Bacteria in Soil Keep Your Hamburger “Healthy”
Abstract(摘要)
“ 在1993年，大肠杆菌的大爆发导致全美国超过700人患病。一种被名为O157:H7菌株的特殊大肠杆菌，它寄生在牛的内脏中并通过粪便传播到水和堆肥里。O157:H7菌株可以在水和堆肥中存活数月，通过蔬菜或肉类抵达人体内部引起疾病。然而，因为大肠杆菌要和土壤中已经存在的多种细菌竞争，所以它们在土壤中存活的时间要比寄生在牛的内脏中要短得多。对土壤中的细菌而言，O157:H7菌株是入侵者。这些入侵者依靠本地生物体 的“残羹冷炙”生存。在越多样化的群落中，所剩余的资源越少（也就是“残羹冷炙”越少），生物体入侵的难度就会越大。这就是为什么O157:H7大肠杆菌在地球上最多样化的土壤环境中却难以生存，这就是土壤细菌对我们健康很重要的诸多因素之一。
In 1993, an outbreak of the bacteriumEscherichia colimade over 700 people ill across the United States. A special kind ofE. coli, called strain O157:H7, inhabits the guts of cattle and spreads to water and compost through cow manure. The strain O157:H7 can survive for many months in the water or compost, until it reaches humans through meat or vegetables, causing disease. However,E. colisurvives a much shorter time in the soil because it must compete with the many kinds of bacteria already present there. To soil bacteria, strain O157:H7 is an invader, and invaders depend on the “leftovers” of the native organisms to survive. In more diverse communities, fewer resources are left behind, and it is harder for organisms to invade. This is whyE. coliO157:H7 is least successful in soil, the most diverse environment on Earth, and it is one of many reasons why soil bacteria are important for our health.
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ESCHERICHIA COLI ATTACKS!
大肠杆菌的攻击
在1993年，大肠杆菌的大爆发导致全美国超过700人得重症。导致这场大爆发的罪魁祸首是那些未煮熟的牛肉馅饼。另一起大肠杆菌的爆发事件致使一大批预包装的菠菜被大规模召回，该爆发的源头是种植菠菜的农场附近的一个养牛场。自那以后，造成大肠杆菌的大爆发的原因是食用了乳酪、洋葱、大豆和生菜。这些大爆发往往是由同一种细菌引起的：大肠杆菌O157:H7菌株（菌株解释：细菌亚型的一种，其细菌与同种细菌的其他菌株略有不同）。那么这个细菌到底是什么，以及为什么它仍然可以造成疾病的大爆发？阅读下文，你将会有不一样的见解！
In 1993, an outbreak of the bacterium Escherichia coli caused over 700 people to become seriously ill across the United States. The culprit was uncooked beef patties. Thirteen years later, another E. coli outbreak caused massive recalls of prepackaged spinach across the country. This time, the source was a cattle ranch next to a spinach farm. Since then, E. coli outbreaks have started from the consumption of cheese, onions, soy, and most recently, romaine lettuce. These outbreaks were always caused by the same bacterium: E. coli strain（A subtype of a bacterial species that has slight differences in its genes from other strains in the same species.）O157:H7. Who is this bacterium and why is it still causing disease outbreaks? Keep reading to learn more!
大肠杆菌⊙∀⊙！（可不可爱～）
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THE HISTORY AND TRAITS OF E. COLI
大肠杆菌的历史和特性
我们今天所知道的大多数细菌都是在近十年时间内被发现。然而，大肠杆菌是个例外。这种细菌是1885年儿科医生Theodor Escherich 在健康人的结肠中发现的，大肠杆菌的名字就是由他的名字命名的。“Coli”指的就是这种细菌生活的地方，即结肠（colon）。因为大肠杆菌在实验室的条件中生长的很好，所以微生物学家一直在研究大肠杆菌，以了解细菌是如何生长的以及其会对周围的环境做出怎样的反应。
大肠杆菌的许多特征让它成为引人着迷的生物学研究对象，也使它（在众多研究对象中）显得尤为突出。首先，如果给大肠杆菌提供合适的食物资源，它们会生长得很好—而且有很多食物资源都适合这种细菌的生长繁殖。当它们拥有了足够充足的食物，就可以以惊人的速度增长：它们可以在仅仅的7个小时里数量上从1个增殖分裂到一百万个！其次，细菌可以改变它们的基因，大肠杆菌正是最擅长如此。基因是细胞的说明书，与其他更大的生物体（例如动物）不同的是，细菌之间可以相互交换基因，也可以接受病毒的基因，还可以在生存环境中获取基因（基因的解释：构成蛋白质的DNA片段）。当一个细菌的基因发生变化时，其品行也会随之发生变化。而这些基因的后代，也继承了同样的基因，成为特定品系的成员———这就好比你是家庭中的一员，你与你家人之间有许多共同的特征。菌株不是以家族姓氏命名，而是由字母和数字组成的代码来被我们所标识的，就如O157:H7。
Most of the bacteria we know about today were discovered in the last 10 years. However, E. coli is the exception. This bacterium was discovered in the colon of healthy humans in 1885, by pediatrician Theodor Escherich, after whom the bacterium is named. Coli refers to their habitat, the colon. Because it grows so well in the laboratory, microbiologists have continued to study E. coli to understand how bacteria grow and respond to their surroundings.
Many of the characteristics that make E. coli so attractive as a study organism also make this bacterium stand out. First, E. coli grows very well if it is given the right food sources—and there are many food sources that are “right” for this bacterium. With enough food, E. coli can grow very quickly: from a single cell to a million cells within 7 hours! Second, bacteria can change their genes（A DNA segment containing instructions for building a protein.）
, and E. coli is especially good at this (Figure 1). Genes are the cell’s instruction manual, and unlike larger organisms like animals, bacteria can trade genes with each other, receive genes from a virus, or pick up genes from the environment. When a bacterium changes its genes, its behaviors and abilities change too, and its descendants, which inherit the same new genes, become members of a specific strain—much like you are a member of your family and share many characteristics with them. Instead of family names, strains are usually identified by a code name of letters and numbers, like O157:H7.
Figure 1 - Bacteria, unlike most other organisms, can change their genes.
图1-细菌与其他大部分生物体不同的是，细菌之间可以相互交换基因
(A)Escherichia colistrain O157:H7 has genes that were left behind by a virus that infected it（A）大肠杆菌O157:H7菌株有病毒感染后留下的基因。(B) O157:H7 has also taken up genes from the environment. Bacteria can also get genes from other bacteria.（B） O157:H7也从环境中获取了基因，细菌还可以从其他细菌中获取基因。
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THE SUPER STRAIN O157:H7
超级菌株O157:H7
数以千计来自不同菌株的大肠杆菌生活在健康的人类肠道中，保护我们免受沙门氏菌等其他病原体（或称致病菌）的侵害, 但O157:H7菌株并不是这样的。大肠杆菌菌株O157:H7于1983年首次被发现，现在仅在美国每年就有约7.3万人被感染。这种菌株的独特之处在于它获得了一组基因：这组基因可以使O157:H7菌株具有产生志贺毒素（Shiga toxin）的能力，而志贺毒素是一种能使感染者生重病的有毒物质。所产生的这些毒素还并不完全足以威胁到我们的身体健康，O157:H7菌株还有一种使其成为病原体（病原体解释：一个可以导致疾病发生的生物体）的行为方式：它积极地尝试把自己传播出去。并非所有的大肠杆菌菌株都会这样做，这种传播行为也是从环境中拾取基因的结果。（图1）
自1993年以来，几乎每年都会有由O157:H7引起的疾病大爆发。为什么这种事情仍然会有所发生呢？简而言之就是大肠杆菌可以接触到食物的途径太多了。如果用来制作汉堡的牛肉是来源于一头受O157:H7感染的牛，那么你的汉堡很可能受到了O157:H7的污染，但这都不是什么问题，因为我们从来不会生吃汉堡包。当你把汉堡包烤熟后，里面的大肠杆菌会被高温杀死，所以肉是可以安全食用的。但是像生菜这些蔬菜我们经常会选择生吃它们，如此一来，在你吃的时候那些细菌可能还活着。
正常情况下，大肠杆菌会在牛的内脏中生活数周至数月，在那里它不会使牛生病。这些动物的粪便中含有许多大肠杆菌，受感染的牛的一克粪便中可能含有超过5000万个大肠杆菌细胞，这些大肠杆菌一旦随着粪便离开牛体内，就极难清除。粪便可容纳这些细菌的时间超达21个月，这使细菌将有大量的机会进入土壤。如果粪便进入水中，那么细菌可能会在那里存活8个月以上。在此期间，当这些水被用作灌溉农作物时，它们也就可能进入土壤。大肠杆菌一旦进入土壤，就可能会接触到作物植物导致水果蔬菜因此受到污染。
Thousands of E. coli cells from different strains live in the healthy human gut and protect us from other pathogenic, or disease-causing, bacteria like Salmonella. But that is not what strain O157:H7 does. First discovered in 1983, E. coli strain O157:H7 now infects ~73,000 people a year in the United States alone [1]. What makes this strain unique is the set of genes it has acquired: one set of genes gives strain O157:H7 the ability to produce Shiga toxin, which is the poisonous substance that makes infected people sick. Producing poison is not quite enough to become a threat to our health. Strain O157:H7 also behaves in a way that makes it apathogen（An organism that can cause disease）.it actively tries to spread. Not allE. colistrains do this. This spreading behavior is also a result of genes picked up from the environment (Figure 1).
Since 1993, there have been almost yearly outbreaks of disease caused by O157:H7. Why do they still happen? The simple answer is that there are too many ways that E. coli can reach your food. If the beef used to make your hamburger came from an infected cow, your burger is probably contaminated, but this is not a problem, because hamburgers are never eaten raw. When you cook your hamburger, the E. coli in it is killed by the heat, and the meat is safe to eat. But vegetables like lettuce are often eaten raw, and in that case, the bacteria may be alive when you eat them.
E. colinormally lives in the guts of cattle for weeks to months, where it does not cause disease (Figure 2). The feces of these animals contain manyE. colicells: a single gram of feces from an infected cow can contain over 50 millionE. colicells, and it is extremely difficult to get rid of them once they leave the cow as manure. Manure can host these bacteria for over 21 months, giving the bacteria plenty of opportunity to reach the soil. If the manure reaches the water, then the bacteria may survive there for more than 8 months, and during this time, they may also get into the soil, when the water is used to irrigate crops. Once in the soil,E. colimay contact crop plants, result in contaminated fruits and vegetables.
Figure 2 - Many pathways to a hamburger.图2-通往汉堡包的许多路径
Beef from infected cows ends up in in raw hamburger patties, andEscherichia coliis shed from the cow gut onto the soil as manure, where the native bacteria compete with it. IfE. colipersists and can grow in the soil, then it may contaminate crops like lettuce, spinach, and onions.
来自受感染的牛的牛肉最终会进入生的汉堡包饼中，而大肠杆菌则作为粪便从奶牛肠道排除到土壤中，在土壤中与原生细菌竞争。如果大肠杆菌持续存在并能在土壤中生长，那么它可能会污染生菜、菠菜和洋葱等农作物。
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SOIL BACTERIA, A SOLUTION
土壤细菌，解决方法
既然这些细菌能活那么久，又容易传播，那为什么大肠杆菌却比较少见呢？答案是：为了沾污我们的蔬菜，大肠杆菌必须要在土壤中生存，但是它在土壤中生存的能力是十分有限的。大肠杆菌在土壤中只能生存3个月。科学家们认为，土壤细菌的多样性（多样性解释：一个群落中不同物种的数量），或者说是自然生活在土壤里的不同种类的细菌的数量使得一切变得不同。没有任何环境比土壤更多样化。一把土壤就可以包含了1万种不同的细菌，而且很多时候，大部分是大肠杆菌的非传染性菌株。在一些实验中，科学家已证明，土壤的多样性越高，危险细菌就越难成功入侵。其原因似乎是入侵细菌生存所需资源的可用性。细菌的资源消耗与动物的食物偏好相似，不同菌种所消耗的资源也不同。当土壤中环境里的原生细菌的多样性很高时，细菌群落就会消耗各种各样的资源到最后什么都没有留下。当大肠杆菌在这种环境生活时，它无法进食，也无法生长，所以就会随之死亡。而多样性较差的细菌群落无法把土壤那里的所有资源都消耗掉，就会留下“残羹冷炙”，大肠杆菌就利用这些“残羹冷炙”进行生长繁殖和传播。
Given how long these bacteria can live and how easily they spread, why is E. coli relatively rare? The answer: soil bacteria. To contaminate our vegetables, E. coli must survive in the soil, but its ability to do so is limited. In soil, E. coli can only survive for 3 months. Scientists think that the diversity （The number of different species in a community.）of soil bacteria, or the number of different kinds of bacteria naturally living there, make all the difference . No environment is more diverse than soil. A single handful of soil can contain 10,000 different bacteria , and very often, many of them are non-infectious strains of E. coli. In several experiments, scientists have shown that the more diversity a soil has, the harder it is for dangerous bacteria to successfully invade it. The reason for this seems to be the availability of resources that the invading bacteria need to survive . Resource consumption for bacteria is similar to food preferences in animals, and different strains of bacteria consume different resources. When an environment like the soil has a high diversity of natural bacteria, the bacterial community consumes a wide range of resources, leaving nothing behind. When E. coli lands on this environment, it is not able to feed or grow, and so it dies. Less diverse groups of bacteria cannot consume all the resources, leaving “leftovers,” which E. coli can use to grow and spread.
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HOW ANTIBIOTICS HELP E. COLI
抗生素是如何帮助大肠杆菌的？
那么，现在你已经知道土壤中细菌的多样性是如此的重要，因为它能确保留给致病细菌的资源少之又少。不幸的是，土壤细菌不断地受到抗生素的威胁。人类使用抗生素来防治动物和自身的疾病，但土壤以我们最初没有想到的方式暴露于抗生素。想一想土壤是如何被致病性大肠杆菌菌株污染的：牛的粪便（就是前文说的）。为了防止疾病大爆发，奶牛通常会被注射大量的抗生素。这些抗生素并没有被它们的身体所消耗完，剩余的抗生素便可以通过牛的尿液和粪便释放到环境中。但这仅仅只是个开始。污水中含有大量的抗生素，人类和养鱼场的水也以同样的方式释放出大量的抗生素。这些水流入河流，这些水又在农业上被用来灌溉土壤。一旦抗生素接触到土壤，就会杀死大部分土壤中的有益的细菌，留下那些有助于致病菌迅速生长繁殖的资源，便有可能会传播疾病。世界上越来越多的国家已经制定了限制对牛等动物使用抗生素的相关法律，这样可以减少抗生素在环境中的传播蔓延，在改善了公民身体健康的同时也改善了野生动物们的健康。
So, now you know that the diversity of bacteria in soil is important because it ensures that there are few resources left for disease-causing bacteria to use. Unfortunately, soil bacteria are constantly threatened by antibiotics. Humans use antibiotics to combat diseases in animals and in themselves, but soils are exposed to antibiotics in ways we did not initially expect. Consider how soil can become contaminated with the pathogenic E. coli strain: cattle feces. To prevent disease outbreaks, cows often receive large amounts of antibiotics. These are not fully used up by their bodies and can be released into the environment through the cow’s urine and feces. But that is just the beginning. Sewage contains lots of antibiotics released in the same way by humans and by the water from fish farms, which is also high in antibiotics. These waters mix into rivers, which are then used to irrigate soils for agriculture. Once the antibiotics reach the soil, they kill most of the good soil bacteria, leaving behind resources that pathogenic bacteria can use to grow and multiply, potentially spreading disease. A growing group of countries around the world have created laws to limit the use of antibiotics on animals like cattle, as a way to reduce the spread of antibiotics in the environment and to improve the health of their citizens but also of wildlife
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BACTERIA: THE TINY ROAD AHEAD
细菌：狭小的前路
自19世纪以来人类就已经知道细菌可以引发疾病，但我们仍在探究细菌帮助我们预防疾病的方法。事实上，在过去的20年里，我们才开始看到细菌多样性的全部范围。我们曾经认为，干净的环境就是一个无菌的，不存在任何细菌的环境。当我们收集到越来越多关于细菌世界的信息，我们对“干净”的定义也随之发生改变。从强调没有细菌到强调要有“正确”的细菌，而这些“正确”的细菌便是可以防止致病菌成功入侵。我们现在已经知道细菌无处不在且没有细菌将无法生存。我们的研究正在从试图让这个世界维持没有细菌转向到研究如何挑选出“正确”的细菌——那些有助于改善我们环境和保持身体健康的细菌。目前仍有许多疑问还未得到解答，就比如：谁是“正确”的细菌？是什么让它们如此的特殊？
Humans have known that bacteria cause diseases since the 1800s, but we are still learning the ways in which bacteria can prevent diseases. In fact, we have only started to see the full extent of bacterial diversity over the past 20 years. We used to think that a clean environment was a sterile one, without any bacteria. As we gather more and more information about the bacterial world, our definition of what is “clean” is changing, from an emphasis on the lack of bacteria to a focus on having the “right” bacteria who can prevent the pathogenic bacteria from successfully invading. We now know that bacteria are everywhere, and it is not possible to live without them. Our research is shifting from trying to keep our world free of bacteria, to learning how to select the right ones: those that help our environments and our bodies to stay healthy. There are still many unanswered questions. For example, who are the “right” bacteria, and what makes them so special?