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Sci Rep. 2019 Dec 27;9(1):19834. doi: 10.1038/s41598-019-56065-y.

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

Author information

1
Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands. Tom.Ederveen@radboudumc.nl.
2
Department of Dermatology, RIMLS, Radboudumc, Nijmegen, The Netherlands. Tom.Ederveen@radboudumc.nl.
3
NIZO, Ede, The Netherlands. Tom.Ederveen@radboudumc.nl.
4
Department of Dermatology, RIMLS, Radboudumc, Nijmegen, The Netherlands.
5
Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.
6
NIZO, Ede, The Netherlands.

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.

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