生物与医学2015cell.com
纽约地铁系统 DNA 的城市级分子图谱
A city-scale molecular profile of DNA collected from NYC's subway system
入门 · 约 45 分钟读完前置知识：基础生物学、宏基因组学概念
导读
这篇论文对纽约市整个地铁系统、Gowanus 运河和公园的表面 DNA 进行了城市规模的宏基因组测序。结果发现约 48% 的 DNA 无法匹配任何已知生物，已识别的物种涵盖 1,688 种细菌、病毒、古菌和真核生物，且多为皮肤相关的无害菌；人类 DNA 的祖先特征还能重现美国人口普查的人口结构，细菌特征甚至能反映车站的历史（如被飓风淹没车站中的海洋菌）。作者认为这一基线微生物图谱可用于疾病监测、生物恐怖威胁防范和城市环境健康管理。
HN 关注点：宏基因组学这一新兴技术揭示的“未知生命”，以及地铁里发现炭疽、鼠疫等病原体证据是否意味着危险。
HN 评论精选
这几条评论里：补充 4
补充解释宏基因组学技术为何能发现大量未知微生物
这是符合预期的结果。过去科学家只能对可在实验室培养的物种测序（测序需要大量 DNA），而超过 90% 的微生物无法培养，因此一直未知。近几年出现了新一代测序技术（宏基因组学和单细胞测序），消除了培养环节，能从单条 DNA 链扩增，几乎可以对一切测序，在许多领域有巨大潜力。
mlu查看英文原文
This is the result what one would expect. Scientists (until recently) have only been able to sequence species which can be cultured in the laboratory (you need massive amounts of DNA for sequencing). But in fact, more than 90 percent of all microbial species cannot be cultured in the lab and hence (until recently) could not be sequenced and stayed unknown. However, in the past few years, "Next next generation sequencing" (that's how I like to call it) techniques emerged and we are now able to sequence nearly everything. The umbrella terms "metagenomics" and "single-cell sequencing" are often used for such new methods and have huuuge potential in many, many fields. Basically, the new methods eliminate the culturing step and instead have novel techniques for amplifying DNA from only a single strand.
补充为无法打开 PDF 的读者提供论文摘要
摘要：环境中的微生物影响人类健康，尤其在城市，但从未在城市尺度上做过宏基因组分析。我们对整个纽约地铁系统、Gowanus 运河和公园的表面 DNA 进行了测序。近一半 DNA（48%）不匹配任何已知生物；已识别物种涵盖 1,688 个细菌、病毒、古菌和真核生物类群，多为与皮肤相关的无害菌属（如不动杆菌）。地铁表面人类 DNA 的祖先预测可重现美国人口普查数据，细菌特征可揭示车站历史，如被飓风淹没车站中的海洋菌。发现了一些病原体证据（炭疽杆菌），但纽约没有相关病例报告，说明这些病原体属于正常城市微生物组。这一基线图谱可用于疾病监测、生物恐怖威胁防范和城市健康管理。
comboy查看英文原文
Abstract for no-PDFers: The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g.,Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
补充指出不可培养微生物的成因可能有新解释
我听过对土壤甚至人类肠道也有类似说法。关键在于我们已能分离极微小的 DNA 片段，但周围很多生物还无法识别，因为科学家一直只能分离完整生物体并培养它们。另外不久前有文章提到，有人发现高压灭菌的标准培养基会产生微量杂质化学物质，抑制了许多被认为不可培养的细菌的生长。
acjohnson55查看英文原文
I've heard similar things said for dirt, and even the human gut. The big story is that we have this incredible ability to isolate insanely tiny fragments of DNA, but there are a lot of organisms all around us we can't yet identify, because scientists have been able to isolate the organisms themselves, intact, and grow them. Although there was an article on here not too long ago about how a guy discovered that autoclaving standard growth media was found to be producing tiny amounts of unwanted chemicals that had been inhibiting the growth of many types of bacteria thought to be unculturable.
补充引用论文讨论部分澄清：DNA 片段不等于活病原体，地铁总体安全
读第 10 页的讨论可知，这些主要是无法溯源的 DNA 片段。论文强调：这些数据并不表明这些生物是活的，检测到的细菌 DNA 片段可能来自人类以外的来源（昆虫、老鼠或其他哺乳动物）。约一半高质量序列无法匹配任何已知生物，与其他研究报道的范围相似，说明我们指尖下还有大量未知生命待发现。虽然发现了炭疽、鼠疫、MRSA 等 CDC 传染病原的证据，但结果并不表明鼠疫或炭疽流行，也不表明纽约居民面临风险——每年全美约报告 7 例人类鼠疫病例，近期纽约及周边没有。总体而言地铁表面基本是安全的。
acomjean查看英文原文
Reading the discussion (page 10 after the pretty graphs), it seems mostly fragments of DNA that they can't source "Most importantly, none of these data indicate that these organisms are alive, and the fragments of bacterial DNA detected in these data may have arisen from sources other than humans (insects, rats, mice, or other mammals)." How many creatures have we sequenced vs we know about? Not surprising a lot of unkonwns. Bateria are everywhere, including millions of them inside us. " half of our high-quality sequence reads do not match any known organism, which is similar to the range reported in other studies (Yooseph et al., 2013) and demonstrates the large, unknown catalog of life directly beneath our fingertips that remains to be discovered and characterized." Millions ride (and complain about) the NY subway daily. They found some intersting stuff (anthrax, plague?!) Although they point out we evolved with some nasty bacteria and we don't get sick from it often (thankfully). "Indeed, these data indicate that the subway, in general, is primarily a safesurface. Although evidence of B.anthracis,Y.pestis, MRSA, and other CDC infectious agents was found on the subway system in multiple stations, the results do not suggest that the plague or anthrax is prevalent, nor do they suggest that NYC residents are at risk.... Approximately seven hu- man plague cases are reported a year, and none recently in NYC or anywhere near NYC,..... This finding further supports the notion that humans have interacted (and potentially evolved) with their environment in such a way that even low levels of Yersinia pestis (plague) or Bacillus anthracis (anthrax) will not necessarily confer a risk of acquiring these pathogens.
历次讨论
- 2015Hacker News 讨论帖145 分 · 37 评
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