Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.
Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.
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DOI：
10.1186/s40793-023-00467-z
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发表时间：
2023-03-30
影响因子：
7.9
通讯作者：
中科院分区：
文献类型：
--
作者：
根据联合国的数据，世界上超过一半的人口居住在城市地区，预计到2050年，这一比例将接近70%。我们的城市由人类建造，也为人类服务，但它们也是复杂的、具有适应性的生物系统，涉及多种其他生物物种。这些物种中的大多数是看不见的，构成了城市的微生物群落。我们对建筑环境的设计决策塑造了这些看不见的种群，而作为居民，我们经常与它们相互作用。越来越多的证据表明，人类的健康和福祉依赖于这些相互作用。事实上，多细胞生物的发育和表型的重要方面归因于它们与微生物——细菌或真菌——的相互作用，它们与这些微生物不断地交换和共生。因此，绘制我们所居住城市的微生物图谱是有意义的。虽然环境微生物群落样本的处理和测序可以是高通量的，但采集样本仍然是劳动密集型和耗时的，并且可能需要动员大量志愿者来获取一个城市微生物景观的快照。
在此我们假设蜜蜂可能是采集城市微生物群样本的有效合作者，因为它们每天在蜂巢半径2英里范围内觅食。我们描述了在纽约布鲁克林的三个屋顶蜂巢进行的一项试点研究的结果，在那里我们评估了各种蜂巢材料（蜂蜜、杂物、蜂巢拭子、蜜蜂身体）揭示周围宏基因组景观信息的潜力，并得出结论：蜜蜂杂物是最丰富的基质。基于这些结果，我们通过收集的蜂巢杂物对另外4个城市进行了分析：悉尼、墨尔本、威尼斯和东京。我们表明，从蜜蜂的视角看，每个城市都呈现出独特的宏基因组图谱。这些图谱提供了与蜂巢健康相关的信息，例如已知的蜜蜂共生体和病原体。此外，我们表明这种方法可用于人类病原体监测，我们用一个概念验证示例证明了这一点，在该示例中我们恢复了猫立克次氏体（一种已知导致“猫抓热”的病原体）的大部分毒力因子基因。
我们表明这种方法提供了与蜂巢健康和人类健康相关的信息，提供了一种在城市规模上监测环境微生物群落的策略。在此我们展示这项研究的结果，并从建筑影响以及这种方法用于疫情监测的潜力方面对其进行讨论。
网络版包含补充材料，可在10.1186/s40793 - 023 - 00467 - z获取。
Over half of the world’s population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by 2050. Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city’s microbiome. Our design decisions for the built environment shape these invisible populations, and as inhabitants we interact with them on a constant basis. A growing body of evidence shows us that human health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms—bacteria or fungi—with which they live in continual exchange and symbiosis. Therefore, it is meaningful to establish microbial maps of the cities we inhabit. While the processing and sequencing of environmental microbiome samples can be high-throughput, gathering samples is still labor and time intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city. Here we postulate that honeybees may be effective collaborators in gathering samples of urban microbiota, as they forage daily within a 2-mile radius of their hive. We describe the results of a pilot study conducted with three rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (honey, debris, hive swabs, bee bodies) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities through collected hive debris: Sydney, Melbourne, Venice and Tokyo. We show that each city displays a unique metagenomic profile as seen by honeybees. These profiles yield information relevant to hive health such as known bee symbionts and pathogens. Additionally, we show that this method can be used for human pathogen surveillance, with a proof-of-concept example in which we recover the majority of virulence factor genes for Rickettsia felis, a pathogen known to be responsible for “cat scratch fever”. We show that this method yields information relevant to hive health and human health, providing a strategy to monitor environmental microbiomes on a city scale. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance. The online version contains supplementary material available at 10.1186/s40793-023-00467-z.
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影响因子：
3.2
作者：
Eugenia Farias, Maria;Revale, Santiago;Vazquez, Martin P.
通讯作者：
Vazquez, Martin P.
影响因子：
9.8
作者：
Bordenstein SR;Theis KR
通讯作者：
Theis KR
DOI：
10.1099/ijs.0.043489-0
发表时间：
2013-04-01
影响因子：
2.8
作者：
Alvarez-Perez, Sergio;Lievens, Bart;Herrera, Carlos M.
通讯作者：
Herrera, Carlos M.
DOI：
10.1016/j.scitotenv.2021.150327
发表时间：
2022-01-20
期刊：
The Science of the total environment
影响因子：
--
作者：
Cilia G;Bortolotti L;Albertazzi S;Ghini S;Nanetti A
通讯作者：
Nanetti A
影响因子：
64.5
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
通讯作者：
International MetaSUB Consortium