Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association
Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association
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在全球范围内注释未知的城市微生物物种揭示了新的功能多样性和当地环境关联。
DOI：
10.1016/j.envres.2021.112183
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发表时间：
2022-01-28
影响因子：
8.3
通讯作者：
Shi, Tieliu
中科院分区：
文献类型：
--
作者：
Wu, Jun;Danko, David;Shi, Tieliu
在城市生态系统中，微生物在维持直接支持人类健康和城市生活的主要生态功能方面发挥着关键作用。然而，关于城市环境中涉及的物种组成和功能的知识仍然有限，这在很大程度上是由于缺乏宏基因组研究中的参考基因组，包括超过一半的未分类读数。在这里，我们发现了732个新的细菌物种从4728个样本收集的各种常见的表面与匹配的材料在公共交通系统在60个城市的Metastasis财团。新物种数量与城市人口显著正相关，皮肤相关样本中可鉴定出更多的新物种。对新基因目录的深入分析表明，功能词具有显著的地理可译性。此外，我们发现，更多的生物合成基因簇（BGC）可以在新物种中发现。BGCs与属的共现关系以及BGCs的地理特异性也可以为天然产物的合成途径提供更多的信息。扩大了已知的城市微生物组多样性，并提出了城市微生物组分类和功能表征的额外机制。考虑到城市微生物群落对人类生活的巨大影响，我们的研究也可以促进人类与城市环境之间微生物相互作用的分析。
In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The cooccurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.