Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression

Grith Miriam Maigaard Hermansen, Pavelas Sazinas, Ditte Kofod, Andrew Millard, Paal Skytt Andersen, Lars Jelsbak*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Interspecies interactions between bacterial pathogens and the commensal microbiota can influence disease outcome. In the nasal cavities, Staphylococcus epidermidis has been shown to be a determining factor for Staphylococcus aureus colonization and biofilm formation. However, the interaction between S. epidermidis and S. aureus has mainly been described by phenotypic analysis, and little is known about how this interaction modulates gene expression.This study aimed to determine the interactome of nasal S. aureus and S. epidermidis isolates to understand the molecular effect of interaction. After whole-genome sequencing of two nasal staphylococcal isolates, an agar-based RNA sequencing setup was utilized to identify interaction-induced transcriptional alterations in surface-associated populations. Our results revealed differential expression of several virulence genes in both species. We also identified putative non-coding RNAs (ncRNAs) and, interestingly, detected a putative ncRNA transcribed antisense to esp, the serine protease of S. epidermidis, that has previously been shown to inhibit nasal colonization of S. aureus. In our study, the gene encoding Esp and the antisense ncRNA are both downregulated during interaction with S. aureus. Our findings contribute to a better understanding of pathogen physiology in the context of interactions with the commensal microbiota, and may provide targets for future therapeutics.
Original languageEnglish
Article numberfny004
JournalFEMS Microbiology Letters
Volume365
Issue number5
Number of pages9
ISSN0378-1097
DOIs
Publication statusPublished - 2018

Keywords

  • Staphylococcus aureus
  • Staphylococcus epidermidis
  • Non-coding RNA
  • Pathogen-commensal interaction
  • Transcriptome
  • RNA-seq

Cite this

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title = "Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression",
abstract = "Interspecies interactions between bacterial pathogens and the commensal microbiota can influence disease outcome. In the nasal cavities, Staphylococcus epidermidis has been shown to be a determining factor for Staphylococcus aureus colonization and biofilm formation. However, the interaction between S. epidermidis and S. aureus has mainly been described by phenotypic analysis, and little is known about how this interaction modulates gene expression.This study aimed to determine the interactome of nasal S. aureus and S. epidermidis isolates to understand the molecular effect of interaction. After whole-genome sequencing of two nasal staphylococcal isolates, an agar-based RNA sequencing setup was utilized to identify interaction-induced transcriptional alterations in surface-associated populations. Our results revealed differential expression of several virulence genes in both species. We also identified putative non-coding RNAs (ncRNAs) and, interestingly, detected a putative ncRNA transcribed antisense to esp, the serine protease of S. epidermidis, that has previously been shown to inhibit nasal colonization of S. aureus. In our study, the gene encoding Esp and the antisense ncRNA are both downregulated during interaction with S. aureus. Our findings contribute to a better understanding of pathogen physiology in the context of interactions with the commensal microbiota, and may provide targets for future therapeutics.",
keywords = "Staphylococcus aureus, Staphylococcus epidermidis, Non-coding RNA, Pathogen-commensal interaction, Transcriptome, RNA-seq",
author = "Hermansen, {Grith Miriam Maigaard} and Pavelas Sazinas and Ditte Kofod and Andrew Millard and Andersen, {Paal Skytt} and Lars Jelsbak",
year = "2018",
doi = "10.1093/femsle/fny004",
language = "English",
volume = "365",
journal = "F E M S Microbiology Letters",
issn = "0378-1097",
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Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression. / Hermansen, Grith Miriam Maigaard; Sazinas, Pavelas; Kofod, Ditte; Millard, Andrew; Andersen, Paal Skytt; Jelsbak, Lars.

In: FEMS Microbiology Letters, Vol. 365, No. 5, fny004, 2018.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression

AU - Hermansen, Grith Miriam Maigaard

AU - Sazinas, Pavelas

AU - Kofod, Ditte

AU - Millard, Andrew

AU - Andersen, Paal Skytt

AU - Jelsbak, Lars

PY - 2018

Y1 - 2018

N2 - Interspecies interactions between bacterial pathogens and the commensal microbiota can influence disease outcome. In the nasal cavities, Staphylococcus epidermidis has been shown to be a determining factor for Staphylococcus aureus colonization and biofilm formation. However, the interaction between S. epidermidis and S. aureus has mainly been described by phenotypic analysis, and little is known about how this interaction modulates gene expression.This study aimed to determine the interactome of nasal S. aureus and S. epidermidis isolates to understand the molecular effect of interaction. After whole-genome sequencing of two nasal staphylococcal isolates, an agar-based RNA sequencing setup was utilized to identify interaction-induced transcriptional alterations in surface-associated populations. Our results revealed differential expression of several virulence genes in both species. We also identified putative non-coding RNAs (ncRNAs) and, interestingly, detected a putative ncRNA transcribed antisense to esp, the serine protease of S. epidermidis, that has previously been shown to inhibit nasal colonization of S. aureus. In our study, the gene encoding Esp and the antisense ncRNA are both downregulated during interaction with S. aureus. Our findings contribute to a better understanding of pathogen physiology in the context of interactions with the commensal microbiota, and may provide targets for future therapeutics.

AB - Interspecies interactions between bacterial pathogens and the commensal microbiota can influence disease outcome. In the nasal cavities, Staphylococcus epidermidis has been shown to be a determining factor for Staphylococcus aureus colonization and biofilm formation. However, the interaction between S. epidermidis and S. aureus has mainly been described by phenotypic analysis, and little is known about how this interaction modulates gene expression.This study aimed to determine the interactome of nasal S. aureus and S. epidermidis isolates to understand the molecular effect of interaction. After whole-genome sequencing of two nasal staphylococcal isolates, an agar-based RNA sequencing setup was utilized to identify interaction-induced transcriptional alterations in surface-associated populations. Our results revealed differential expression of several virulence genes in both species. We also identified putative non-coding RNAs (ncRNAs) and, interestingly, detected a putative ncRNA transcribed antisense to esp, the serine protease of S. epidermidis, that has previously been shown to inhibit nasal colonization of S. aureus. In our study, the gene encoding Esp and the antisense ncRNA are both downregulated during interaction with S. aureus. Our findings contribute to a better understanding of pathogen physiology in the context of interactions with the commensal microbiota, and may provide targets for future therapeutics.

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KW - Staphylococcus epidermidis

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KW - Pathogen-commensal interaction

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