title: Hierarchical oligonucleotide primer extension as a time- and cost-effective approach for quantitative determination of Bifidobacterium spp. in infant feces.
abstract: The Bifidobacterium spp. present in 10 infant fecal samples (4 from infants with eczema and 6 from healthy infants) were quantified with both hierarchical oligonucleotide primer extension (HOPE) and fluorescence in situ hybridization-flow cytometry. The relative abundances of Bifidobacterium longum and B. catenulatum with respect to the total bifidobacteria had a poor correlation (rho, <0.600; P value, >0.208), presumably due to differences in primer specificity and the level of hybridization stringency of both methods. In contrast, the relative abundances of organisms of the genus Bifidobacterium against the total amplified 16S rRNA genes and those of B. adolescentis, B. bifidum, and B. breve against the genus Bifidobacterium exhibited a good statistical correlation (rho, >0.783; P value, <0.066). This good comparability supports HOPE as a method to achieve high-throughput quantitative determination of bacterial targets in a time- and cost-effective manner.
authors.affiliation: Division of Environmental Science and Engineering, National University of Singapore, Singapore 117576, USA.
authors.forename: Pei-Ying
authors.initials: PY
authors.lastname: Hong
authors.forename: Gaik Chin
authors.initials: GC
authors.lastname: Yap
authors.forename: Bee Wah
authors.initials: BW
authors.lastname: Lee
authors.forename: Kaw Yan
authors.initials: KY
authors.lastname: Chua
authors.forename: Wen-Tso
authors.initials: WT
authors.lastname: Liu
mesh_terms: D001644:Bifidobacterium / Q000235:genetics / Q000302:isolation & purification*; D015169:Colony Count, Microbial / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D005243:Feces / Q000382:microbiology*; D005434:Flow Cytometry / Q000379:methods; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D007223:Infant; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013997:Time Factors
chemical_list: D017931:DNA Primers; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S