Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany.
Cell. 2021 Jun 24;184(13):3376-3393.e17. doi: 10.1016/j.cell.2021.05.002. Epub 2021 May 26.
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
我们呈现了一个全球图谱，其中包含 60 个城市的大规模交通系统中的 4728 个宏基因组样本，这代表了对城市微生物生态系统进行的首次系统的、全球性的编目。该图谱提供了微生物菌株、功能特征、抗生素耐药性（AMR）标记和遗传元件的注释地理空间分布，包括 10928 种病毒、1302 种细菌、2 种古菌和 838532 个未在参考数据库中发现的 CRISPR 数组。我们鉴定出 4246 种已知的城市微生物物种，以及在 97%的样本中发现的 31 种一致的物种，这些物种与人类共生生物不同。城市之间的 AMR 基因的类型和密度差异很大。城市表现出不同的微生物分类特征，这些特征是由气候和地理差异驱动的。这些结果构成了一个高分辨率的全球宏基因组图谱，能够发现新的生物体和基因，突出了潜在的公共卫生和法医应用，并提供了城市中 AMR 负担的无培养观点。
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