Commensal Science For Non-Scientists

Did you know your body contains more bacterial cells than human cells? About 100 trillion of these microscopic creatures live in your body and outnumber your 10 trillion human cells. Your intestines alone, where most of the bacteria in your body live, can contain up to 100 billion bacterial cells. These normally harmless bacteria are referred to as commensal bacteria. Commensal bacteria help keep our bodies healthy in many ways: they help us to digest foods and acquire nutrients such as vitamins B and K, encourage your immune system to develop and prevent the colonization of bacterial pathogens that cause disease by competing with them.

Click on the body to the right to find out more about where these beneficial organisms live in your body.  Mouth - Even though you brush your teeth every day, commensal bacteria still live among the tiny crevices of your teeth and gums. The mouth is a favorable environment for bacteria because they can feast on the constant supply of food and skin [2]. Also, the mouth provides prime conditions for organisms that like to grow in low levels of oxygen. Examples of bacteria in the mouth are Streptococcus mitis, Proteus species, and Veillonellae species. Harmless commensals in your mouth compete for food with pathogens you are exposed to, preventing illnesses like Strep throat. Stomach - Very few bacteria colonize this organ because of its highly acidic environment. Those that are capable of living in highly acidic conditions, called acid-tolerant bacteria, colonize the walls of the stomach. Acid-tolerant Lactobacillus and Streptococcus species can be found here [3]. Small intestine - The first part of the small intestine, called the duodenum, contains few commensals because of its closeness to the stomach’s acidic environment. Farther down the small intestine, at the ileum, the population of commensals increases and becomes similar to that of the large intestine [2]. Large intestine - Your large intestine contains an amazing diversity of commensal bacteria. Between 300-500 different species can exist here and their numbers can range from 1 billion (109) to 100 billion (1011) cells [1]. Examples of commensal bacteria living here are Bacteroides fragilis, Lactobacillus species, and Escherichia coli [4]. These commensals help you to absorb certain nutrients in the food you eat, produce essential vitamins, and compete with pathogens. Commensal bacteria in your gut are so important that when you kill them by taking antibiotics, you may suffer diarrhea as a side effect. Respiratory tract - Most commensals colonize the upper respiratory tract because of its close proximity to the mouth. Organisms enter when you inhale and attach to mucous membranes of your nose, throat, and pharynx [1]. Examples include Streptococcus salivarius, Staphylococcus aureus, and Neisseria species [2]. Unlike your upper respiratory tract, if you are healthy your lower respiratory tract (trachea and lungs) does not contain any bacteria. This is because microbes become trapped in your nasal hairs or mucus membranes of your upper respiratory tract or they are pushed back into the upper tract by the beating of cilia, tiny hair-like structures that line your trachea [3]. Urogenital tract - Except for the urethra and the vagina, this area of the body is completely devoid of any bacteria. The urethra can harbor organisms such as S.epidermidis, E.coli, and Proteus mirabilis [3,4]. Microbes in the vagina will vary based upon a women’s age. Adult females tend to have Lactobacillus acidophilius, while girls who have not reached puberty and women who have experienced menopause tend to have species such as Staphylococcus, Streptococcus, and Corynebacterium present [3]. The balance of bacteria and other organisms in the vagina is important for preventing yeast infections. Skin - Commensal bacteria are found mostly on warm, moist areas on your skin surface. Popular places for bacteria to live are the armpit, perineum, palms, and toe webs. Other surfaces that are less colonized are drier areas such as your face, arms, legs, and trunk. Types of bacteria found on skin surfaces are Staphylococcus epidermidis, Micrococcus species, and Corynebacterium species [1].

Although these commensal bacteria are beneficial to our body, they can carry genes that cause them to become resistant to antibiotics.  Additionally, other harmless bacteria living in animals and the environment may carry these genes. When these bacteria are exposed to antibiotics these genes spread to more bacteria and become more common. In the body or in the environment, commensals may transfer these genes to pathogenic bacteria.  Once pathogens obtain these antibiotic resistance genes, it becomes difficult or impossible for doctors to treat the infections they cause.

This transfer of genes from one bacterium to another is called Horizontal Gene Transfer. In order to understand how commensals transfer antibiotic resistance genes to pathogenic bacteria, it is important to understand horizontal gene transfer and its role in antibiotic resistance.

Horizontal gene transfer can occur via three different mechanisms: transformation, conjugation and transduction. 

Transformation occurs when a bacterium picks up pieces of genetic material directly from its environment and inserts the genetic material into its own genome.  This genetic material can come from a ruptured bacterial cell from the same or unrelated species, as illustrated in the image to the left. 

Conjugation can be thought of as ‘bacterial sex’ and involves direct cell-to-cell contact as genetic material is transferred from donor to recipient.  The genetic material that is transferred is often in the form of a closed loop of DNA known as a plasmid.

Transduction is more complex and involves the transfer of genetic material from one bacterium to another by a virus. 

If a pathogen causing illness acquires an antibiotic resistance gene from commensal bacteria, the pathogen becomes resistant to the antibiotic. The illness can no longer be treated using that antibiotic and the doctor has to choose a different antibiotic. As a result, the illness is often longer, more severe, more expensive, and more often fatal. There are some pathogenic bacteria that are now resistant to every single available antibiotic! Untreatable infections caused by antibiotic resistant bacteria are now a common cause of death in the United States.

The current scientific evidence shows that the origin of this deadly resistance in pathogens may lie in harmless commensal bacteria. The Reservoirs of Antibiotic Resistance Network (ROAR) is working to understand the origin of resistance in pathogens by examining the abundance, diversity and distribution of antibiotic resistance in human, animal and environmental commensal bacteria.

Our goal is to understand how commensals acquire antibiotic resistance genes, how they pass these genes to pathogens, and use this information to predict and prevent the emergence of resistance in pathogens. As a citizen, consumer and patient, you can do many things to minimize the threat of antibiotic resistance. Visit the APUA website for more information.

1. Albrecht T, et al.  “Bacteriology:  Normal Flora.”  Medical Microbiology, 4th Edition.  University of Texas.  1996 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.section.508.
2. Champonux JJ, Drew WL, Falkow S, Neidhardt FC, Plorde JJ, Ray CG.  Sherris Medical Microbiology:  An Introduction to Infectious Diseases.  Connecticut:  Appleton & Lange, 1994.
3. Madigan MT, Martinko JM, Parker J.  Brock Biology of Microorganisms, 8th Edition.  New Jersey:  Prentice Hall, 1997. 
4. Todar K.  “The Bacterial Flora of Humans.”   Todar’s Online Textbook of Bacteriology.  University of Wisconsin.  2006 http://textbookofbacteriology.net/normalflora.html.