A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota.

ABSTRACT: We present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. As TaxPhlAn requires the SLST targets identified to fit the phylogenetic pattern as determined through comprehensive evolutionary reconstruction of input genomes, TaxPhlAn allows for the identification and phylogenetic inference of new biodiversity. Here, we present a clinically relevant case study of high-resolution Staphylococcus profiling on skin of atopic dermatitis (AD) patients. We demonstrate that SLST enables profiling of cutaneous Staphyl

SUBMITTER: Ederveen THA 

PROVIDER: S-EPMC6934516 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature