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Bacteria in the Large Intestine: Potential Effects on Health

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

Bacteria in Our 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 the bacteria. Many of our intestinal 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.

It's often said that there are around ten times more bacterial cells in our body than human ones. There have been recent criticisms that this ratio is too high, but researchers agree that the microbes outnumber our 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.

Intestinal bacteria co-exist with us, living out their lives in our large intestine and reproducing to make new bacteria. The community of microbes in this area 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.

The Human Microbiome Project

Microbes 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.

Importance of Gut Bacteria

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

Potential Health Benefits of Intestinal Bacteria

Certain intestinal bacteria are known or suspected to:

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

Microorganisms in Humans

Consult a Doctor If Necessary

It's important to remember that bacteria are living things that may have significant effects in our body. Anyone with questions about intestinal bacteria or about attempts to influence the bacterial population in the intestine should discuss the situation with a doctor.

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 either 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 can suppress C. diff.

The donated feces is screened for the presence of specific bacteria that are harmful before a transplant is performed. The people involved generally work carefully in order to get a safe sample for donation and are often successful. There is a chance that harmful bacteria in the sample will be missed, however, depending on the tests that are done.

Be Careful!

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 helpful for certain disorders. When done incorrectly, it could be harmful.

Clostridium difficile and Fecal Transplantation

Fecal transplantation is also known as fecal microbiota transplantation, or FMT. 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 (at least in my part of the world), 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.

A C. diff Patient Helped by a Fecal Transplant

Super Donors

Researchers have found that some people produce stool with a high concentration of beneficial bacteria. They call these people "super donors." A group of scientists has explored the literature and found that stool from super donors produces a higher rate of success in fecal transplants than stool from other donors.

Safety of Fecal Transplants

Sadly, in June, 2019, someone in the United States died after receiving a fecal transplant. The patient received a harmful, antibiotic-resistant strain of a bacterium called Escherichia coli in the donated feces. The patient was immunocompromised (that is, their immune system wasn't working effectively). Despite receiving "aggressive" treatment for the infection, they died.

The case is discussed in the NPR reference below and in the second ScienceDaily news service one. The latter article says that the capsule with the donated stool was created and frozen in late 2018 and came from a healthy donor. Testing stool for the drug-resistant form of E. coli "was not adopted into screening protocols until January 2019."

Anyone who is thinking of getting a fecal transplant should consult their doctor and investigate the procedures used at the clinic or hospital where they will receive the transplant. They should also discuss the fatality with the doctor, who should know about the details of the case. The details are important in order to understand why the recipient died.

The fatality is the only death from the procedure that I've heard about, but even one death is tragic. Fecal transplants seem to have the wonderful potential to help someone with debilitating health problems, but safety is important.

Crohn's Disease and 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 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 significant benefit from a stool transplant. The number of participants in the trial was so small that the results should be interpreted cautiously, however. Overall, evidence that the procedure is a good treatment for people with Crohn's disease is lacking at the moment. The link between a fecal transplant and a benefit in a C. diff infection is much stronger.

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.)

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

Microbes and Health

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.


When a harmful microbe is multiplying in a community, washing the hands is important in other cases besides the ones mentioned above. An epidemic or a pandemic is a special case that requires special hygiene procedures.

Antibiotics Made by Gut Bacteria

Antibiotic Effects on 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 may kill some of our good bacteria as well as the bad bacteria that are making us sick, however, which could be a problem. Nevertheless, we need to take an antibiotic when we have a serious bacterial infection and take all the pills in the container (unless a doctor recommends a different procedure).

Although following a doctor’s prescription with respect to antibiotics is important, some scientists are worried because they say that the medications are being prescribed too often and in situations where they're not needed. The use of the medications not only kills helpful bacteria but may also result in some harmful bacteria becoming resistant to the effects of antibiotics. If a few of the harmful bacteria have a gene or genes that give them resistance to the antibiotic, the rest of their species may be killed by the medicine, but the resistant cells will survive and be able to reproduce. This process may spread the gene (or genes) for resistance through the population.

Effects of Probiotics

Treating Disease by Altering Our 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 soon be overcome. Probiotic foods, drinks, and supplements may one day be designed for specific health problems. Studying intestinal bacteria in the future might be just as important as studying new medications in order to treat diseases.


  • Fecal transplant success in treating C. diff from the CBC (Canadian Broadcasting Corporation)
  • The super donor phenomenon in fecal transplants from the ScienceDaily news service
  • Patient death after a fecal transplant from NPR (National Public Radio)
  • Screening for drug-resistant E. coli in capsulized fecal transplants from ScienceDaily
  • Fecal transplantation and Crohn's disease from WebMD
  • Fecal transplant news from Medical Xpress (starting with the most recent news release)
  • Gut bacteria linked to obesity and metabolic syndrome identified from the Medical Xpress news service
  • Interaction between gut bacteria and diet from the NIH (National Institutes of Health
  • Good bacteria and Type 1 diabetes from EurekAlert (an online publication of the American Association for the Advancement of Science)
  • Gut bacteria and rheumatoid arthritis from the NIH

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

Question: Is the flora in the large intestine also in the small intestine?

Answer: 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


Linda Crampton (author) from British Columbia, Canada on August 01, 2017:

Thanks for the comment, JaneanOverman.

Janean Overman from Virginia on August 01, 2017:

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

Linda Crampton (author) from British Columbia, Canada on January 27, 2013:

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 and sherry from south Florida on January 27, 2013:

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.

Linda Crampton (author) from British Columbia, Canada on January 25, 2013:

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.

Deb Hirt from Stillwater, OK on January 25, 2013:

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.

Linda Crampton (author) from British Columbia, Canada on January 21, 2013:

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

Dianna Mendez on January 21, 2013:

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

Linda Crampton (author) from British Columbia, Canada on January 21, 2013:

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.

Helen Murphy Howell from Fife, Scotland on January 21, 2013:

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!!

Linda Crampton (author) from British Columbia, Canada on January 20, 2013:

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 from Alberta, Canada on January 20, 2013:

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