FISH (Fluorescence in situ Hybridization) is a powerful microscopic technique that combines molecular biology, fluorescence microscopy, and histology. Fluorescent probes bind specifically to the ribosomal RNA (rRNA) of microorganisms, allowing bacteria and fungi to be visualized and identified at the genus or species level. For instance, probes can detect all bacteria, all staphylococci, or specifically Staphylococcus aureus. FISH also assesses the (residual) activity of microorganisms based on ribosome content at the single-cell level, enabling visualization, identification, and quantification of microbes in tissue by number, location, and activity. For sequencing, targeted regions of microbial DNA—such as parts of the 16S rRNA gene—are amplified using PCR (Polymerase Chain Reaction). In mono-species infections, Sanger sequencing is then used to determine the precise identity of the microorganisms.

Microbiome analysis allows us to study all microorganisms present in a sample. The workflow includes DNA extraction, amplification, barcoding, and Next-Generation Sequencing (NGS) with bioinformatic evaluation. This method is ideal for mixed cultures or samples with multiple microbes, such as mixed biofilms. We combine microbiome analysis with FISH to provide a spatial view of microorganisms in tissue and to ensure accurate, contamination-free results.

FISH (Fluorescence in situ Hybridization) is a powerful microscopic method that combines molecular biology, fluorescence microscopy, and histology. It enables visualization and identification of microorganisms within tissue, and allows quantification by number, location, and activity. Using fluorescent probes that bind specifically to the ribosomal RNA (rRNA) of microorganisms, FISH can detect bacteria and fungi at the genus or species level—for example, all bacteria, all staphylococci, or specifically Staphylococcus aureus. FISH also measures microbial activity at the single-cell level based on ribosome content. Following treatment with an antimicrobial substance, the fluorescence signal decreases compared to active biofilms, allowing direct measurement of antimicrobial effectiveness by assessing the reduction in FISH-positive cells and overall biofilm mass. Effect quantification is performed using digital image analysis, making FISH an ideal tool for biofilm research, testing antimicrobial substances on biofilms, and developing innovative biofilm-resistant materials.

We identify microorganisms in culture or tissue samples using pan-bacterial 16S rRNA gene amplification followed by sequencing. During PCR (Polymerase Chain Reaction), selected regions of microbial DNA are amplified, and sequencing—either Sanger sequencing or microbiome analysis—is then used to determine the identity of the microorganisms.

Microbiome analysis allows us to study all microorganisms in a sample. The process includes DNA extraction, amplification, barcoding, and Next-Generation Sequencing (NGS) with bioinformatic evaluation. This method is ideal for mixed cultures or samples with multiple microbes, such as mixed biofilms.