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- Title
A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota.
- Authors
Ederveen, Thomas H. A.; Smits, Jos P. H.; Hajo, Karima; van Schalkwijk, Saskia; Kouwenhoven, Tessa A.; Lukovac, Sabina; Wels, Michiel; van den Bogaard, Ellen H.; Schalkwijk, Joost; Boekhorst, Jos; Zeeuwen, Patrick L. J. M.; van Hijum, Sacha A. F. T.
- 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 Staphylococcus members at (sub)species level and provides higher resolution than current 16S-based techniques. With the higher discriminative ability provided by our approach, we further show that the presence of Staphylococcus capitis on the skin together with Staphylococcus aureus associates with AD disease.
- Subjects
BACTERIAL loci; BIOINFORMATICS; BACTERIAL genomes; BACTERIA phylogeny; ATOPIC dermatitis
- Publication
Scientific Reports, 2019, Vol 9, Issue 1, p1
- ISSN
2045-2322
- Publication type
Article
- DOI
10.1038/s41598-019-56065-y