Isolation of Bacterial RNA from Foods Inoculated with Pathogens

  • Deepti Tyagi
  • Autumn L. Kraft
  • Teresa M. BergholzEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1918)


One strategy bacteria use to acclimate to changing environmental conditions is modulation of gene expression. Alterations in gene expression are indicative of activation or repression of certain physiological responses. In order to understand which genetic responses are utilized to cope with various environmental conditions by analyzing transcriptomes, obtaining RNA of high quality, yield, and integrity is paramount. Here, we describe an acid phenol–chloroform method employed to extract RNA from laboratory grown cell cultures, as well as cultures inoculated onto complex matrices such as lettuce and cold-smoked salmon. The method results in high-quality RNA, which can be used for various downstream processes such as cDNA library construction, RNA sequencing, real-time quantitative PCR, and northern analysis. Extraction of RNA from bacterial foodborne pathogens in conjunction with transcriptome sequencing is a useful technique to elucidate pathogens’ transcriptional responses.

Key words

RNA extraction RNA sequencing Transcriptional response Foodborne pathogens 



Teresa M. Bergholz and the work in her lab are partially supported by the National Institute of Food and Agriculture, US Department of Agriculture, under project no. ND02426.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Deepti Tyagi
    • 1
  • Autumn L. Kraft
    • 1
  • Teresa M. Bergholz
    • 1
    Email author
  1. 1.Department of Microbiological SciencesNorth Dakota State UniversityFargoUSA

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