Development of multi-color FISH method for analysis of seven Bifidobacterium species in human feces

We have developed a multi-color fluorescence in situ hybridization (FISH) method which detects, by a single reaction, all seven species of Bifidobacterium (B. adolescentis, B. angulatum, B. bifidum, B. breve, B. catenulatum, B. dentium, and B. longum), the dominant bacteria in human feces. First, eight new types of oligonucleotide probe were designed, complementary with the 16S rRNA sequence specific to genus Bifidobacterium and each bifidobacterial species described above. Using whole cell hybridization, the fluorescent intensity was measured against the bacterial species targeted by each probe, to show that each probe is specific to the targeted bacteria and that the relative fluorescent intensity (RFI) as an indicator of probe accessibility is high at 61-117%. Then, bacterial species-specific probes were labeled with fluorochromes (FITC, TAMRA and Cy5) in seven different ways, singly or in combination. Using these probes, seven species of Bifidobacterium were differentially stained in mixed samples of cultured bacteria and feces from adult volunteers, proving the efficacy of this technique.