3. Fluorescent in situ hybridization (FISH) for image analysis of specific microorganisms in the digestive tract

FISH with fluorescently labelled oligonucleotides targeting bacterial rRNAs can be a very powerful tool for detecting specific bacteria in various environmental samples such as active sludge, stool, clinical specimens, animal tissues and so on (Wagner et al. 2003, Amann and Fuchs 2008). In this chapter, we describe a basic FISH protocol suitable for the detection of specific bacteria in the honey bee gut (Fig. 3) and probably also applicable for other insect samples. We provide useful tips and mention important points to be considered when performing these experiments.

Fig. 3. Micrograph using fluorescent in situ hybridization (FISH) of Snodgrassella alvi (green) and Firm-5 (blue) in an oblique section of the honey bee ileum.  The fluorescent tags used here were linked to probes hybridizing with 16S rRNA specific to these bacterial types. In addition, a DNA stain (white) was used to stain the honey bee nuclei. Image prepared by W Kwong.



3.4. Hybridization