Application of RNA-seq and Bioimaging Methods to Study Microbe–Microbe Interactions and Their Effects on Biofilm Formation and Gene Expression

  • Cristina Isabel AmadorEmail author
  • Claus Sternberg
  • Lars Jelsbak
Part of the Methods in Molecular Biology book series (MIMB, volume 1734)


Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. We describe two different experimental approaches to study microbe–microbe interactions in in vitro systems containing surface-associated microbial populations. One method is the application of RNA sequencing (RNA-seq) to determine the transcriptional changes in pathogenic bacteria in response to microbial interspecies interactions. The other method combines flow cell devices for bacterial cultivation and growth with high-resolution bioimaging to analyze the microscale structural organization of interacting microbial populations within mixed-species biofilms.

Key words

Microbe–microbe interactions Bacterial physiology Interspecies interactions RNA sequencing Bacterial pathogens Biofilms 



We acknowledge Christina Hansen (DTU Bioengineering) for assistance in generating biofilm images. The Villum Foundation provided funding for this study to Lars Jelsbak (Grant number VKR023113).


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Cristina Isabel Amador
    • 1
    Email author
  • Claus Sternberg
    • 1
  • Lars Jelsbak
    • 1
  1. 1.Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark

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