Health Benefits and Effects of Bacteria in the Large Intestine

Updated on May 17, 2019
AliciaC profile image

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

The human digestive system
The human digestive system | Source

Bacteria in the Large Intestine

Our large intestine is home to a huge bacterial population. The environment in the intestine is warm, moist, and rich in nutrients—the ideal surroundings for bacteria. Many of these bacteria are believed to have important health benefits. Researchers have shown that manipulating the population to increase the number of beneficial microbes can help to relieve specific health problems.

Intestinal bacteria co-exist with us, living out their lives in our large intestine and reproducing to make new bacteria. There are said to be around ten times more bacterial cells in our body than human cells. We contain about 100 trillion bacterial cells and only around 10 trillion human cells. The bacteria are smaller than our cells and normally live in body cavities that have contact with the outer world, such as the mouth, nose, intestine, urinary tract, and reproductive tract. They also live on our skin.

The community of microbes in the large intestine is known as the gut flora or the intestinal microbiome. "Gut" is a general name for the digestive tract (or gastrointestinal tract). It's most often used to refer to either the small intestine or the large intestine. The word bowel is sometimes used instead of intestine.

A Discussion About the Human Microbiome Project

Bacteria Living in the Human Body

The Human Microbiome Project (HMP) aims to identify and characterize all the microscopic creatures that live in or on the healthy human body. The project is run by the National Institutes of Health, an agency of the United States Government.

Until the Human Microbiome Project reported its first results in June 2012, it was thought that about 700 species of bacteria inhabited the large intestine. Now scientists say that at least 10,000 species of bacteria and other microbes inhabit the human body, a lot of them in the large intestine. They also say that almost everyone—even when they're healthy—has pathogenic microbes (those that can cause disease) inside their body. In healthy people these potentially harmful microbes seem to cause no problems. Most microorganisms in the body are bacteria, but yeasts and viruses are also present.

Although there are variations in the microbiomes of humans, the bacterial community in healthy people has certain features in common. Knowing the composition of the gut flora in healthy humans will hopefully enable researchers to identify microbe communities that can cause problems.

Research into identifying gut bacteria and discovering how they affect our lives is intensifying. Under normal circumstances, the good bacteria dominate and keep the bad ones under control. In some disorders, however, the effects of the harmful bacteria become noticeable.

Our Helpful Microbiome

Health Benefits of Intestinal Bacteria

Intestinal bacteria are known to:

  • make vitamins that we use (including vitamin k and biotin)
  • digest proteins, lipids, and carbohydrates in our food, enabling us to absorb some of the resulting products
  • help our immune system to function effectively
  • make anti-inflammatory chemicals
  • make other biochemicals that improve our health
  • help to keep us lean (possibly)
  • keep harmful microbes under control

Microbes in the Human Body

A Clostridium difficile Infection

Clostridium difficile, or C. diff, is a harmful gut bacterium. It can cause diarrhea, which may be debilitating, as well as colitis and abdominal pain. Colitis is inflammation of the colon. Our large intestine is made of two main sections: the colon followed by the shorter rectum.

C. diff is thought to live harmlessly in many of us. When a large number of our good bacteria die, such as during antibiotic treatment, C. diff can sometimes multiply out of control. The infection is most often found in hospitals and care homes but may also be found in the general community.

Some unlucky people have a persistent C. diff infection or a recurring condition that resists treatment. Experimental treatments by some doctors have found that fecal transplants cure many cases of these life-altering infections. In a fecal transplant, or fecal transplantation, a small sample of feces is taken from a healthy volunteer. Feces is also known as stool. It's released from a person's large intestine and contains intestinal bacteria. The donated feces or a liquid containing fecal bacteria is inserted into the colon of the sick person. The good bacteria in the feces multiply rapidly, spread through the intestine, and suppress C. diff.

Clostridium difficile
Clostridium difficile | Source

Treating Clostridium difficile by Fecal Transplantation

Until recently, individual patients infected by C. diff have reported wonderful results when they've found a doctor willing to do a fecal transplant, but the treatment hasn't been generally accepted by the medical profession. The attitude is currently changing and fecal transplants are becoming more common.

The results of a randomized and controlled trial published in The New England Journal of Medicine in 2013 are very interesting. Patients were randomly assigned to receive a fecal transplant, an antibiotic called vancomycin, or a bowel lavage followed by vancomycin treatment. The bowel lavage was used to cleanse the colon. The results of the experiment were as follows.

  • Out of 16 patients who received a fecal transplant, 13 were cured after one treatment.
  • 2 of the remaining patients were cured by a transplant from a different donor.
  • Only one patient was not cured, resulting in a cure rate of 94%.
  • 13 patients received vancomycin as a treatment.
  • 4 of these patients were cured, a cure rate of 31%.
  • 13 patients were treated by a bowel lavage and vancomycin.
  • 3 of these patients were cured, giving a cure rate of 23%.

After the first trial, 18 people who were not cured by vancomycin received a fecal transplant. 11 of these people were cured by the first transplant. 4 more people were cured by a second fecal transplant. This news is wonderful for people who are desperate to be rid of C. diff.

It's very important that fecal transplants are done by a doctor and that donated feces is carefully screened for dangerous microbes. When performed correctly, the procedure could be very helpfulful for certain disorders. When done incorrectly, it could be harmful.

A C. diff Patient Helped by a Fecal Transplant

Treating Crohn's Disease With a Fecal Transplant

Crohn's disease is a type of inflammatory bowel disease. The lining of the digestive tract becomes inflamed, resulting in abdominal pain. The pain is often severe. The patient may also experience diarrhea and other unpleasant symptoms. The inflammation most often occurs in the lower part of the small intestine, called the ileum, and in the large intestine. It's currently thought that Crohn's disease is an autoimmune condition—one in which the body's immune system attacks the lining of the digestive tract by mistake.

The use of fecal transplants for Crohn's disease hasn't been as well studied as their use for C. diff infections. Some individuals have reported dramatic relief from Crohn's disease after fecal transplantation, however. A small trial was conducted by Seattle Children's Hospital. Seven of nine children with the disease experienced a very significant benefit from a stool transplant.

Gut Bacteria and Morbid Obesity

Intestinal Bacteria and Obesity

Researchers have discovered that lean people have a different intestinal biome from obese people. This doesn't prove that bacteria cause obesity; it could mean that when people become obese the population of bacteria in their intestine changes. Still, it's an interesting observation.

Scientists at the University of Maryland School of Medicine have discovered 26 species of gut bacteria that seem to be linked to not only obesity but also metabolic syndrome. Symptoms of metabolic syndrome include high blood sugar levels, insulin resistance (inability of the cells to respond to insulin), a high blood cholesterol level, high blood triglycerides, and increased blood pressure. Metabolic syndrome increases the risk of heart problems, strokes, and type 2 diabetes. The researchers also noticed that people with the problem bacteria had increased inflammation in their bodies and were missing the bacteria that are reported to make anti-inflammatory substances.

Researchers at the Washington University School of Medicine have also made a discovery linking gut bacteria to obesity. They've found that obese and lean human twins have different microbe communities in their gut. The community in obese twins is less diverse. In a lab experiment, the researchers added bacteria from lean and obese twins to mice. The mice with donated bacteria from obese twins gained weight; those with a donation from a lean twin didn't. The researchers also found that a healthy diet helped the "lean" bacteria to survive.

Insulin is made by beta cells in the pancreatic islets, which are also called the islets of Langerhans. (The acini make digestive enzymes.)
Insulin is made by beta cells in the pancreatic islets, which are also called the islets of Langerhans. (The acini make digestive enzymes.) | Source

Intestinal Bacteria and Type 1 Diabetes

Type 1 diabetes is a disease in which the pancreas stops producing a hormone called insulin. It's an autoimmune condition. The immune system attacks and destroys the beta cells in the pancreas, which make the insulin. Insulin is an important hormone because it stimulates the entry of glucose into cells. The cells use the glucose to produce energy.

Researchers at The Hospital for Sick Children performed an experiment with female mice that had a high genetic risk for developing type 1 diabetes. When the females were given intestinal bacteria from normal male mice early in their lives, they were strongly protected against diabetes. It's important to be cautious about results in mouse experiments and their relevance to human health. The results often apply to humans, but this is not always the case.

The researchers suspect that a difference in intestinal bacteria could at least partially explain why human females are more susceptible to certain autoimmune diseases, including rheumatoid arthritis, than human males. More research is required in order to prove this idea.

Gut Bacteria and Rheumatoid Arthritis

It's important that we don't fall into the trap of thinking that bad gut bacteria are responsible for everything that ails us and that good gut bacteria can always help us. The microbes in our intestine may be involved in more aspects of our health than we realize, however.

The Hygiene Hypothesis

One theory about the increasing prevalence of certain diseases in the human population—especially autoimmune diseases—is the so-called hygiene hypothesis. This hypothesis says that our environment is so much cleaner than in the past and that we are so concerned with avoiding germs today that we are limiting the microbe diversity in and on our body.

Most of us have moved away from an agricultural lifestyle where we were in contact with soil and farm animals and shared microbes with them. We now live in a much more sterile environment. According to the hygiene hypothesis, children's immune systems aren't being trained to recognize and deal with potentially harmful microbes and their immune systems aren't developing properly.

Scientists are very careful when they refer to the hygiene hypothesis because they don't want people to get the wrong idea. We must wash our hands after a high-risk situation such as visiting a washroom. Dangerous bacteria can escape from washrooms and make us very sick. Washing the hands after cleaning up human or animal feces and body fluids, before eating, before preparing food, and after touching something known to be dangerous is also very important. However, some scientists wonder if we're being too careful with hygiene in other situations.

Antibiotics Made by Gut Bacteria

Antibiotics and Good Bacteria

Another topic that scientists talk about carefully is the use of antibiotics. They don't want people to refuse to take these medications when they're necessary. Antibiotics kill some of our good bacteria as well as the bad bacteria that are making us sick, which could be a problem. Nevertheless, we need to take an antibiotic when we have a serious bacterial infection. Scientists say that the medications are being prescribed too often and in situations where they're not needed, however. Their use not only kills helpful bacteria but also results in some harmful bacteria becoming resistant to the effects of antibiotics.

Effects of Probiotics

Treating Disease by Altering the Intestinal Microbiome

Some scientists say that so many microbes live in our intestine and that they seem to be so important in our lives that the intestinal microbiome should be classified as an organ. Our microbes have evolved with us; we are partners in life.

Discovering how the bacteria in our intestine affect our health is an interesting topic, but it's also one with great practical importance. In the future we may be able to treat diseases by adding specific bacteria to the intestine in order to produce a specific effect. Some people already try to do this. They ingest probiotics to add bacteria and yeasts to their intestine. The probiotic products that exist today contain only a few species out of the huge variety of organisms that live in our gut, however.

Most of our gut microbes haven't been grown successfully outside the body, which limits the types of probiotics that can be produced. Hopefully this problem will be overcome. Probiotic foods, drinks, and supplements may one day be designed for specific health problems. Studying intestinal bacteria in the future may be just as important as studying new medications in order to treat diseases.


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.

Questions & Answers

  • Is the flora in the large intestine also in the small intestine?

    The small intestine does contain some of the microbes found in the large intestine. The number of microbes in the small intestine is far lower than in the large intestine, however. The identity and the location of intestinal microorganisms are still being studied, so our knowledge of the flora may change.

© 2013 Linda Crampton


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    • AliciaC profile imageAUTHOR

      Linda Crampton 

      2 years ago from British Columbia, Canada

      Thanks for the comment, JaneanOverman.

    • JaneanOverman profile image

      Janean Overman 

      2 years ago from Virginia

      Nice hub. Learned a lot. Very thorough. Thanks for sharing.

    • AliciaC profile imageAUTHOR

      Linda Crampton 

      6 years ago from British Columbia, Canada

      Thank you very much for the comment and the vote, drbj!! I think that this information is fascinating, too. The relationship between our bacteria and our body is very interesting to study.

    • drbj profile image

      drbj and sherry 

      6 years ago from south Florida

      Absolutely, positively fascinating information, Alicia. The Human Microbiome Project and fecal transplants are particularly awesome. You give bacteria a good name, m'dear. Thanks you for this amazing research. Voted Up.

    • AliciaC profile imageAUTHOR

      Linda Crampton 

      6 years ago from British Columbia, Canada

      Hi, Deb. Yes, fecal transplants and their success rates are amazing. It will be great to have probiotics that are designed to treat specific health problems. Thanks for the visit.

    • aviannovice profile image

      Deb Hirt 

      6 years ago from Stillwater, OK

      A fecal transplant! How amazing that is. It makes sense that it would usually work, too. Sounds fascinating that we will be able to treat more ailments with probiotics.

    • AliciaC profile imageAUTHOR

      Linda Crampton 

      6 years ago from British Columbia, Canada

      Thank you so much for the comment and the vote, Dianna. I appreciate them both!

    • teaches12345 profile image

      Dianna Mendez 

      6 years ago

      I learned so much from this, especially about fecal transplants and how bacteria can help with many ailments. Very well done! Voted up+++

    • AliciaC profile imageAUTHOR

      Linda Crampton 

      6 years ago from British Columbia, Canada

      Thank you very much, Seeker7! I appreciate your comment and the vote. The hygiene hypothesis is interesting. I've read reports saying that children who grow up on farms have fewer autoimmune problems than other children. It does seem that exposure to a little dirt is helpful for the development of the immune system.

    • Seeker7 profile image

      Helen Murphy Howell 

      6 years ago from Fife, Scotland

      Fantastic hub about bacteria in the gut! There are a few thing new to me such as the fecal transplantation - this is very interesting indeed!

      It's also interesting about scientists wondering if we are being too hygienic. There was an old saying in Scotland that 'a dirty child was a healthy child' - this didn't mean the child was unwashed, only that the kids who were allowed the freedom to make mud-pies and so on seemed to have great resistance to many illnesses.

      This was a thoroughly enjoyable and fascinating hub + voted up!!

    • AliciaC profile imageAUTHOR

      Linda Crampton 

      6 years ago from British Columbia, Canada

      Thank very much for the comment, jaydene! I appreciate your visit. Fecal transplants are very interesting - they may sound disgusting, but they are proving to be a wonderful treatment for some serious conditions.

    • jaydene profile image


      6 years ago from Alberta, Canada

      Hi, I heard something on the news about the fecal transplant. It is such interesting information, as well as how it relates to crones disease and the many ways that our bodies can heal from rebalancing the bacteria in our bodies and intestines.

      Incredibly informative article. Lots to think about.

      Thank you for publishing this hub


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