A global network of coexisting microbes from environmental and whole-genome sequence data
A global network of coexisting microbes from environmental and whole-genome sequence data
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DOI：
10.1101/gr.104521.109
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发表时间：
2010-07-01
期刊：
影响因子：
7
通讯作者：
von Mering, Christian
中科院分区：
文献类型：
--
作者：
Chaffron, Samuel;Rehrauer, Hubert;von Mering, Christian
微生物是地球上最丰富和最多样化的生物。与宏观生物相比，它们的环境偏好和生态相互依赖性仍然难以评估，需要在不同的采样地点进行艰苦的分子调查。在这里，我们提出了一个全球性的荟萃分析以前采样的微生物谱系的环境。我们将公开可用的16S核糖体RNA序列分组为不同分辨率水平的操作分类单位，并系统地搜索这些在不同环境中的共现。自然发生的微生物确实表现出许多重要的谱系间关联。这些范围从相对特定的群体，包括只有几个谱系，更大的组合与共同的栖息地偏好的微生物。许多共存的谱系在遗传学上密切相关，但也观察到大量的远亲关系。完全测序的基因组的增加使我们第一次能够寻找这种生态关联的基因组相关性。从共存的微生物的基因组往往是更相似的比预期的机会，无论是在途径内容和基因组大小，并从这些趋势的离群值进行了讨论。我们假设谱系分组通常是古老的，并且它们可能对基因组进化产生了显着影响。
Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic organisms, their environmental preferences and ecological interdependencies remain difficult to assess, requiring laborious molecular surveys at diverse sampling sites. Here, we present a global meta-analysis of previously sampled microbial lineages in the environment. We grouped publicly available 16S ribosomal RNA sequences into operational taxonomic units at various levels of resolution and systematically searched these for co-occurrence across environments. Naturally occurring microbes, indeed, exhibited numerous, significant interlineage associations. These ranged from relatively specific groupings encompassing only a few lineages, to larger assemblages of microbes with shared habitat preferences. Many of the coexisting lineages were phylogenetically closely related, but a significant number of distant associations were observed as well. The increased availability of completely sequenced genomes allowed us, for the first time, to search for genomic correlates of such ecological associations. Genomes from coexisting microbes tended to be more similar than expected by chance, both with respect to pathway content and genome size, and outliers from these trends are discussed. We hypothesize that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.