Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.
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DOI：
10.1101/gr.236000.118
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发表时间：
2018-10
期刊：
影响因子：
7
通讯作者：
Relman DA
中科院分区：
文献类型：
--
作者：
Goltsman DSA;Sun CL;Proctor DM;DiGiulio DB;Robaczewska A;Thomas BC;Shaw GM;Stevenson DK;Holmes SP;Banfield JF;Relman DA
最近的研究表明，微生物组对妊娠健康和结局有影响。然而，妊娠相关微生物组的表征在很大程度上依赖于基于16 S rRNA基因扩增子的调查。在这里，我们描述了一个组装驱动的，基于宏基因组学的，纵向研究的阴道，肠道和口腔微生物组在292个样本从10个受试者在整个怀孕期间每三周采样。非人类序列的量为1.53 Gb组装成支架，并预测功能基因的基因和路径为基础的分析。将阴道组装体分箱到97个草案质量基因组中。在所有三个身体部位的微生物群落组成的RDA分析（RDA）显示，胎龄是基因丰度模式变化的重要来源。此外，健康并发症与口腔和肠道中社区功能基因组成的变化有关。与大多数其他阴道群落类型不同，阴道中乳杆菌占主导地位的群落的多样性随胎龄显著增加。在来自两名受试者的样品中回收了具有预测的不同功能的共同存在的加德纳菌菌株的基因组。在七名受试者中，肠道样本含有在同一受试者阴道群落中占主导地位的相同乳杆菌属菌株，而不是其他乳杆菌属菌株;然而，这些宿主内菌株是不同的。CRISPR间隔区分析表明跨身体部位和个体共享噬菌体和质粒群体。这项工作强调了怀孕期间微生物组的动态行为，并表明了解这种行为的来源对胎儿发育和妊娠结局的潜在重要性。
Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.
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影响因子：
5.8
作者：
Gardner, Shea N.;Slezak, Tom;Hall, Barry G.
通讯作者：
Hall, Barry G.
DOI：
10.1126/science.1224203
发表时间：
2012-06-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Costello EK;Stagaman K;Dethlefsen L;Bohannan BJ;Relman DA
通讯作者：
Relman DA
影响因子：
17.1
作者：
Gajer P;Brotman RM;Bai G;Sakamoto J;Schütte UM;Zhong X;Koenig SS;Fu L;Ma ZS;Zhou X;Abdo Z;Forney LJ;Ravel J
通讯作者：
Ravel J
影响因子：
5.8
作者：
Huber, T;Faulkner, G;Hugenholtz, P
通讯作者：
Hugenholtz, P
影响因子：
11
作者：
Abeles, Shira R.;Robles-Sikisaka, Refugio;Pride, David T.
通讯作者：
Pride, David T.