Application of a neutral community model to assess structuring of the human lung microbiome.
Application of a neutral community model to assess structuring of the human lung microbiome.
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DOI：
10.1128/mbio.02284-14
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发表时间：
2015-01-20
期刊：
影响因子：
6.4
通讯作者：
Schmidt TM
中科院分区：
文献类型：
--
作者：
Venkataraman A;Bassis CM;Beck JM;Young VB;Curtis JL;Huffnagle GB;Schmidt TM
从系统发育多样的微生物中提取的DNA通常从健康人的肺部提取，并用于确定肺部微生物组。这种DNA来自适应肺部的微生物的比例，与从身体其他部位和大气中分散到肺部的微生物的比例相反，尚不清楚。我们使用群落生态学的中性模型来区分肺部微生物组的成员，这些成员的存在与来自其他身体部位的分散一致，而那些偏离模型的成员，表明这些微生物在肺部具有竞争优势。我们发现健康肺部微生物组的组成与中性模型的预测一致，反映了口腔微生物分散在塑造健康肺部微生物群落中的重要作用。相比之下，患病肺部的微生物组很容易被区分为处于主动选择状态。我们还通过各种培养基和孵育条件的培养评估了肺样品中微生物的生存能力。从健康肺部培养中恢复的细菌代表了包含61%来自支气管肺泡灌洗液样本的16S rrna编码基因序列的物种。微生物的中性分布是健康肺部微生物组的一个显著特征，其中来自口腔的细菌的不断扩散压倒了细菌的差异生长。在健康的肺中，没有细菌种类总是偏离模型预测，尽管许多分散物种的代表很容易培养。相比之下，患病肺部的细菌种群被确定为处于主动选择之下。量化选择和中性过程（如扩散）在塑造健康肺部微生物组中的相对重要性是了解其对宿主健康影响的第一步。微生物的中性分布是健康肺部微生物组的一个显著特征，其中来自口腔的细菌不断扩散覆盖了细菌的差异生长。在健康的肺中，没有细菌种类总是偏离模型预测，尽管许多分散物种的代表很容易培养。相比之下，患病肺部的细菌种群被确定为处于主动选择之下。量化选择和中性过程（如扩散）在塑造健康肺部微生物组中的相对重要性是了解其对宿主健康影响的第一步。
DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. Importance Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health. Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health.