Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
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DOI：
10.1128/aem.68.10.5064-5081.2002
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发表时间：
2002-10-01
影响因子：
4.4
通讯作者：
Wagner, M
中科院分区：
文献类型：
--
作者：
Loy, A;Lehner, A;Wagner, M
为了独立于培养检测硫酸盐还原原核生物 (SRP)，设计了由 132 个 16S rRNA 基因靶向寡核苷酸探针 (18-mers) 组成的寡核苷酸微阵列，该微阵列具有分层和平行（相同）特异性，用于检测硫酸盐还原原核生物的所有已知谱系 (SRP-PhyloChip)，并随后用 41 个合适的 SRP 纯培养物进行评估。通过使用来自牙周牙袋和来自 Solar Lake（埃及西奈）的超盐蓝藻垫趋化素的样品，测试了 SRP-PhyloChip 在环境和临床样品中 SRP 多样性筛选的适用性。与之前的研究一致，SRP-PhyloChip 表明存在 Desulfomicrobium spp。齿袋中存在 Desulfonema 和 Desulfomonile 样 SRP（与其他 SRP 一起）在垫的趋化素中。 SRP-PhyloChip 结果通过多种独立于 DNA 微阵列的技术得到证实，包括 SRP 16S rRNA 基因和编码异化（双）亚硫酸盐还原酶 (dsrAB) 的基因的特异性 PCR 扩增、克隆和测序。
For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).