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Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis


Traditional cultivation-based methods to quantify microbial abundance are not suitable for analyses of microbial communities in environmental or medical samples, which consist mainly of uncultured microorganisms. Recently, different cultivation-independent quantification approaches have been developed to overcome this problem. Some of these techniques use specific fluorescence markers, for example ribosomal ribonucleic acid targeted oligonucleotide probes, to label the respective target organisms. Subsequently, the detected cells are visualized by fluorescence microscopy and are quantified by direct visual cell counting or by digital image analysis. This article provides an overview of these methods and some of their applications with emphasis on (semi-)automated image analysis solutions.

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The development of image analysis approaches and software by our group has been financially supported by the Deutsche Forschungsgemeinschaft (DFG; grant Schl 120/14-1) and the Vienna Science and Technology Fund (WWTF; grant LS 216).

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Correspondence to Holger Daims.

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Daims, H., Wagner, M. Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis. Appl Microbiol Biotechnol 75, 237–248 (2007).

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  • Uncultured microorganisms
  • Quantification
  • Fluorescence in situ hybridization
  • Digital image analysis
  • Microbial ecology