First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.
First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.
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DOI：
10.1128/mbio.00824-17
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发表时间：
2017-11-14
期刊：
影响因子：
6.4
通讯作者：
Moissl-Eichinger C
中科院分区：
文献类型：
--
作者：
Koskinen K;Pausan MR;Perras AK;Beck M;Bang C;Mora M;Schilhabel A;Schmitz R;Moissl-Eichinger C
人类相关的古细菌在微生物组研究领域仍未得到充分研究，尽管特别是产甲烷的古细菌被发现是人类肠道的常规共生体，它们是代谢过程中的关键物种。关于与人类相关的古菌的丰富度和多样性的知识极其有限，对它们的功能、它们在人类健康中的总体作用，或它们与胃肠道和口腔以外的人体部分的关系知之甚少。目前，方法学问题阻碍了对人类古菌群的全面评估，因为细菌靶向方案不适合表征古菌的全谱。本研究的目的是建立基于特异性古菌靶向的保守方案，基于pcr的方法来检索人类胃肠道，肺，鼻子和皮肤的古菌群。古细菌的检测高度依赖于引物的选择和序列处理管道的使用。我们的研究结果使我们能够检索到人类古菌组的新图像，因为我们首次发现甲烷杆菌和Woesearchaeota （DPANN超门）分别与人类胃肠道和人类肺部有关。与细菌相似，人类相关的古细菌群落在生物地理上分组，形成(i)古细菌皮肤景观，（ii）（甲烷）euryarchaeal胃肠道，（iii）鼻子的混合皮肤-胃肠道景观，以及（iv）研究肺部景观。在我们使用的协议的基础上，我们能够检测到与不同身体部位相关的古细菌的出乎意料的高多样性。综上所述，我们的研究突出了引物和NGS数据处理管道用于研究人类古组的重要性。我们能够建立方案，揭示了以前未被检测到的古菌存在于所有被调查的组织样本中，并在胃肠道、皮肤和呼吸道（即鼻子和肺部）中首次检测到人类古菌群的生物地理模式。我们的结果为进一步研究人类古菌群，并从长远来看，发现古菌在人类健康和疾病中的潜在作用奠定了坚实的基础。
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts. In summary, our study highlights the importance of the primers and NGS data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract, on the skin, and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.