taxref and Amy Taylor (both Creative Commons)

上周纽约科学院（NYAS）主持了一个令人兴奋的研讨会城市中的微生物：映射城市基因组that was a jammed-packed day full of research science, policy discussion and glimpses into the promising future of the metagenomics field. Microbiome research aims to identify the microbial citizens of our cities, environments or any place amenable to swabbing or sampling, seemingly only limited by resources and the imagination of investigators. Microbes are everywhere; turns out, you just need to look.

Our Microbes, Ourselves

There are about ten times more bacterial cells in your body than human cells, making us more microbe than human. You have an estimated 3-5 lbs of commensal bacteria that live with you and that are essential for the proper functioning of many aspects of your biology. In that sense, you and your microbiota are a “super-organism”, with all the genes that the microbes contain and all the metabolites that they produce being part of you.

This personal microbiome has become an attractive thing to study due to recent advances in sequencing technology and data analysis, as well as the implications that the microbiome can affect things like weight gain, disease susceptibility and even mood. The mysteries of the human microbiome are being unraveled, but the high degree of complexity of these microbial communities themselves as well as their interactions with each other and their hosts remain far from being fully understood.

我们的内部和局部微生物群与我们密切相关，但显然我们在环境中也遇到了微生物。我们日常生活中会遇到什么微生物？城市环境的微生物生态如何影响我们？我们如何影响它？这些有趣的问题导致了一些非常有趣的研究，使我们深入了解了城市蓬勃发展和动态的微生物世界的杰出构成。

Urban Genomes

“Everything is everywhere, but the environment selects”. This tenet holds true for the microbes found in soil, deep sea vents or intestines, but it applies just as equally to our urban environments, whether those be high rise buildings, wastewater treatment plants or mass transit systems. Therefore, discovering what microbes are present can in fact tell us about the environment in which they are found.

Identifying those microbes is fraught with challenges, but with the advances of genomics, we can sequence complex communities and characterize the “metagenome” of a sample, cataloguing its microbial makeup. We aren’t just talking about bacteria, either; fungi, viruses, protists and unicellular organisms also encompass an urban microbiome.

宏基因组学侦探

A wealth of research is being done in the area of urban metagenomics, as was highlighted at this NYAS event. Some of the scientists in this exciting field discussed their own “Urban Genome Projects”, including the sampling of New York City sewage treatment plants (Jane Carlton, New York University), the New York City subway (Christopher Mason, Weill Cornell Medical College), the Boston subway (Curtis Hottenhower, MIT), bed bug- and cockroach-infested areas (Coby Schal, North Carolina State University), the Chicago River (Rachel Poretsky, University of Illinois at Chicago), homes and hospitals (Jack Gilbert, Argonne National Laboratory) and practically the entire city of Austin (Juan P. Maestre, University of Texas at Austin).

这些努力代表了科学家和志愿者的巨大努力，以准确地收集和分类大量样本，有时不便或荒凉的地方。需要对大量数据进行处理，分析和存储，以创建特定位置的微生物剖面，并且在共享，开放和可用的资源之后，将有助于比较微生物组合。

The fact that urban microbiomes are being described for so many areas and environments allows us to study patterns of microbial signatures and explore their relationships with one another. In this way, intriguing connections can emerge that inform on how the mutual interactions between humans, microbes and the environment affect our health and behavior. These crucial insights into the microbiology of our world can help us to understand how the design, structure and management of our cities contribute to the organization of life at every scale.

Love for microbes

尽管“细菌”和“虫子”可能会听到不良的说唱，但微生物的无处不在，是我们世界中非常正常且非常重要的特征。Urban Genomics研究向我们讲了很多关于发现哪些微生物的信息，并且可以用作信息工具，以帮助我们看到微生物的广泛存在是我们城市或其他生态系统中不可或缺的一部分。