An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.
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DOI：
10.1101/gr.201863.115
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发表时间：
2016-11
期刊：
影响因子：
7
通讯作者：
Pollard KS
中科院分区：
文献类型：
--
作者：
Nayfach S;Rodriguez-Mueller B;Garud N;Pollard KS
我们提出了宏基因组种内多样性分析系统（MIDAS），这是一个集成的计算管道，用于定量细菌物种丰度和菌株水平的基因组变异，包括基因含量和单核苷酸多态性（snp），来自霰弹枪宏基因组。我们的方法利用了一个超过30,000个细菌参考基因组的数据库，我们将这些基因组聚集到物种组中。这些覆盖了人类微生物组中大多数丰富的物种，但只有一小部分微生物在其他环境中，包括土壤和海水。我们将MIDAS应用于98名瑞典母亲及其婴儿一年以上的粪便宏基因组，并使用罕见的snp来追踪宿主之间的菌株。使用这种方法，我们发现尽管母亲和婴儿的物种组成随着时间的推移而趋同，但品系水平的相似性却出现了分歧。具体来说，早期的定植细菌通常是从婴儿的母亲那里传播的，而晚期的定植细菌通常是从环境中的其他来源传播的，并且富含孢子形成基因。我们还将MIDAS应用于全球分布的198个海洋宏基因组，并使用基因含量来显示许多流行细菌物种具有与地理位置相关的种群结构。在宏基因组中存在的菌株水平的遗传变异清楚地揭示了广泛的结构和动态，当数据以较粗的分类分辨率进行分析时，这些结构和动态是模糊的。
We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution.
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影响因子：
64.5
作者：
Greenblum S;Carr R;Borenstein E
通讯作者：
Borenstein E
影响因子：
46.9
作者：
Luo C;Knight R;Siljander H;Knip M;Xavier RJ;Gevers D
通讯作者：
Gevers D
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
56.9
作者：
Li, Simone S.;Zhu, Ana;Bork, Peer
通讯作者：
Bork, Peer
DOI：
10.1098/rstb.2006.1920
发表时间：
2006-11-29
影响因子：
6.3
作者：
Konstantinidis, Konstantinos T.;Ramette, Alban;Tiedje, James M.
通讯作者：
Tiedje, James M.