ArticleScientific reports2019
A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 41 citations in OpenAlex.
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- Novel methodologies for host-microbe interactions and microbiome-targeted therapeutics in 3D organotypic skin models.Microbiome · 2023Article
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- Model-Based Meta-Analysis to OptimizeJID innovations : skin science from molecules to population health · 2022Article
- Interspecies Regulation BetweenFrontiers in microbiology · 2022Article
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- Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin.BMC microbiology · 2021Article
- Skin microbiota in health and disease: From sequencing to biology.The Journal of dermatology · 2020Review
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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