Bacteria in Soil Keep Your Hamburger “Healthy”

Abstract(摘要)

“?在1993年，大腸桿菌的大爆發導致全美國超過700人患病。一種被名為O157:H7菌株的特殊大腸桿菌，它寄生在牛的內臟中并通過糞便傳播到水和堆肥里。O157:H7菌株可以在水和堆肥中存活數月，通過蔬菜或肉類抵達人體內部引起疾病。然而，因為大腸桿菌要和土壤中已經存在的多種細菌競爭，所以它們在土壤中存活的時間要比寄生在牛的內臟中要短得多。對土壤中的細菌而言，O157:H7菌株是入侵者。這些入侵者依靠本地生物體 的“殘羹冷炙”生存。在越多樣化的群落中，所剩余的資源越少（也就是“殘羹冷炙”越少），生物體入侵的難度就會越大。這就是為什么O157:H7大腸桿菌在地球上最多樣化的土壤環境中卻難以生存，這就是土壤細菌對我們健康很重要的諸多因素之一。

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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01

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ESCHERICHIA COLI?ATTACKS!

大腸桿菌的攻擊

在1993年，大腸桿菌的大爆發導致全美國超過700人得重癥。導致這場大爆發的罪魁禍首是那些未煮熟的牛肉餡餅。另一起大腸桿菌的爆發事件致使一大批預包裝的菠菜被大規模召回，該爆發的源頭是種植菠菜的農場附近的一個養牛場。自那以后，造成大腸桿菌的大爆發的原因是食用了乳酪、洋蔥、大豆和生菜。這些大爆發往往是由同一種細菌引起的：大腸桿菌O157:H7菌株（菌株解釋：細菌亞型的一種，其細菌與同種細菌的其他菌株略有不同）。那么這個細菌到底是什么，以及為什么它仍然可以造成疾病的大爆發？閱讀下文，你將會有不一樣的見解！

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!

大腸桿菌⊙?⊙！（可不可愛～）

02

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THE HISTORY AND TRAITS OF?E. COLI

大腸桿菌的歷史和特性

? ?我們今天所知道的大多數細菌都是在近十年時間內被發現。然而，大腸桿菌是個例外。這種細菌是1885年兒科醫生Theodor Escherich ?在健康人的結腸中發現的，大腸桿菌的名字就是由他的名字命名的。“Coli”指的就是這種細菌生活的地方，即結腸（colon）。因為大腸桿菌在實驗室的條件中生長的很好，所以微生物學家一直在研究大腸桿菌，以了解細菌是如何生長的以及其會對周圍的環境做出怎樣的反應。

?大腸桿菌的許多特征讓它成為引人著迷的生物學研究對象，也使它（在眾多研究對象中）顯得尤為突出。首先，如果給大腸桿菌提供合適的食物資源，它們會生長得很好—而且有很多食物資源都適合這種細菌的生長繁殖。當它們擁有了足夠充足的食物，就可以以驚人的速度增長：它們可以在僅僅的7個小時里數量上從1個增殖分裂到一百萬個！其次，細菌可以改變它們的基因，大腸桿菌正是最擅長如此。基因是細胞的說明書，與其他更大的生物體（例如動物）不同的是，細菌之間可以相互交換基因，也可以接受病毒的基因，還可以在生存環境中獲取基因（基因的解釋：構成蛋白質的DNA片段）。當一個細菌的基因發生變化時，其品行也會隨之發生變化。而這些基因的后代，也繼承了同樣的基因，成為特定品系的成員———這就好比你是家庭中的一員，你與你家人之間有許多共同的特征。菌株不是以家族姓氏命名，而是由字母和數字組成的代碼來被我們所標識的，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.

圖1-細菌與其他大部分生物體不同的是，細菌之間可以相互交換基因

(A)Escherichia colistrain O157:H7 has genes that were left behind by a virus that infected it（A）大腸桿菌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也從環境中獲取了基因，細菌還可以從其他細菌中獲取基因。

03

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THE SUPER STRAIN O157:H7

超級菌株O157:H7

??數以千計來自不同菌株的大腸桿菌生活在健康的人類腸道中，保護我們免受沙門氏菌等其他病原體（或稱致病菌）的侵害, 但O157:H7菌株并不是這樣的。大腸桿菌菌株O157:H7于1983年首次被發現，現在僅在美國每年就有約7.3萬人被感染。這種菌株的獨特之處在于它獲得了一組基因：這組基因可以使O157:H7菌株具有產生志賀毒素（Shiga toxin）的能力，而志賀毒素是一種能使感染者生重病的有毒物質。所產生的這些毒素還并不完全足以威脅到我們的身體健康，O157:H7菌株還有一種使其成為病原體（病原體解釋：一個可以導致疾病發生的生物體）的行為方式：它積極地嘗試把自己傳播出去。并非所有的大腸桿菌菌株都會這樣做，這種傳播行為也是從環境中拾取基因的結果。（圖1）

??? 自1993年以來，幾乎每年都會有由O157:H7引起的疾病大爆發。為什么這種事情仍然會有所發生呢？簡而言之就是大腸桿菌可以接觸到食物的途徑太多了。如果用來制作漢堡的牛肉是來源于一頭受O157:H7感染的牛，那么你的漢堡很可能受到了O157:H7的污染，但這都不是什么問題，因為我們從來不會生吃漢堡包。當你把漢堡包烤熟后，里面的大腸桿菌會被高溫殺死，所以肉是可以安全食用的。但是像生菜這些蔬菜我們經常會選擇生吃它們，如此一來，在你吃的時候那些細菌可能還活著。

? ? 正常情況下，大腸桿菌會在牛的內臟中生活數周至數月，在那里它不會使牛生病。這些動物的糞便中含有許多大腸桿菌，受感染的牛的一克糞便中可能含有超過5000萬個大腸桿菌細胞，這些大腸桿菌一旦隨著糞便離開牛體內，就極難清除。糞便可容納這些細菌的時間超達21個月，這使細菌將有大量的機會進入土壤。如果糞便進入水中，那么細菌可能會在那里存活8個月以上。在此期間，當這些水被用作灌溉農作物時，它們也就可能進入土壤。大腸桿菌一旦進入土壤，就可能會接觸到作物植物導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.圖2-通往漢堡包的許多路徑

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.

來自受感染的牛的牛肉最終會進入生的漢堡包餅中，而大腸桿菌則作為糞便從奶牛腸道排除到土壤中，在土壤中與原生細菌競爭。如果大腸桿菌持續存在并能在土壤中生長，那么它可能會污染生菜、菠菜和洋蔥等農作物。

04

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SOIL BACTERIA, A SOLUTION

土壤細菌，解決方法

? ? 既然這些細菌能活那么久，又容易傳播，那為什么大腸桿菌卻比較少見呢？答案是：為了沾污我們的蔬菜，大腸桿菌必須要在土壤中生存，但是它在土壤中生存的能力是十分有限的。大腸桿菌在土壤中只能生存3個月。科學家們認為，土壤細菌的多樣性（多樣性解釋：一個群落中不同物種的數量），或者說是自然生活在土壤里的不同種類的細菌的數量使得一切變得不同。沒有任何環境比土壤更多樣化。一把土壤就可以包含了1萬種不同的細菌，而且很多時候，大部分是大腸桿菌的非傳染性菌株。在一些實驗中，科學家已證明，土壤的多樣性越高，危險細菌就越難成功入侵。其原因似乎是入侵細菌生存所需資源的可用性。細菌的資源消耗與動物的食物偏好相似，不同菌種所消耗的資源也不同。當土壤中環境里的原生細菌的多樣性很高時，細菌群落就會消耗各種各樣的資源到最后什么都沒有留下。當大腸桿菌在這種環境生活時，它無法進食，也無法生長，所以就會隨之死亡。而多樣性較差的細菌群落無法把土壤那里的所有資源都消耗掉，就會留下“殘羹冷炙”，大腸桿菌就利用這些“殘羹冷炙”進行生長繁殖和傳播。

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.

05

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HOW ANTIBIOTICS HELP?E. COLI

抗生素是如何幫助大腸桿菌的？

那么，現在你已經知道土壤中細菌的多樣性是如此的重要，因為它能確保留給致病細菌的資源少之又少。不幸的是，土壤細菌不斷地受到抗生素的威脅。人類使用抗生素來防治動物和自身的疾病，但土壤以我們最初沒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腸桿菌菌株污染的：牛的糞便（就是前文說的）。為了防止疾病大爆發，奶牛通常會被注射大量的抗生素。這些抗生素并沒有被它們的身體所消耗完，剩余的抗生素便可以通過牛的尿液和糞便釋放到環境中。但這僅僅只是個開始。污水中含有大量的抗生素，人類和養魚場的水也以同樣的方式釋放出大量的抗生素。這些水流入河流，這些水又在農業上被用來灌溉土壤。一旦抗生素接觸到土壤，就會殺死大部分土壤中的有益的細菌，留下那些有助于致病菌迅速生長繁殖的資源，便有可能會傳播疾病。世界上越來越多的國家已經制定了限制對牛等動物使用抗生素的相關法律，這樣可以減少抗生素在環境中的傳播蔓延，在改善了公民身體健康的同時也改善了野生動物們的健康。

? ? 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

06

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BACTERIA: THE TINY ROAD AHEAD

細菌：狹小的前路

自19世紀以來人類就已經知道細菌可以引發疾病，但我們仍在探究細菌幫助我們預防疾病的方法。事實上，在過去的20年里，我們才開始看到細菌多樣性的全部范圍。我們曾經認為，干凈的環境就是一個無菌的，不存在任何細菌的環境。當我們收集到越來越多關于細菌世界的信息，我們對“干凈”的定義也隨之發生改變。從強調沒有細菌到強調要有“正確”的細菌，而這些“正確”的細菌便是可以防止致病菌成功入侵。我們現在已經知道細菌無處不在且沒有細菌將無法生存。我們的研究正在從試圖讓這個世界維持沒有細菌轉向到研究如何挑選出“正確”的細菌——那些有助于改善我們環境和保持身體健康的細菌。目前仍有許多疑問還未得到解答，就比如：誰是“正確”的細菌？是什么讓它們如此的特殊？

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?