Bacteria in Soil - A Source of New Antibiotics
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.
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.
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.
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
Analyzing the DNA in Soil Bacteria
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.
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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