A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.
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DOI：
10.1371/journal.pone.0036466
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Versalovic J
中科院分区：
文献类型：
--
作者：
Aagaard K;Riehle K;Ma J;Segata N;Mistretta TA;Coarfa C;Raza S;Rosenbaum S;Van den Veyver I;Milosavljevic A;Gevers D;Huttenhower C;Petrosino J;Versalovic J
虽然目前主要的国家研究工作（即，NIH人类微生物组计划）将使得能够对成年人类微生物群进行全面的宏基因组表征，这些不同的微生物群落如何以及何时在宿主中以及在生殖生命期间驻留在种群水平上是未探索的。由于微生物丰度和多样性可能在怀孕期间不同，我们试图在胎龄层中产生比较宏基因组签名。从阴道（阴道口、后穹窿、阴道中段）分离DNA，并对细菌16S rRNA基因的V5V3区域进行测序（454FLX Titanium平台）。将来自24名健康孕妇（18至40周确认）的68个样本与301名非妊娠对照（60名受试者）进行比较。将生成的序列数据进行质量过滤、分类学分箱、标准化，并通过同源性组织成操作分类单位（OTU）;将所得β多样性测量的主坐标分析（PCoA）用于与样品临床元数据相关的可视化和分析。总共产生了包含> 250万个读段（平均6，837个序列/长度为493 nt的样品）的1.4千兆字节的数据用于计算分析。尽管在筛选时没有由于后穹窿pH> 4.5而排除孕妇科，但是使用系统发育、非系统发育、监督和非监督方法的组合观察并确认了包括几种特定OTU和更高水平进化枝的独特阴道微生物组特征。总体多样性和丰富度在怀孕期间都降低了，乳酸杆菌属物种（L。iners crispatus、jensenii和johnsonii，以及乳杆菌目（和乳杆菌科）、梭菌目、拟杆菌目和放线菌目。使用严格的标准化采样方案和分析方法进行的组间比较提供了有力的初步证据，表明阴道微生物16S rRNA基因目录在妊娠中存在独特的差异，阴道亚位点和胎龄之间的分类群存在差异。
While current major national research efforts (i.e., the NIH Human Microbiome Project) will enable comprehensive metagenomic characterization of the adult human microbiota, how and when these diverse microbial communities take up residence in the host and during reproductive life are unexplored at a population level. Because microbial abundance and diversity might differ in pregnancy, we sought to generate comparative metagenomic signatures across gestational age strata. DNA was isolated from the vagina (introitus, posterior fornix, midvagina) and the V5V3 region of bacterial 16S rRNA genes were sequenced (454FLX Titanium platform). Sixty-eight samples from 24 healthy gravidae (18 to 40 confirmed weeks) were compared with 301 non-pregnant controls (60 subjects). Generated sequence data were quality filtered, taxonomically binned, normalized, and organized by phylogeny and into operational taxonomic units (OTU); principal coordinates analysis (PCoA) of the resultant beta diversity measures were used for visualization and analysis in association with sample clinical metadata. Altogether, 1.4 gigabytes of data containing >2.5 million reads (averaging 6,837 sequences/sample of 493 nt in length) were generated for computational analyses. Although gravidae were not excluded by virtue of a posterior fornix pH >4.5 at the time of screening, unique vaginal microbiome signature encompassing several specific OTUs and higher-level clades was nevertheless observed and confirmed using a combination of phylogenetic, non-phylogenetic, supervised, and unsupervised approaches. Both overall diversity and richness were reduced in pregnancy, with dominance of Lactobacillus species (L. iners crispatus, jensenii and johnsonii, and the orders Lactobacillales (and Lactobacillaceae family), Clostridiales, Bacteroidales, and Actinomycetales. This intergroup comparison using rigorous standardized sampling protocols and analytical methodologies provides robust initial evidence that the vaginal microbial 16S rRNA gene catalogue uniquely differs in pregnancy, with variance of taxa across vaginal subsite and gestational age.
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影响因子：
9.4
作者：
Kim, Tae Kyung;Thomas, Susan M.;Wilson, Brenda A.
通讯作者：
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影响因子：
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作者：
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影响因子：
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作者：
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DOI：
10.1073/pnas.1002601107
发表时间：
2010-06-29
影响因子：
11.1
作者：
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通讯作者：
Knight, Rob
DOI：
10.1073/pnas.1000162107
发表时间：
2010-04-06
影响因子：
11.1
作者：
Fierer, Noah;Lauber, Christian L.;Knight, Rob
通讯作者：
Knight, Rob