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Bacteria in Soil - A Source of New Antibiotics

Updated on January 25, 2015
AliciaC profile image

Linda Crampton has an honors degree in biology. She finds the study of microorganisms and viruses fascinating.

Soil may be a wonderful source of bacteria that can make new antibiotics.
Soil may be a wonderful source of bacteria that can make new antibiotics. | Source

Bacteria are fascinating and abundant creatures that live in almost every habitat on Earth, including our bodies. Although some are harmful and others seem to have no influence on our lives, many bacteria are very useful. Researchers have recently discovered a new bacterium in soil and have also found that it makes an antibiotic that destroys other bacteria. This could be a very significant discovery. We desperately need new antibiotics to fight bacterial infections in humans, since the ones that we have are losing their effectiveness.

Healthy soil is a rich source of bacteria. Research suggests that there may be many soil bacteria which make chemicals that could be used as human medicines. Scientists are eagerly investigating this largely untapped resource. In the United States, they have even enlisted the public's help in finding soil samples to analyze.

Cultures of soil bacteria growing in Petri dishes in a laboratory
Cultures of soil bacteria growing in Petri dishes in a laboratory | Source

How do Antibiotics Work?

Bacteria are microscopic organisms. They are also unicellular, although they sometimes join together to form chains or clusters. Scientists are discovering that despite their apparent simplicity, bacteria are more complex than we realized.

One of the most useful abilities of bacteria as far as humans are concerned is to make antibiotics. An antibiotic is a chemical made by certain bacteria or fungi that either kills other bacteria or inhibits their growth or reproduction. Doctors prescribe antibiotics to destroy harmful bacteria that are causing disease.

The current antibiotics work by interfering with an aspect of bacterial biology that isn't part of human biology. This means that they hurt harmful bacteria but don't damage our cells. Some antibiotics block the production of the cell wall in bacteria. Human cells don't have a cell wall, so they are unharmed. Other antibiotics stop structures called ribosomes from making proteins inside the bacterial cell. Our cells have ribosomes, too. There are important differences between bacterial and human ribosomes, however, so our ribosomes aren't injured by the antibiotics. Still other antibiotics work by breaking up bacterial DNA (but not our DNA) as the DNA is being copied. DNA is the genetic material in cells. It replicates before cell division so that each daughter cell can get a copy of the DNA.

The Wonder of Antibiotics and the Dangers of Resistance

How Do Bacteria Become Resistant to Antibiotics?

We need to repeatedly find new antibiotics because of a phenomenon known as antibiotic resistance. In this situation, an antibiotic that once killed a harmful bacterium no longer works. The bacterium is said to have become resistant to the antibiotic.

Antibiotic resistance develops due to genetic changes in bacteria. These changes are a natural part of a bacterium's life. Exchange of genes between bacteria and mutations (alterations in genes) give bacteria new characteristics. It also means that the bacteria in a species are not completely identical genetically.

When a bacterial species is attacked by an antibiotic, some of the bacteria may survive. A few of the bacterial cells may have a gene (or genes) that enables them to resist the chemical attack. When they reproduce, the resistant bacteria will produce offspring that also have the helpful gene. Over time, the entire population of the bacterium will become resistant to the antibiotic.

Antibiotic resistance is very worrying. If we can't find new antibiotics or new ways to kill bacteria, some infections may become untreatable, as they were before the discovery of antibiotics. Some serious diseases have already become much harder to treat. The search for new antibiotics made by soil bacteria is therefore very important.

What Causes Antibiotic Resistance?

Finding New Antibiotics in Soil

Most of our present antibiotics originated from bacteria that live in the soil, which in most places is teeming with microscopic life. One teaspoon of healthy soil contains millions or even billions of bacteria. It's extremely difficult to grow these bacteria in laboratory equipment, however, causing antibiotic discovery to be a slow process.

Researchers at the Northeastern University in Boston, Massachusetts, have recently created a new method for growing captive bacteria in soil. The bacteria are housed in specially designed containers that are placed in the soil instead of in a laboratory. The containers allow nutrients and other chemicals in the soil to reach the bacteria.

As a result of their technique, the researchers have discovered twenty-five new antibiotics made by soil bacteria. It's unlikely that all of these antibiotics will be suitable medicines, however. An antibiotic needs to kill or inhibit specific bacteria. It also needs to be potent instead of only weakly antibacterial in order to be medically useful. The latest antibiotic discovered by the research team seems to fit these requirements, however, and looks very promising.

Soil and its Importance

Teixobactin - A New Antibiotic?

The newest antibiotic discovered in soil has been named teixobactin. It seems to be quite different from other antibiotics. In lab tests, it has been found to destroy a dangerous dose of the MRSA bacterium in mice without harming the animals. It has also been found to kill Mycobacterium tuberculosis, which causes TB or tuberculosis. Teixobactin needs to be tested in humans to see if it has the same effects in us as it does in mice.

MRSA stands for methicillin-resistant Staphylococcus aureus. It produces a very problematic infection because it's resistant to many common antibiotics. The infection can still be treated, but the treatment is often difficult because the number of antibiotics that affects the bacterium is decreasing. The discovery of teixobactin and the hints that soil bacteria produce other antibiotics has excited scientists. Some scientists have even called the discovery a "game changer". I very much hope that this is true.

A colourized photo taken with a scanning microscope showing neutrophils (a type of white blood cell) engulfing MRSA bacteria
A colourized photo taken with a scanning microscope showing neutrophils (a type of white blood cell) engulfing MRSA bacteria | Source

Drugs From Dirt and Citizen Science

Finding new antibiotics is an urgent problem. The discovery of new bacteria in soil may help us solve this problem. It would be very time consuming and expensive for researchers to travel around the world to collect soil samples in the hope of finding useful bacterial chemicals, however.

Sean Brady, a professor at Rockefeller University, has created a potential solution for this problem. His solution also offers people the wonderful opportunity to contribute to an important scientific endeavour, even if they're not scientists themselves.

Brady has created the Drugs From Dirt website to help him with his quest for new bacteria. He's asking people to send him soil samples from every state in the United States. Eventually he will extend his campaign to other countries. Individuals and groups can sign up for the process on the website. If they are chosen to collect soil, they will be emailed instructions regarding the collection and shipping of the soil sample. They will also be sent a report describing what was found in the soil.

Brady and his team are particularly interested in getting soil samples from unusual places, such as in caves and near hot springs. They are also hoping to work with science classes from schools as well as with individuals.

A section of a DNA molecule; each nucleotide is composed of a phosphate, a sugar called deoxyribose and a nitrogenous base (adenine, thymine, cytosine or guanine)
A section of a DNA molecule; each nucleotide is composed of a phosphate, a sugar called deoxyribose and a nitrogenous base (adenine, thymine, cytosine or guanine) | Source

What is DNA?

The scientists behind Drugs From Dirt won't be extracting novel chemicals from the soil and then testing them to see if they are antibiotics, as might be expected. Instead, they will extract pieces of DNA from the soil and analyze them

Deoxyribonucleic acid, or DNA, is the chemical that makes up the genes of living things. It consists of a long, double stranded molecule that is colied to make a helix. The strands of a DNA molecule are made of "building blocks" known as nucleotides. Each nucleotide contains a phosphate group, a sugar known as deoxyribose and a nitrogenous base.

Four different bases are present in DNA - adenine, thymine, cytosine and guanine. The order of the bases on one strand of the DNA molecule forms the genetic code, somewhat like the order of letters in a written language forms meaningful words and sentences. The DNA code controls the characteristics of an organism by directing the production of proteins. A gene is a segment of DNA that codes for one specific protein.

Only the coding strand of the DNA molecule is "read" during protein synthesis. The other strand is known as the template strand. This strand is required during DNA replication, which takes place before a cell divides.

The Structure of DNA and Nucleotides

Source

Analyzing the DNA in Soil Bacteria

Sequencing DNA

The DNA of soil bacteria is present in their cells while they are alive and released into the soil when they die. The Drugs from Dirt scientists will extract this DNA from the soil that they receive, replicate it and then sequence it with the aid of a specialized lab instrument called a DNA sequencer. "Sequencing" DNA means determining the order of bases in a piece of DNA.

The researchers will look for interesting and possibly significant base (or nucleotide) sequences in the DNA from soil. What often happens next in experiments like this is that the DNA is transplanted into lab bacteria. These bacteria often incorporate the transplanted DNA into their own DNA and carry out its instructions, sometimes making new and useful chemicals as a result.

A Sequence Database

The Drugs From Dirt project won't involve DNA transplants into bacteria. Instead, the researchers will create a digital database of the base sequences that they discover. Other scientists will be able to access this database and use the information in their own research.

Fertile soil is likely to contain many bacteria.
Fertile soil is likely to contain many bacteria. | Source

The International Year of Soils

The 68th United Nations General Assembly has declared 2015 to be the International Year of Soils.

Hope for the Future - New Medicines from Soil Bacteria

The analysis of soil and its bacteria is proving to be exciting. The two techniques dscribed in this article - creating captive bacterial cultures in soil and sequencing the DNA of soil bacteria - may become very important.

We need to learn as much as we can about soil bacteria. We also need to understand the development of antibiotic resistance in bacteria in more detail. It would be a great shame if bacteria become resistant to any new antibiotics that we discover.

Time will tell whether the bacteria in soil live up to our expectations. The situation is certainly hopeful. Soil bacteria may play an important and even essential role in our future.

© 2015 Linda Crampton

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    • tobusiness profile image

      Jo Alexis-Hagues 2 years ago from Bedfordshire, U.K

      Great hub, interesting and well presented with lots of important information. Well done.

    • DDE profile image

      Devika Primić 2 years ago from Dubrovnik, Croatia

      This is very interesting information. I did not give much thought to soil bacteria. You presented this hub to perfection. Voted up!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much for the comment, Jo. I appreciate your visit.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thanks for the comment and the vote, Devika. I suspect that many people don't give much thought to soil bacteria!

    • Lee Hansen profile image

      Lee Hansen 2 years ago from Vermont

      It really adds a new perspective to ."ashes to ashes, dust to dust" - healthy soil is the foundation of sustainable agriculture so it makes sense to learn that antibiotics develop in healthy soil. Thanks for this great article.

    • billybuc profile image

      Bill Holland 2 years ago from Olympia, WA

      Well, it's not a new cake recipe, but it was still interesting. LOL I'm joking of course. Fascinating information, my friend, and so interesting. Thank you for writing a quality article.

    • AliciaC profile image
      Author

      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Lee. Yes, healthy soil plays a very important role in our lives. We need to think more about the way we treat it! Thank you very much for the comment.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Bill. I doubt that I'll be writing many cake recipes! Thank you very much for the comment. I appreciate it, as always.

    • MartieCoetser profile image

      Martie Coetser 2 years ago from South Africa

      Very interesting hub about bacteria in soil and the development of new antibiotics. I am in awe of the mikro universe! Thank you, Alicia, we always learn from you :)

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much, Martie. I always appreciate your visits!

    • FlourishAnyway profile image

      FlourishAnyway 2 years ago from USA

      Fascinating. The need for new antibiotics affects us all. I have a cat who struggled for well over a year with a MSRA-related infection that nearly killed him. I took him to vet specialists and spent a small fortune on him and he was just declared MSRA-free a few weeks ago. (Yay!) The need for new antibiotics is urgent, and wherever they can find them, I'm in support. Great hub, and I find it interesting that the scientist is asking for soil samples.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      I'm so glad that your cat has beaten the infection, Flourish. It's horrible when a pet that we love is so ill. The fact that he was fighting the infection for over a year is scary! Thank you very much for the comment.

    • Faith Reaper profile image

      Faith Reaper 2 years ago from southern USA

      This is exciting news here! We certainly do need new antibiotics no doubt about it and now there is hope through soil; how fascinating.

      You are always educating us with such interesting topics.

      Up +++ tweeting, pinning, G+ and sharing

      Blessings always

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      I agree, Faith - it is exciting news! Thank you so much for the comment, the votes and the shares. Blessings and best wishes to you, too.

    • Don Bobbitt profile image

      Don Bobbitt 2 years ago from Ruskin Florida

      I'm a retired EE and I appreciated reading your article. Very interesting. Let me tell you a little story.

      When I was a child, my brother and I crawled under my grandmothers house. It was just another adventure for a couple of boys, but by the time we had crawled back out, we were filthy; even our faces were black with the dirt we had crawled around in.

      Well.my Mom began chewing us out, but our grandmother came to our rescue with an old Southern adage.

      She told my Mom; "Leave the boys alone. They have to eat a Peck of dirt before they die."

      t didn't make a lot of sense to me but it saved us from whipping.

      Now, as I see more and more families isolating themselves and their children from the outside world, I wonder if this lack of contact with the variety of bacteria in nature might not be the cause of there being so many children with allergies and even other diseases?

      Just a thought,

      DON

    • AudreyHowitt profile image

      Audrey Howitt 2 years ago from California

      This is fascinating and very exciting !

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Don. Thank you for sharing your story. I've heard of the interesting theory that you describe before. I think there might be something to it!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Audrey. Thanks for commenting. I agree - the news is very exciting!

    • Mark Johann profile image

      Mark Johann 2 years ago from Italy

      I understand a lot of things on your hub. Thanks. Bacteria is sometimes helpful. I remember the good bacteria called lacto bacillus that is present in our stomach.

      So, I guess, there is a big part in all of these soil bacteria.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Mark. Thank you very much for the comment. Bacteria can definitely be helpful for us. Many of the ones in our small intestine, like the Lactobacillus that you mention, are especially beneficial. I hope lots of bacteria in the soil prove useful as well!

    • Hendrika profile image

      Hendrika 2 years ago from Pretoria, South Africa

      Very interesting. I think we have to try to make sure that once these antibiotics are available not to over use them again and cause the same to happen again. These super bugs are really becoming a big problem. On of my friends were prescribed and antibiotic for an infects last week and it had no effect at all and the infection is still there!

    • ChitrangadaSharan profile image

      Chitrangada Sharan 2 years ago from New Delhi, India

      Excellent hub with lots of information!

      I am glad you wrote about antibiotic resistance. This is something, I have been hearing a lot. Many patients are getting affected by this issue and months and months have passed and their infection etc. could not be cured by a particular antibiotic or several others.

      There is a need to discover new antibiotics and the soil bacteria is a very appropriate source to this.

      Thanks for sharing the information, voted up, shared on HP and pinned!

    • Rota profile image

      Rota 2 years ago

      Interesting well researched hub!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Hendrika. Overuse of antibiotics has become a serious problem. It's scary to hear that an antibiotic had no effect on your friend's infection. I hope that he or she is prescribed a new medicine that works!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much for the comment, the vote and the shares, ChitrangadaSharan. It's definitely scary that some infections are taking so long to cure. We are heading towards a very serious situation with respect to curing disease unless we can find new treatments.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much, Rota!

    • vespawoolf profile image

      vespawoolf 2 years ago from Peru, South America

      I also have great hope for this research. I found this article very interesting. I didn´t realize scientists were studying the bacterial and antibiotics found in soil. I know there are probiotics made from soil, too, which can be very beneficial when taken for the digestive tract. Thank you for sharing!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, vespawoolf. Thanks for commenting. I hope the research pays off. We need to solve the antibiotic problem somehow!

    • Karine Gordineer profile image

      Karine Gordineer 2 years ago from Upstate New York

      Very well researched hub and interesting information! Promising research for sure.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much, Karine! The research is definitely promising. I hope it leads to some useful discoveries.

    • Mel Carriere profile image

      Mel Carriere 2 years ago from San Diego California

      As always, a fantastically researched and informative hub. This offers great hope for medicine at a time when many diseases are on the rebound due to vaccine dissenters and antibiotic resistance. Great job!

    • heidithorne profile image

      Heidi Thorne 2 years ago from Chicago Area

      Super interesting! So glad to hear about these new advances that are, surprisingly, all around us. Voted up, useful and interesting!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you so much, Mel. I appreciate your comment a great deal!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thanks for the comment and the votes, Heidi! I'm happy that new discoveries are being made, too.

    • RoadMonkey profile image

      RoadMonkey 2 years ago

      Good place to look for more help on novel antibiotics. We definitely need them!

    • AliciaC profile image
      Author

      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, RoadMonkey. I agree! We badly need new antibiotics, and the bacteria in soil could provide them. Thanks for the visit.

    • aviannovice profile image

      Deb Hirt 2 years ago from Stillwater, OK

      As kids, we played in the soil, as well as the mud. This was beneficial and healthy, as most of us we very healthy as a result of getting this natural bacteria in and on our skin.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Deb. Thanks for the interesting comment. The idea that children need to be exposed to bacteria in the natural environment in order to be healthy is certainly thought provoking! There's some research that supports the idea, too.

    • susi10 profile image

      Susan W 2 years ago from The British Isles, Europe

      Wow, I never really knew that the bacteria in soil could be a new source of antibiotics. That truly is amazing.

      I think there is definitely a sense of urgency in the world to find a completely new strain of bacteria that could potentially become an antibiotic. Because if they don't, the international community will definitely have a serious issue at hand. But through soil, this could lead to the next antibiotic, which is very inspiring for the future.

      Thanks for writing this hub. It's so well written. Shared. :-)

    • AliciaC profile image
      Author

      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much for the comment and the share, susie10. I agree with you - the search for new antibiotics is definitely urgent!

    • Sam Montana profile image

      Sam Montana 2 years ago

      Great article. There has always been a lot of truth when our parents told us getting a little dirty won't hurt. There is a theory that people that played in the dirt as kids have a stronger immune system than those that never did.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Hi, Sam. Thank you for the comment. That's an interesting theory!

    • Minnetonka Twin profile image

      Linda Rogers 2 years ago from Minnesota

      Thank you Alicia for the hard work on this interesting and fact filled hub. I think nature is so fascinating. Glad you shared the information on bacteria in soil and new antibiotics with us.

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much, Linda. I think nature is fascinating, too!

    • AVailuu profile image

      A. Cristen Vailuu 2 years ago from Augusta, Ga

      Awesome hub! I just published one that is very similar to yours, but yours is so well written and easy to understand. You did a great job of breaking down the information and making it more digestible to the general population. Voted up for excellence!

    • AliciaC profile image
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      Linda Crampton 2 years ago from British Columbia, Canada

      Thank you very much, AVailuu. I appreciate your comment. It's nice to meet you!

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