa
- Metagenome
- Metagenomics
- Microbial Consortia
- Phylogeny
- Skin