title: Molecular approaches for the detection and identification of bifidobacteria and lactobacilli in the human gastrointestinal tract.
abstract: In this review an overview of various molecular techniques and their application for the detection and identification of bifidobacteria and lactobacilli in the gastrointestinal (GI) tract is presented. The techniques include molecular typing techniques such as amplified ribosomal DNA restriction analysis (ARDRA), randomly amplified polymorphic DNA (RAPD), pulsed field gel electrophoresis (PFGE), ribotyping and community profiling techniques such as PCR coupled to temperature and denaturing gradient gel electrophoresis (PCR-TGGE and PCR-DGGE, respectively). Special attention is given to oligonucleotide probes and primers that target the ribosomal RNA (rRNA) sequences and their use in PCR and different hybridisation techniques such as DNA microarrays and fluorescent in situ hybridisation (FISH). In addition, recent findings based on the molecular studies of bifidobacteria and lactobacilli in the GI-tract are reviewed.
authors.affiliation: VTT Biotechnology, Espoo, Finland. reetta.satokari@vtt.fi
authors.forename: Reetta M
authors.initials: RM
authors.lastname: Satokari
authors.forename: Elaine E
authors.initials: EE
authors.lastname: Vaughan
authors.forename: Hauke
authors.initials: H
authors.lastname: Smidt
authors.forename: Maria
authors.initials: M
authors.lastname: Saarela
authors.forename: Jaana
authors.initials: J
authors.lastname: Mättö
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods; D001644:Bifidobacterium / Q000145:classification* / Q000166:cytology / Q000302:isolation & purification* / Q000378:metabolism; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D016521:Electrophoresis, Gel, Pulsed-Field; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D007778:Lactobacillus / Q000145:classification* / Q000166:cytology / Q000302:isolation & purification* / Q000378:metabolism; D009693:Nucleic Acid Hybridization; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D019105:Random Amplified Polymorphic DNA Technique; D021521:Ribotyping; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal