Bacteriophages: Viruses in Bacteria and the Gut Microbiome - Owlcation - Education
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Bacteriophages: Viruses in Bacteria and the Gut Microbiome

Linda Crampton is a writer and teacher with a first-class honors degree in biology. She often writes about the scientific basis of disease.

An internal and external depiction of a T-even phage (T2, T4, and T6)

An internal and external depiction of a T-even phage (T2, T4, and T6)

Bacteriophages and the Gut Microbiome

Bacteriophages (or phages) are viruses that infect bacteria, including the ones that live in our gut. Phages don't infect our cells, but by affecting our gut bacteria they may indirectly affect our lives. They may also affect us while they are in our gut but outside cells. Influencing the types and behaviour of phages in our body might be beneficial.

Bacteria are widely studied, especially the species that directly affect our lives. The viruses that infect our cells or those of animals are also widely studied since they can make us and the animals that we care for ill. The viruses that infect bacteria haven't been given as much attention until relatively recently. Scientists are now discovering the fascinating features and variety in the bacteriophage group.

In this article, I provide an overview of phages and their activity. I also describe some of their known effects and some of their possible effects in our gut microbiome. The gut or intestinal microbiome is the community of microorganisms that lives in our digestive tract. This community influences our lives in multiple ways. Many of the effects are beneficial, but not all of them are.

T4 phage structure and summary of action

T4 phage structure and summary of action

The Structure of Viruses

Viruses consists of a coat of protein known as a capsid that encloses the genetic material, or nucleic acid. The genetic material is either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). Some viruses have a lipid coat outside the capsid.

Bacteriophages have three basic shapes, which in simple terms can be described as a head with a tail (as in the T phages), a head on its own, and a filament. Based on our current knowledge, the vast majority of phages lack a lipid coat. Their nucleic acid is double-stranded or single-stranded DNA or RNA.

The nucleic acid of phages contains genes, as it does in other organisms. A gene is a section of nucleic acid that codes for a protein. This coding ability is why genes are able to control an organism's body. A huge variety of proteins exist in living things. They contribute to both the structure and the function of the body.

In most organisms, including humans, the genes are stored in DNA and the RNA is a helper chemical in the process of protein synthesis. In some viruses, RNA stores the genes, however.

T Phages: An Interesting and Common Type

T phages were the first bacteriophages to be discovered and are very often shown as the model type. They are numbered from T1 to T7. They are sometimes said to resemble a lunar lander in appearance. The virus has a polyhedral "head" region that is attached to an elongated "tail". The tail has spikes at the bottom that resemble the legs of a lunar lander.

The virus attaches to a bacterium with its tail spikes. It then contracts the core part of its tail as it injects its nucleic acid into the bacterium. At some point in the bacterium's life cycle, the viral nucleic acid forces the cell to make new virus particles.

Though T phages receive most of the publicity with respect to bacteriophages, researchers have discovered other types. Multiple families of phages exist. A casual reader may not realize this since a T4 phage illustration is often used to represent the entire bacteriophage group. T4 is found in our gut, however. In addition, the tailed phage group seems to be the most common type living in the gut, so the viruses are relevant with respect to our lives.

The Lytic Cycle of Viruses

Bacterial cells (and the cells of other organisms) contain genes as well as the chemicals and structures needed to carry out the instructions in the genes. Viruses also contain genes encoding instructions, but they don't have the chemicals or the equipment needed to act on the instructions. A virus must have the help of a cell in order to reproduce.

In the lytic cycle, the viral DNA that has been injected into a bacterial cell triggers the bacterium to make new viral nucleic acid and protein and then assemble the chemicals to make new virions (individual viruses). The virions break out of the bacterial cell, destroying it in the process. The destruction of the cell is known as lysis. The process is summarized in the video above.

A representation of the capsid  of an MS2 phage (which has no tail); the different colours represent different protein chains

A representation of the capsid of an MS2 phage (which has no tail); the different colours represent different protein chains

The Lysogenic Cycle

In some phages or in some viral infections, a lysogenic cycle takes place instead of a lytic one. In a lysogenic cycle, the viral genes are incorporated into the bacterial nucleic acid and reproduce with it. While the viral genome (gene collection) is part of the bacterial one, it's known as a prophage. It was once thought that the prophage was inactive while it remained part of the bacterium's genetic material. Researchers have discovered that this is not always the case.

If the bacterium bearing the viral genes is stimulated in an appropriate way, such as by a stress of some kind, the prophage leaves the host's DNA and triggers the host to make new virions. This is followed by lysis of the bacterium and the release of the phages. The activation of the prophage is known as induction. Finding ways to activate prophages or to force them to remain inactive might be beneficial for us.

M13 is a filamentous phage, or an inovirus. The purple colour in this illustration represents single-stranded DNA. The other colours (except for the yellow) represent different kinds of proteins.

M13 is a filamentous phage, or an inovirus. The purple colour in this illustration represents single-stranded DNA. The other colours (except for the yellow) represent different kinds of proteins.

Our Gut or Intestinal Microbiome

Our digestive tract, gastrointestinal tract, or gut is a continuous passageway that leads from the mouth to the anus. Inside the body, the wall of the digestive tract separates it from its surroundings. The wall is not a complete barrier, however. Substances pass through it in either direction.

The term "gut" with reference to the microbiome refers to the small and large intestine. Many bacteria and other microorganisms live in the gut, especially in the small intestine. Some of the bacteria have phages inside them. Bacteriophages are also found outside the bacteria after they have been released during lysis.

Most of the phages in the gut appear to be ones containing DNA, not RNA. They are much smaller than bacteria and are often difficult to study, especially when they are hiding in bacterial cells. They appear to be numerous, however.

Researchers have learned that the bacteria living in our gut can have major effects on our lives. Many scientists are studying them. Now interest in exploring the role of gut phages is increasing. They may be an important contributor to human health or disease.

The human digestive tract and related structures

The human digestive tract and related structures

The gut microbiome is a complex, interconnected ecosystem of species.

— Brigham and Women's Hospital, via phys.org

Effects of Bacteriophages in the Mouse Gut

Researchers at Brigham and Women's Hospital have found that phages "can have a profound impact on the dynamics of the gut microbiome", at least in mice. The researchers used mice that had no microorganisms in their gut before the experiment was started.

The scientists added gut bacteria and phages found in humans to the intestines of the mice. They found that the phages killed the bacteria that they could infect, as was expected. They also found other changes in the bodies of the mice, however.

One observed change was that the populations of the bacterial species that weren't killed by the phages increased dramatically. There was also a change in the gut metabolome of the mice. The metabolome is the collection of chemicals (or metabolites) produced in an organism and present in a sample obtained from it, such as intestinal fluid.

By examining the gut metabolome of the mice with the added bacteria, the researchers detected an alteration in the level of neurotransmitters, bile acids, and some other molecules. Neurotransmitters are produced by our nervous system. Some are also made by certain bacteria. They control the passage of a nerve impulse from one neuron (nerve cell) to another. Bile acids or bile salts emulsify fats in the intestine, making them easier to digest. Bile acids are produced by the liver from cholesterol and exist in different forms. Some bacteria can change the form of bile acids, which may be a significant effect for us.

The investigation was performed in mice, not humans, which is an important point to consider. Nevertheless, the research might be important with respect to our intestine. The scientists plan to do more investigations in order to better understand the links between gut phages and health or disease.

An artistic representation of the effect of phages on the mouse metabolome

An artistic representation of the effect of phages on the mouse metabolome

Obesity and Type 2 Diabetes in Mice

Researchers at the University of Copenhagen have performed an interesting experiment. They transferred stool viruses from lean mice to mice that were following an unhealthy diet. The majority of the viruses that were transferred were phages as opposed to non-phage viruses.

The mice receiving the phages continued to eat an unhealthy diet during the experiment. Some mice eating the diet were not given transplanted viruses. The mice that received the phages gained significantly less weight over a six-week period that the mice without the phage transplant. They also had a significantly reduced chance of developing glucose intolerance. The condition includes an increased blood glucose level and is associated with type 2 diabetes.

When obese mice who were following an unhealthy diet and had glucose intolerance were given the phages, the intolerance to glucose disappeared. The researchers stress that humans with the health problem should change their lifestyle in an attempt to help their condition (and, of course, seek their doctor's advice). It's unknown whether a phage transplant will help humans or if it does when it will be available for use. Clinical trials in humans are required in order to determine the usefulness of the technique for us. The trials could be very worthwhile.

Oregano is often considered to be an antibacterial herb.

Oregano is often considered to be an antibacterial herb.

Antibacterial Foods and Phage Release

Researchers at San Diego State University have discovered some interesting information about certain foods that are often considered to be antibacterial (including oregano). In the lab, oregano and some other foods triggered the activation of prophages in certain bacteria that are found in the human gut. This caused new phages to be produced and the death of the bacteria as the phages escaped from them. The released bacteriophages were then able to attack and kill other bacteria. This may be the way or at least one way in which the foods are able to fight bacteria in our body. Once again, however, the experiment wasn't performed in humans.

The research report raises a concern. Some foods in the scientists' test list appear to be broad-spectrum antibacterials. This means that they may affect multiple kinds of gut bacteria, perhaps including helpful ones. Eating the foods in excessive amounts may therefore be harmful as well as beneficial with respect to the gut community. The researchers certainly aren't recommending that we avoid the foods, though. Discovering how the foods activate prophages (assuming they do this in our bodies) might be very useful.

Phage Therapy

The discoveries about the potential benefits of phages for health problems have been made in lab animals and lab equipment. They may apply to our body as well, but we need clinical trials in order to confirm this.

An exception to the lack of evidence in the human body is a treatment called phage therapy. As its name suggests, during this therapy, a phage or a collection of phages aimed at destroying the bacteria causing an infection is administered to the patient in an appropriate way. A liquid contained suitable phages may be gargled, swallowed, or sprayed over an area, for example. The treatment is used for the treatment of gut problems and for problems outside the gut.

The therapy was developed in the country of Georgia, which is located on the border between Europe and Asia. It appears to be popular there. It has been used successfully outside of Georgia, but special permission to use the therapy is generally required in this situation. Western scientists, health professionals, and health agencies want to explore the treatment in more detail before they agree to its general use. As bacterial resistance to antibiotics increases, more scientists are investigating phage therapy.

Bacteriophages can be seen under an electron microscope. This is the gamma phage.

Bacteriophages can be seen under an electron microscope. This is the gamma phage.

Exploring the Role of Phages in Our Lives

Viruses are microscopic and don't consist of cells, but this doesn't mean that they are simple entities. I think the study of phages is exciting. It offers many possibilities. These include the ability to reduce the population of a target bacterium without the use of antibiotics that may affect more than one species and without increasing antibiotic resistance.

Obtaining detailed knowledge about how specific phages behave in our body and about their possible effects is important. Researchers are investigating whether our gut phages have any effect on us while they are outside bacterial cells. Evidence suggests that some types may trigger inflammation in this situation. There are uncertainties and questions related to the activities of phages in the gut, but enough research has been done to suggest that at least some of them might be very useful for us.

Scientists say that exploring the phages in our gut is not as easy as studying the bacteria that live there and that it can be a very challenging process. They are working on ways to overcome this challenge. Some of the phage types that they have discovered were unknown before their research. Learning more about bacteriophages and using them to improve our health or to obtain other benefits is a tantalizing idea.

References

  • Information about bacteriophages from the Khan Academy
  • Bacteriophage facts from the Encyclopedia Britannica
  • Phages in the gut microbiome from the phys.org news service
  • Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model by Bryan B.Hsu et al, Cell Host and Microbe journal
  • New insights into intestinal phages from the Nature journal
  • Considering the other half of the gut microbiome from the ASM (American Society for Microbiology):
  • Phages from feces can fight obesity and diabetes in mice from the Medical Xpress news service
  • Foods and bacteria level in the gut from the ScienceDaily news service
  • Potential benefits and problems linked to phage therapy from CTV News

This content is accurate and true to the best of the author’s knowledge and does not substitute for diagnosis, prognosis, treatment, prescription, and/or dietary advice from a licensed health professional. Drugs, supplements, and natural remedies may have dangerous side effects. If pregnant or nursing, consult with a qualified provider on an individual basis. Seek immediate help if you are experiencing a medical emergency.

© 2020 Linda Crampton

Comments

Linda Crampton (author) from British Columbia, Canada on June 28, 2020:

Hi, Denise. Flatulence can be caused by the action of bacteria on certain substance that we haven't digested, though there are some other causes of the condition.

Linda Crampton (author) from British Columbia, Canada on June 28, 2020:

Hi, Miebakagh. I'm not willing to say that we'll never be able to identify all of the bacteria, viruses, and fungi in the digestive tract. We may be able to identify them in the distant future when science and technology are sufficiently advanced. Our intestinal microbiome certainly has some mysterious aspects at the moment, though.

Denise McGill from Fresno CA on June 28, 2020:

I heard once that bacteria in the gut is what causes flatulence. Do you think that is true?

Blessings,

Denise

Miebakagh Fiberesima from Port Harcourt, Rivers State, NIGERIA. on June 28, 2020:

Apart from the teeth and tongue, the gut, the small and large intestines has the key to healthy working of the body as far as digestion is concern. We will never know all the virus and bacteria involve. It is as mysterious as the universe.

Linda Crampton (author) from British Columbia, Canada on June 28, 2020:

Hi, Manatita. Thanks for commenting. Our gut is certainly important. I think the latest discoveries about the activities inside it are fascinating to explore. The potential health benefits of the substances that you've mentioned are interesting to investigate, too.

manatita44 from london on June 28, 2020:

A very indept study and some aspects of it are beyond me. I try to relate it to the gut, which seems to have been a subject of health and ill heath for quite some time, especially 'leaky' gut.

Some naturopaths, are making pre-biotics to work in a different way from the pro-biotics. Interesting that the viruses attack bacteria and yes, the small and large bowel may hold many mysteries. Seems that Omega 3 fatty acids, are as useful as the oregano.

Miebakagh Fiberesima from Port Harcourt, Rivers State, NIGERIA. on June 26, 2020:

Well noted, please. And thanks.

Linda Crampton (author) from British Columbia, Canada on June 26, 2020:

Thanks for the visit, Nithya. I think using phages to help people is exciting, too. I'm looking forward to reading about new discoveries related to bacteriophages.

Nithya Venkat from Dubai on June 26, 2020:

I hope the research "Obesity and Type 2 Diabetes in Mice" helps to find a solution for diabetes. Phage therapy is something new and exciting, and it has a lot of potentials to help cure diseases. I learned a lot today by reading your article. Thank you for sharing.

Linda Crampton (author) from British Columbia, Canada on June 24, 2020:

Thanks, Peggy. I hope the research leads to more therapies. That would be a wonderful outcome of the studies.

Peggy Woods from Houston, Texas on June 24, 2020:

As we are developing more resistance to antibiotics, perhaps these new studies will offer more therapies in the future. Your articles always provide fascinating insights into subjects. Thanks for the education!

Linda Crampton (author) from British Columbia, Canada on June 23, 2020:

I find the research fascinating, too. Gut phages are difficult to study, but I hope it's not too long before they can be used to help people.

Blessings to you, Denise.

Denise McGill from Fresno CA on June 23, 2020:

What fascinating research. I can't wait to hear more. It could be years, I'm guessing, but I'll have to keep my eyes open about it.

Blessings,

Denise

Linda Crampton (author) from British Columbia, Canada on June 23, 2020:

Hi, Adrienne. I think viruses are fascinating as well as confusing. They are certainly strange entities!

Adrienne Farricelli on June 23, 2020:

Viruses are such weird entities, I still feel confused when I read they can't define whether viruses are live or non-live entities. I am always interested in reading about gut bacteria. It seems like they play such a big role in our immune system including fighting allergies and infections.

Linda Crampton (author) from British Columbia, Canada on June 23, 2020:

It would be wonderful if the research improves our lives. Thanks for the visit, Devika.

Linda Crampton (author) from British Columbia, Canada on June 23, 2020:

I hope the research is useful, too, Miebakagh.

Devika Primic on June 23, 2020:

Linda this is an interesting and a fascinating research of a unique topic So much going on around us I tend to forget of other new researches such as this one. hope it works out and improves our lives for the illnesses one carries with.

Miebakagh Fiberesima from Port Harcourt, Rivers State, NIGERIA. on June 23, 2020:

Thank you, Linda, thank you. I hope the researchs were positive.

Linda Crampton (author) from British Columbia, Canada on June 22, 2020:

Hi, Flourish. Yes, the information about oregano is interesting, but it's not yet certain that it's antibacterial within our body. I hope researchers clarify the situation soon.

I was thinking about fecal transplants as I was creating the article. I've seen speculation that in some cases the phages in the donated feces might contribute to the success or failure of a transplant. That's another point that I hope researchers are able to clarify soon.

FlourishAnyway from USA on June 22, 2020:

The oregano insight was interesting, and I would love to learn more about how much, how often, whether it's taken raw, etc. This article made me think of the rather gross but real fecal transplant procedure option for people with C diff and other serious gastro problems. I also wonder how much our addiction to hand sanitizer growing up contributes to poor health.

Miebakagh Fiberesima from Port Harcourt, Rivers State, NIGERIA. on June 22, 2020:

I agreed.

Linda Crampton (author) from British Columbia, Canada on June 22, 2020:

Thank you for the kind comment, Venkatachari.

Venkatachari M from Hyderabad, India on June 22, 2020:

Very interesting article, Linda. Great information has been provided by you in this article. Thanks for sharing.

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Thank you very much, Linda. If oregano kills bacteria in the body, it could be very useful. I'm looking forward to seeing more discoveries about the herb.

Linda Chechar from Arizona on June 21, 2020:

What a wonderful article Linda. I think oregano would be a great antibacterial herb!

Miebakagh Fiberesima from Port Harcourt, Rivers State, NIGERIA. on June 21, 2020:

Mel, great post!

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Thanks for the comment, Mel. I think phages might have many uses in our lives, but we need to understand their behaviour in more detail. I'm looking forward to reading about future discoveries.

Mel Carriere from San Diego California on June 21, 2020:

Another fascinating review about a subject with endless potential applications to our own lives. Our bad western diets I think have caused the creation of unhealthy microbiomes in our digestive tract, and this may have to be reprogrammed with microphages. Great article.

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Hi, Eric. Your comment is amusing, but you've also also raised some excellent points. It's amazing that something so small might have such important effects!

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

I appreciate your comment very much, Pamela. The study of phages is complicated, but it could offer us many benefits. I hope it eventually helps us in many ways.

Eric Dierker from Spring Valley, CA. U.S.A. on June 21, 2020:

Really educational and full of nuggets. Phages? What a huge deal for something so small.

This could not help but get me to think of how in the heck does the body make it so far?

I am off to wash my hands, this made me feel viral ;-)

Pamela Oglesby from Sunny Florida on June 21, 2020:

This is a fascinating article. If they could cure people of diabetes that would be so wonderful. There has obvousy been a great deal of research but a lot more must be done. This is a complicated topic and I appreciate the careful explanations you have written.

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Hi, Liz. It's interesting that such tiny creatures can have such big effects on our lives. Thank you for the visit.

Liz Westwood from UK on June 21, 2020:

This is an interesting article. Much more is said these days about good and bad bacteria in the gut, so it's good to discover more information in your article.

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Hi, Mary. A healthy gut is always valuable! Good luck with your efforts.

Mary Norton from Ontario, Canada on June 21, 2020:

Linda, this article is of interest to me as I am trying to make my gut healthy. I haven't understood the complexity of our gut microbiome as studies continue to come up. I am glad you wrote about this.

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Hi, Liza. I agree. Science is fascinating. It seems that the more we discover, the more there is to learn! Thanks for the comment.

Liza from USA on June 21, 2020:

Science is a fascinating subject, and the amount of research and study that we can do is endless. For example, it leads us to this scientific and knowledge about our bodies. I have a little learning about how much bacteria was influencing our life when I was in high school. Your article is the depth with knowledge, Linda. Thanks for sharing!

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Hi, Bill. Yes, the thought of phages and their action does make one realize that many factors contribute to our health. It's interesting to think about the microscopic events occurring in the gut.

Bill Holland from Olympia, WA on June 21, 2020:

I read an articled like this one, Linda, and I am left with the realization and appreciation for just how lucky I am to have this body of mine. My good health is not easily explained, but it sure is appreciated daily.

Linda Crampton (author) from British Columbia, Canada on June 21, 2020:

Thank you for the comment, Miebakagh. I think that bacteria and viruses are fascinating. They are important, too.

Miebakagh Fiberesima from Port Harcourt, Rivers State, NIGERIA. on June 21, 2020:

Linda, your article is a study and informational. I am very interested and immersed in it. Right in my school days and at university, bacteria always fascinated me. I must agreed with you that doctors must have a good knowledge of the study of the gut bacteria. Thanks for sharing.

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