Highlight talk – Theme: Genome
Abstract
Microbial species comprise strains with largely different set of genes and functional potential. Identifying microbial strains and characterizing their genes is thus essential for pathogen discovery, epidemiology and population genomics. Here we present a novel computational strain-level metagenomic profiling tool, called PanPhlAn, for identifying the gene composition and in-vivo transcriptional activity of individual strains from metagenomic and metatranscriptomic samples. PanPhlAn enables both the identification of known organisms and the characterization of previously unseen strains. Applied to the 2011 German E. coli outbreak, we demonstrate the ability of PanPhlAn to recognize outbreak strains and identify their associated virulence and resistance factors. Based on almost two thousand samples, PanPhlAn produced the largest strain-level, culture-free population genomic study of human-associated microbial species. In a large cohort of preterm infants, PanPhlAn enabled the identification of disease-associated strain-level genetic biomarkers. PanPhlAn is available at http://segatalab.cibio.unitn.it/tools/panphlan.
Authors
Matthias Scholz, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
Doyle V. Ward, Center for Microbiome Research, University of Massachusetts Medical School, Worcester, Massachusetts, United States
Edoardo Pasolli, Centre for Integrative Biology, University of Trento, Italy
Thomas Tolio, Centre for Integrative Biology, University of Trento, Italy
Moreno Zolfo, Centre for Integrative Biology, University of Trento, Italy
Francesco Asnicar, Centre for Integrative Biology, University of Trento, Italy
Duy Tin Truong, Centre for Integrative Biology, University of Trento, Italy
Adrian Tett, Centre for Integrative Biology, University of Trento, Italy
Ardythe L. Morrow, Cincinnati Children’s Hospital Med. Ctr, Perinatal Institute, Cincinnati, Ohio, United States
Nicola Segata, Centre for Integrative Biology, University of Trento, Italy