RRC ID 5154
著者 Hong PY, Wu JH, Liu WT.
タイトル Relative abundance of Bacteroides spp. in stools and wastewaters as determined by hierarchical oligonucleotide primer extension.
ジャーナル Appl Environ Microbiol
Abstract A molecular method, termed hierarchical oligonucleotide primer extension (HOPE), was used to determine the relative abundances of predominant Bacteroides spp. present in fecal microbiota and wastewaters. For this analysis, genomic DNA in feces of healthy human adults, bovines, and swine and in wastewaters was extracted and total bacterial 16S rRNA genes were PCR amplified and used as the DNA templates for HOPE. Nineteen oligonucleotide primers were designed to detect 14 Bacteroides spp. at different hierarchical levels (domain, order, cluster, and species) and were arranged into and used in six multiplex HOPE reaction mixtures. Results showed that species like B. vulgatus, B. thetaiotaomicron, B. caccae, B. uniformis, B. fragilis, B. eggerthii, and B. massiliensis could be individually detected in human feces at abundances corresponding to as little as 0.1% of PCR-amplified 16S rRNA genes. Minor species like B. pyogenes, B. salyersiae, and B. nordii were detected only collectively using a primer that targeted the B. fragilis subgroup (corresponding to approximately 0.2% of PCR-amplified 16S rRNA genes). Furthermore, Bac303-related targets (i.e., most Bacteroidales) were observed to account for 28 to 44% of PCR-amplified 16S rRNA genes from human fecal microbiota, and their abundances were higher than those detected in the bovine and swine fecal microbiota and in wastewaters by factors of five and two, respectively. These results were comparable to those obtained by quantitative PCR and to those reported previously from studies using whole-cell fluorescence hybridization and 16S rRNA clone library methods, supporting the conclusion that HOPE can be a sensitive, specific, and rapid method to determine the relative abundances of Bacteroides spp. predominant in fecal samples.
巻・号 74(9)
ページ 2882-93
公開日 2008-5-1
DOI 10.1128/AEM.02568-07
PII AEM.02568-07
PMID 18344347
PMC PMC2394900
MeSH Adult Animals Bacteroidetes / classification Bacteroidetes / genetics* Bacteroidetes / isolation & purification* Cattle Colony Count, Microbial / methods DNA Primers / genetics DNA, Bacterial / chemistry DNA, Bacterial / genetics DNA, Ribosomal / chemistry DNA, Ribosomal / genetics Feces / microbiology* Humans Molecular Sequence Data Nucleic Acid Amplification Techniques / methods* Phylogeny RNA, Ribosomal, 16S / genetics Sensitivity and Specificity Sequence Analysis, DNA Sewage / microbiology* Swine
IF 4.016
引用数 36
WOS 分野 BIOTECHNOLOGY & APPLIED MICROBIOLOGY MICROBIOLOGY
リソース情報
一般微生物 JCM12987 JCM12988 JCM6294 JCM9498 JCM10556 JCM13266 JCM12986 JCM6297 JCM5828 JCM12979 JCM12982 JCM5825 JCM9497 JCM13446