The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults.
The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults.
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DOI：
10.1016/j.juro.2015.08.070
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发表时间：
2016-02
期刊：
影响因子：
--
通讯作者：
Blaser MJ
中科院分区：
文献类型：
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作者：
Barnett C;Nazzal L;Goldfarb DS;Blaser MJ
草酸钙形成基因是人类结肠微生物群的成员，在结肠草酸盐净转运和分泌中起主要作用，对草酸钙肾结石的形成具有保护作用。我们现在描述的流行，相对丰度和稳定的O。在美国健康的年轻人中的产甲酸杆菌，如人类微生物组计划（HMP）数据所揭示的，来自242名健康的年轻人的粪便样品，他们进行了1-3次研究访问。样品进行全基因组鸟枪（WGS）测序和/或16 S rRNA测序。研究了可从经处理的序列数据获得的三个数据集：通过与参考基因组（HMSCP）比对或使用MetaPhlAn的WGS宏基因组分析，或V1-3或V3-5 16 S序列的QIME分析。O.使用WGS和16 S rRNA数据在粪便样品中检测到产甲酸杆菌。使用HMSCP分析WGS数据集，显示94名受试者中有29名（31%）为O。V1-3和V3-5分析对O.甲酸杆菌检测当存在时，O.产甲烷菌相对丰度变化在3log 10以上，呈正态分布。对于所有三种方法研究的66个样品，所有检测结果一致58（88%）。14名受试者中O.在基线时甲酸杆菌阳性的13例患者中，13例（93%）在随访访视时阳性，表明定植稳定。O.产甲酸杆菌似乎稳定存在于不到一半的美国健康年轻成人中，并且通过WGS最敏感地检测。
Oxalobacter formigenes, a member of the human colonic microbiota that plays a major role in net colonic oxalate transport and secretion, is protective against formation of calcium oxalate kidney stones. We now describe the prevalence, relative abundance and stability of O. formigenes in healthy young adults in the United States, as revealed by Human Microbiome Project (HMP) data from fecal samples from 242 healthy young adults who had 1-3 study visits. Samples underwent whole-genomic shotgun (WGS) sequencing, and/or 16S rRNA sequencing. Three datasets available from the processed sequence data were studied: WGS metagenomic analysis by alignment to reference genomes (HMSCP) or using MetaPhlAn, or QIIME analysis of the V1-3 or V3-5 16S sequences. O. formigenes was detected in fecal samples using both the WGS and 16S rRNA data. Analysis of the WGS dataset, using HMSCP, showed that 29 (31%) of 94 subjects were O. formigenes-positive while the V1-3 and V3-5 analyses were less sensitive for O. formigenes detection. When present, O. formigenes relative abundance varied over 3 log10, and was normally distributed. For 66 samples studied by all three methods, all assays agreed in 58 (88%). Of 14 subjects who were O. formigenes-positive at baseline, 13 (93%) were positive on follow-up visit, indicating the stability of colonization. O. formigenes appears to be stably present in fewer than half of healthy young USA adults and is most sensitively detected by WGS.