Temporal development of the gut microbiome in early childhood from the TEDDY study.
Temporal development of the gut microbiome in early childhood from the TEDDY study.
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DOI：
10.1038/s41586-018-0617-x
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发表时间：
2018-10
期刊：
影响因子：
64.8
通讯作者：
Petrosino JF
中科院分区：
文献类型：
--
作者：
Stewart CJ;Ajami NJ;O'Brien JL;Hutchinson DS;Smith DP;Wong MC;Ross MC;Lloyd RE;Doddapaneni H;Metcalf GA;Muzny D;Gibbs RA;Vatanen T;Huttenhower C;Xavier RJ;Rewers M;Hagopian W;Toppari J;Ziegler AG;She JX;Akolkar B;Lernmark A;Hyoty H;Vehik K;Krischer JP;Petrosino JF
微生物组从婴儿期到儿童期的发育取决于一系列因素，在这段时间内，微生物免疫串扰被认为参与了后来的疾病的病理生物学，如持续性胰岛自身免疫和1型糖尿病。然而，据我们所知，还没有研究对大型多中心人群中早期生命的微生物群进行广泛的表征。在这里，我们通过16SRRNA基因测序(n = 12,005)和元基因组测序(n = 10,867)分析了903名3至46个月大的儿童的纵向粪便样本，这是青年糖尿病的环境决定因素(Teddy)研究的一部分。我们发现，肠道微生物群的发育经历了三个不同的阶段：发育阶段(3-14个月)、过渡阶段(15-30个月)和稳定阶段(31-46个月)。接受母乳，无论是排他性的还是部分的，是与微生物组结构相关的最重要的因素。母乳喂养与双歧杆菌种类(短双歧杆菌和双歧双歧杆菌)水平较高有关，停止母乳喂养会导致肠道微生物群更快成熟，如Firmicius门所示。出生方式也与发育阶段的微生物群显著相关，这是由阴道分娩的婴儿中较高水平的类杆菌(特别是脆弱杆菌)推动的。无论出生模式如何，类杆菌也与肠道多样性增加和更快成熟有关。环境因素，包括地理位置和家庭暴露(如兄弟姐妹和毛茸茸的宠物)也是重要的协变量。一项嵌套病例对照分析揭示了微生物分类与胰岛自身免疫或1型糖尿病的发展之间的微妙联系。这些数据决定了微生物组在生命早期的结构和功能组装，并为有针对性的机制研究微生物免疫串扰对长期健康的影响提供了基础。作为Teddy研究的一部分，对903名儿童的粪便样本进行的超基因组测序分析表明，母乳喂养是与微生物群结构相关的最重要因素，停止母乳会导致肠道微生物群更快地成熟。
The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial–immune crosstalk during this time thought to be involved in the pathobiology of later life diseases such as persistent islet autoimmunity and type 1 diabetes. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3–14), a transitional phase (months 15–30), and a stable phase (months 31–46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case–control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial–immune crosstalk for long-term health. Metagenomic sequencing analysis of stool samples from 903 children as part of the TEDDY study shows that breastfeeding was the most important factor associated with microbiome structure, and the cessation of breast milk resulted in faster maturation of the gut microbiome.
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影响因子：
3.7
作者：
Hu J;Nomura Y;Bashir A;Fernandez-Hernandez H;Itzkowitz S;Pei Z;Stone J;Loudon H;Peter I
通讯作者：
Peter I
DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
影响因子：
3.7
作者：
Holodniy, Mark;Brown, Sheldon T.;Darbyshire, Janet
通讯作者：
Darbyshire, Janet
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
DIRICHLET多项式混合物：微生物宏基因组学的生成模型。
影响因子：
3.7
作者：
Holmes I;Harris K;Quince C
通讯作者：
Quince C