Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.
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DOI：
10.1126/scitranslmed.aad0917
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发表时间：
2016-06-15
影响因子：
17.1
通讯作者：
Xavier RJ
中科院分区：
文献类型：
--
作者：
Yassour M;Vatanen T;Siljander H;Hämäläinen AM;Härkönen T;Ryhänen SJ;Franzosa EA;Vlamakis H;Huttenhower C;Gevers D;Lander ES;Knip M;DIABIMMUNE Study Group;Xavier RJ
肠道微生物组在人类健康中起着关键作用。这个社区在生命的前三年是动态的，然后稳定到成年状态。然而，人们对环境因素对发育中的人类肠道微生物组的影响知之甚少。在这里，我们报告了一项基于每月粪便样本的DNA序列分析和39名儿童的临床信息的肠道微生物组的纵向研究，其中大约一半的儿童在生命的前三年接受了多个疗程的抗生素。虽然大多数阴道出生的儿童的肠道微生物组以拟杆菌属物种为主，但我们发现，所有四名剖腹产出生的儿童和约20%的阴道出生的儿童在前6至18个月内缺乏拟杆菌属。我们的纵向采样，加上全基因组鸟枪测序，使我们能够检测菌株水平的变化以及抗生素耐药（AR）基因的丰度。接受驱虫治疗的儿童的微生物群在物种和菌株水平上的多样性较低，一些物种通常由单一菌株主导。此外，我们还观察了接受抗生素治疗的儿童的连续样本之间的短期成分变化。微生物染色体上携带的AR基因在抗生素治疗后出现丰度高峰，随后急剧下降，而移动的元件上的一些基因在抗生素治疗结束后持续时间更长。我们的研究结果强调了高分辨率应变曲线的密集纵向研究在研究婴儿肠道微生物组的建立和对扰动的反应中的价值。
The gut microbiome plays a key role in human health. This community is dynamic during the first three years of life, before stabilizing to an adult-like state. However, relatively little is known about the impact of environmental factors on the developing human gut microbiome. Here we report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, approximately half of whom received multiple courses of antibiotics during the first three years of life. While the gut microbiome of most vaginally born children was dominated by Bacteroides species, we found that all four children born by Cesarean section and approximately 20% of vaginally born children lacked Bacteroides in the first six to eighteen months. Our longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed us to detect strain-level variation as well as the abundance of antibiotic resistance (AR) genes. The microbiota of antibiotic-treated children was less diverse at the level of both species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. AR genes carried on microbial chromosomes showed a strong peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes on mobile elements persisted longer after the end of antibiotic therapy. Our results highlight the value of dense longitudinal studies with high-resolution strain profiles in studying the establishment and response to perturbation of the infant gut microbiome.
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影响因子：
7.3
作者：
Arrieta MC;Stiemsma LT;Amenyogbe N;Brown EM;Finlay B
通讯作者：
Finlay B
影响因子：
17.1
作者：
Arrieta, Marie-Claire;Stiemsma, Leah T.;Finlay, B. Brett
通讯作者：
Finlay, B. Brett
影响因子：
30.3
作者：
Backhed, Fredrik;Roswall, Josefine;Jun, Wang
通讯作者：
Jun, Wang
DOI：
10.1073/pnas.1002601107
发表时间：
2010-06-29
影响因子：
11.1
作者：
Dominguez-Bello, Maria G.;Costello, Elizabeth K.;Knight, Rob
通讯作者：
Knight, Rob
DOI：
10.1073/pnas.1219451110
发表时间：
2013-05-28
影响因子：
11.1
作者：
Everard, Amandine;Belzer, Clara;Cani, Patrice D.
通讯作者：
Cani, Patrice D.