A global metagenomic map of urban microbiomes and antimicrobial resistance.
A global metagenomic map of urban microbiomes and antimicrobial resistance.
复制标题
城市微生物组和抗菌素耐药性的全球宏基因组图谱。
DOI：
10.1016/j.cell.2021.05.002
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发表时间：
2021-06-24
期刊：
影响因子：
64.5
通讯作者：
International MetaSUB Consortium
中科院分区：
文献类型：
--
作者：
Danko D;Bezdan D;Afshin EE;Ahsanuddin S;Bhattacharya C;Butler DJ;Chng KR;Donnellan D;Hecht J;Jackson K;Kuchin K;Karasikov M;Lyons A;Mak L;Meleshko D;Mustafa H;Mutai B;Neches RY;Ng A;Nikolayeva O;Nikolayeva T;Png E;Ryon KA;Sanchez JL;Shaaban H;Sierra MA;Thomas D;Young B;Abudayyeh OO;Alicea J;Bhattacharyya M;Blekhman R;Castro-Nallar E;Cañas AM;Chatziefthimiou AD;Crawford RW;De Filippis F;Deng Y;Desnues C;Dias-Neto E;Dybwad M;Elhaik E;Ercolini D;Frolova A;Gankin D;Gootenberg JS;Graf AB;Green DC;Hajirasouliha I;Hastings JJA;Hernandez M;Iraola G;Jang S;Kahles A;Kelly FJ;Knights K;Kyrpides NC;Łabaj PP;Lee PKH;Leung MHY;Ljungdahl PO;Mason-Buck G;McGrath K;Meydan C;Mongodin EF;Moraes MO;Nagarajan N;Nieto-Caballero M;Noushmehr H;Oliveira M;Ossowski S;Osuolale OO;Özcan O;Paez-Espino D;Rascovan N;Richard H;Rätsch G;Schriml LM;Semmler T;Sezerman OU;Shi L;Shi T;Siam R;Song LH;Suzuki H;Court DS;Tighe SW;Tong X;Udekwu KI;Ugalde JA;Valentine B;Vassilev DI;Vayndorf EM;Velavan TP;Wu J;Zambrano MM;Zhu J;Zhu S;Mason CE;International MetaSUB Consortium
我们提供了一个全球地图集，其中包含来自60个城市3年多的公共交通系统的4，728个宏基因组样本，代表了第一个系统的全球城市微生物生态系统目录。该图集提供了微生物菌株、功能特征、抗菌素耐药性（AMR）标记和遗传元件的注释地理空间概况，包括10，928种病毒、1，302种细菌、2种古细菌和838，532种参考数据库中未发现的CRISPR阵列。我们确定了4，246种已知的城市微生物，并在97%的样本中发现了31种与人类微生物不同的物种。AMR基因的分布在不同城市的类型和密度上差异很大。城市显示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，可以发现生物体和基因，突出潜在的公共卫生和法医应用，并提供了城市AMR负担的文化独立视图。城市拥有一套一致的“核心”非人类微生物城市微生物组反映了城市和城市生活的重要特征抗菌素耐药性基因在城市中广泛存在城市包含许多新的细菌和病毒物种这一系统的全球城市微生物组目录代表了一个宏基因组图谱，对于理解城市特定微生物群落的生态学，毒性和抗生素耐药性非常重要。
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. Cities possess a consistent “core” set of non-human microbes Urban microbiomes echo important features of cities and city-life Antimicrobial resistance genes are widespread in cities Cities contain many novel bacterial and viral species This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.
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DOI：
10.1016/s2666-5247(21)00039-2
发表时间：
2021-04
期刊：
The Lancet. Microbe
影响因子：
--
作者：
Afshinnekoo E;Bhattacharya C;Burguete-García A;Castro-Nallar E;Deng Y;Desnues C;Dias-Neto E;Elhaik E;Iraola G;Jang S;Łabaj PP;Mason CE;Nagarajan N;Poulsen M;Prithiviraj B;Siam R;Shi T;Suzuki H;Werner J;Zambrano MM;Bhattacharyya M;MetaSUB Consortium
通讯作者：
MetaSUB Consortium
DOI：
10.1038/nrg.2017.88
发表时间：
2018-01
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Gardy JL;Loman NJ
通讯作者：
Loman NJ
影响因子：
3
作者：
Hoch, Jessica M. K.;Rhodes, Matthew E.;McGuire, Krista L.
通讯作者：
McGuire, Krista L.
影响因子：
12.3
作者：
Breitwieser FP;Baker DN;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
14.9
作者：
Couvin D;Bernheim A;Toffano-Nioche C;Touchon M;Michalik J;Néron B;Rocha EPC;Vergnaud G;Gautheret D;Pourcel C
通讯作者：
Pourcel C