The development and evaluation of a duplex polymerase chain reaction detection of Bifidobacterium spp. And Lactobacillus spp. in duodenum, jejunum, ileum and cecum of broilers

Bifidobacterium spp. and Lactobacillus spp. genera are useful and important microbiota which affect poultry performance. The aim of this study was to develop a method for the direct and simultaneous detection of Bifidobacterium spp. and Lactobacillus spp. by multiplex polymerase chain reaction (PCR). Two pairs of oligonucleotide primers were applied simultaneously to detect two different genera of useful bacteria by duplex PCR in a single tube. Primers were compared with sequences in the GenBank and none were found to have the exact same sequence as the non-targeted sequence. Bacterial source included duodenum, jejunum, ileum and cecum obtained from commercial broilers. All gastrointestinal samples tested including duodenum, jejunum, ileum and cecum showed positive results with the PCR assay for both Bifidobacterium spp. and Lactobacillus spp. There was no cross reactivity among these two closely related microorganisms. All primer pairs showed specificities only for their corresponding target microorganisms.