Applied Microbiology and Biotechnology

, Volume 75, Issue 2, pp 237–248

Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis


DOI: 10.1007/s00253-007-0886-z

Cite this article as:
Daims, H. & Wagner, M. Appl Microbiol Biotechnol (2007) 75: 237. doi:10.1007/s00253-007-0886-z


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.


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

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  1. 1.Department für Mikrobielle ÖkologieUniversität WienViennaAustria

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