Visualization of microorganisms in bioprocesses

Tsuyoshi Yamaguchi, Kengo Kubota

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)


Fluorescence in situ hybridization (FISH) is currently a standard technique for detecting, identifying, and enumerating microorganisms. The method allows for visualization of cell morphology as well as in situ localization of microorganisms at single-cell resolution. Although FISH has been used for more than 20 years, many challenges remain with regard to improving the technique for understanding microbial ecology and physiology. This chapter describes the recent developments in this field, such as improved sensitivity by catalyzed reporter deposition (CARD)-FISH and in situ DNA-hybridization chain reaction (HCR). Highly sensitive methods for detecting mRNA and/or functional genes are also described. Moreover, methods combining isotope probing to reveal microbial metabolic activities are introduced.

Original languageEnglish
Title of host publicationOptimization and Applicability of Bioprocesses
PublisherSpringer Singapore
Number of pages14
ISBN (Electronic)9789811068638
ISBN (Print)9789811068621
Publication statusPublished - 2018 Jan 2


  • Ecology
  • Fluorescence
  • Metabolic activity
  • Microorganisms
  • Phylogeny

ASJC Scopus subject areas

  • Medicine(all)
  • Health Professions(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Engineering(all)
  • Environmental Science(all)
  • Immunology and Microbiology(all)


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