title: Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis.
abstract: 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.
authors.affiliation: Department für Mikrobielle Okologie, Universität Wien, Althanstrasse 14, 1090, Vienna, Austria. daims@microbial-ecology.net
authors.forename: Holger
authors.initials: H
authors.lastname: Daims
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D015169:Colony Count, Microbial; D017753:Ecosystem; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods*; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D012335:RNA, Ribosomal