How Biofilm Works

By: Marianne Spoon  | 
When microbial biofilms bind together sedimentary grains, they can form stromatolites such as these on the coast of Australia.

At first, it's not clear what dental plaque, the persistent slime in your shower drain and a slippery submerged rock have in common besides the fact that they can be a headache — or toothache — to remove. To the naked eye, it's nearly impossible to see what's responsible for these lined surfaces.

If you look closer, with the help of a microscope, you'll realize these slimy aggregations are anything but dull. Each biofilm consists of tiny communities of diverse living microorganisms bound together in a thick adhesive matrix. Who would've guessed the grimy buildup in your toilet bowl is a complex clump of living, communicating cells?


Though Antoni van Leeuwenhoek, the discoverer of bacteria, described similar formations when he studied his own dental plaque in the 17th century, it wasn't until the 20th century that scientists had the tools they needed to take a closer look at how the structures develop [sources: Montana State University CBE, Costerton and Wilson].

These colonies, also called biofilms, form when single microorganisms attach to a hydrated surface and undergo a "lifestyle switch," giving up life as a single cell to live on a surface in an adhesive cell matrix with other microorganisms [source: Lemon et al.]. Some definitions state that biofilm cells "irreversibly attach" to a surface, meaning gentle rinsing can't remove them [source: Donlan].

But why should we care about biofilms?

For starters, they can attach to both living and nonliving surfaces (including humans), create problems in the medical field, alter industrial production practices and even contribute to environmental cleanup. In addition, some researchers estimate that biofilms constitute more than half of the world's biomass [sources: Montana State University CBE; Sturman]. Biofilms are so abundant it's surprising that we don't notice them more.


Biofilm Formation

The building blocks for biofilms are microorganisms, or organisms too small to see with the naked eye. Different species of bacteria, protozoans, algae, yeasts and fungi can form biofilms. With most biofilms ranging from a few microns to hundreds of microns (one micron being one-millionth of a meter) in thickness, it's no wonder scientists prefer to use microscopes to study them.

So, what are the ingredients for biofilm development?


Generally, all you need is a hydrated surface submerged in water or some other aqueous solution, microorganisms and favorable conditions. However, not all biofilms grow at the same rate or even require similar conditions to survive — different types of microbial cells have different needs. Still, some factors that can affect biofilm attachment and growth regardless of species include:

  • The availability of nutrients in the hydrated sample
  • The physical and chemical characteristics of the biofilm surface, including its polarity
  • The thickness of the conditioning layer, or material already attached to the surface
  • pH levels
  • Temperature
  • The amount of shear, or rate of water flow, in the sample
  • Presence of antimicrobial agents
  • The number of species in the sample
  • Whether the microorganisms can move on their own
  • The cellular structures of the microbe (appendages)
  • The types of metabolic interactions between cells

Ultimately, it's essential to understand that microorganisms don't necessarily "think" while forming a biofilm; it just happens if the conditions are favorable. If water flow pushes a microbe or it accidentally bumps into a surface, it may or may not attach the first time—or at all.

It's unclear what causes a cell to attach to a surface, and some researchers say a combination of factors — including shear rates, electrostatic forces, conditioning layers (debris already on the surface) and nutrients available to the microorganism — is more influential than a single factor [source: Sturman].

With microorganisms often at the mercy of their environments, it's incredible how something as small as a bacterium can hold on to a surface to settle in its new home.


Biofilm Colonization and Development

Biofilms often grow as algae around hot springs, creating a display of bright colors.


Microbial Colonization and Biofilm Development

The transition from a free-moving microorganism to an immobile one distinguishes biofilms from cells growing in a test tube. But how can microorganisms stick to a surface long-term?

Gene Control

First, you'll need to know that once a free-floating cell starts a biofilm or becomes part of an existing one, it uses different genes to create proteins and other substances to help it adapt to its new lifestyle.


Switching genes "off" and "on" can change the cell's behavior. For instance, some genes control whether a microbe can move independently, while others can command the cell to go dormant if conditions are harsh. Human genes can do the same thing. For example, genes responsible for producing lactase (the enzyme that allows infants to digest milk) can turn “off” post-weaning, manifesting as lactose intolerance [source: Bowen].

Protecting the Colony

Regardless of species, all biofilms contain an extracellular polymeric substance (EPS) [source: Lemon et al.]. Think of EPS as part of a sticky extracellular (outside-of-the-cell) matrix of sugars, proteins and other genetic material released from cells in biofilm communities. EPSs not only help hold the cells of a biofilm together, but they also play a significant role in protecting the colony. The EPS usually makes up most of a biofilm's mass [source: Christenson and Characklis].

After latching onto a surface, a cell will produce a sticky biofilm matrix with EPSs to root itself better and make it easy for other cells to join the colony. Once other cells stick to the extracellular matrix and decide to stay, they also produce an adhesive matrix.

Communal Life

Before you know it, microbes in the biofilm have created an elaborate, three-dimensional biofilm structure that, when viewed under a microscope, resembles gluey towers.

While some biofilms have only a few cells, others can have millions — and sometimes billions — of cells intertwined in a single biofilm matrix. But as we'll note later, biofilm growth can be slowed or stopped sometimes, primarily by competition among cells and environmental factors [source: Sturman].

Interestingly, communal life also makes it easier for cells to send signals to one another through quorum sensing. This activity helps cells pass information about their neighbors and surrounding environment.

Quorum sensing is known to cause changes in cell behavior and may provide insight into why cells detach from biofilms; however, scientists have yet to fully understand the meanings of these signals [source: Donlan].


Biofilm Interaction: Life Within the Biofilm

In a sense, biofilms are like cities. Similar to city dwellers, microorganisms pass up solitary life to live communally [source: Watnick and Kolter]. We'll use Watnick and Kolter's analogy describing biofilms as "cities of microbes" to understand how cells in a biofilm interact.

Home Sweet Home

As we discussed earlier, microbes colonize surfaces to build the foundation of a biofilm. Before settling down, some cells move around using flagella or other mobile structures until they find a suitable place to stay — much like how new city residents visit different neighborhoods before choosing a home.


After moving in, new residents may add a room to their new home to create more space for people in a crowded house. In comparison, cells in a biofilm will produce those extracellular polymeric substances (EPSs) to include new cells from the outside and others created within the community.

Signals and Boundaries

At a basic level, both cities and biofilms offer their residents protection from outside forces. For biofilm bacteria, these forces can be antibiotic treatment or even the human immune system [source: Lemon et al.]. Scientists think a biofilm's overall thickness and density provide some protection [source: Montana State University CBE].

Also, communicating with your neighbors can be easier if you live closer to them. The same principle applies to cells in a biofilm during quorum sensing, when cells are near enough to signal effectively. Researchers hypothesize biofilms may also use quorum sensing to establish boundaries between different biofilm colonies [source: Watnick and Kolter]. Living in biofilms makes it easier for cells to conjugate, the primary mechanism of horizontal gene transfer.


Another important concept to remember is that biofilm structures are flexible. Most scientists use the term viscoelastic to describe biofilms, meaning they can be stretched like putty when the flow of a liquid pulls or pushes on the colony [source: Montana State University CBE]. These shear forces, or liquid flow rates, can shape a biofilm colony and cause clumps to disconnect or tumble away.


What if our newcomers to the city grow tired of living in a crowded area? They may move somewhere else. Cells in a biofilm can do the same by detaching from the colony, regaining their mobility and continuing life as floating microorganisms. Detaching may be a more challenging task for cells embedded beneath other layers of cells and EPSs.

After detaching, a microbe may start a new biofilm or join another established cell community. We don't know what causes detachment, but scientists say that species type, environmental pressures and competition within the biofilm all play roles. Like humans and other animals, microorganisms often move elsewhere to survive when the going gets tough.


Biofilm and Medical Problems

Biofilm formation in an indwelling catheter, such as this one shown on an electron micrograph, may lead to staph infections.
Image Courtesy CDC/Rodney M. Donlan, Ph.D; Janice Carr


Biofilm and Medical Problems

Have you ever wondered why cleaning your teeth at the dentist is necessary? You already brush your teeth on your own, right?

Microbial Biofilms

Unfortunately, while brushing and flossing your teeth removes some dental plaque, a biofilm found on teeth, you won’t be able to remove everything. If dental plaque builds up in hard-to-reach areas, it can harden, leading to cavities and periodontitis (gum infection).


Outside your mouth, biofilm-related health problems are more common than you might think. Up to 80 percent of human microbial infections are biofilm-associated infections [source: Khatoon et al.]. Biofilms strengthen microbial communities, which is good news for the microbes, but not-so-good news for anyone battling a biofilm infection.

Bacterial Biofilms

The biofilm structure can promote antimicrobial resistance (AMR). Some microbes, like the bacterial species Staphylococcus epidermidis, exhibit “biofilm resistance,” meaning antimicrobial compounds are less effective when the S. epidermidis forms a biofilm than when the bacterial cells are isolated planktonic cells. Unfortunately, antibiotic testing often happens with planktonic bacteria rather than with a bacterial biofilm [source: Koch et al.].

Biofilm-related infections can cause health problems, ranging from a common earache to a specific bacterial infection found in people with a genetic disease called cystic fibrosis.

Biofilms are a particular area of concern for patients with implanted medical devices like:

  • Catheters, or tubes inserted in the body to deliver treatment or remove bodily fluids (especially central venous catheters and urinary catheters)
  • Prosthetic joints
  • Mechanical heart valves
  • Pacemakers
  • Contact lenses
  • Endotracheal tubes, used to help with breathing or administer anesthesia
  • Intrauterine devices used as contraceptives

In hospital settings, microbes can enter a patient's body when transferred to a medical device from visitors, hospital staff, or the patient themselves, which is why hygiene is crucial. Staph infections, for example, can result from infectious biofilms containing Streptococcus bacteria. Staphylococcus aureus biofilms are notorious for their bacterial persistence.

Removing Dangerous Biofilms

Getting rid of a bacterial biofilm, especially if it contains staph bacteria, can be challenging for patients with implants, but there are a few options. Removing the implant will sometimes do the trick, but won't necessarily help with bacterial adhesion to live tissue [source: Donlan].

Other techniques include applying more substantial doses of antimicrobial drugs to the implant's surface before it's placed inside a patient or experimenting with implants lined with silver, which has antimicrobial properties.

Unfortunately, there's no universal treatment for medical biofilms in the long run. Preventing biofilms from forming in the first place is the most promising tactic. Patients should always consult their doctors about possible treatments for biofilm infections.


Biofilm Damage to the Environment

Communal microbes can adapt to live on many surfaces, including our teeth and in our bodies, but the vast majority of biofilms are found in nature. For instance, you may feel the presence of biofilms on rocks in a shallow body of water, creating a slippery surface to traverse. Unlike biofilms studied in the lab, these aggregations occur naturally and are one part of a larger ecosystem.

Today, our impact on the environment often results in imbalances in ecosystems. For example, waste runoff can cause an area to have higher levels of certain nutrients than usual. To some microorganisms, this means more food to eat, and their populations may grow out of control as a result.


In order to break down nutrients, some microbes require oxygen, and they will use more than usual to break down a surplus of nutrients. This removal of oxygen from an ecosystem can cause problems for other organisms that share the same habitat, sometimes resulting in dead zones.

If given the nutrients to grow out of control, both free-floating microorganisms and sedentary biofilms can flourish and use all of the oxygen in an area, making an environment hard or impossible to live in for other microbes and animals.


Biofilm and Industry

In industrial environments, biofilms are a force to be reckoned with. Since most production facilities use water to cool equipment or depend on pipes to transport resources, there's a substantial risk of developing biofilms on these equipment and piping systems.

According to one estimate, biofilms cause well over a billion dollars' worth of damage every year in industrial settings, affecting human health and companies' abilities to manufacture their products efficiently [source: Montana State University CBE; Sturman]. Papermaking facilities are especially at risk for biofilm problems, because manufacturing paper requires a lot of water and provides a warm and nutritious environment for microorganisms to grow [source: Sturman].


Biofilms can also negatively affect the quality of drinking water. After waste water is treated, it flows through clean pipes that transport it to our faucets. But in some cases, biofilms can be a nuisance in this process. Scientists at water treatment facilities found that biofilms still form in the pipes that carry clean water, which recontaminates the water.

After studying the issue, they learned that clean drinking water that has been treated contains organic carbon — a tasty meal for bacteria. Fortunately, removing organic carbon from processed water limits these bacterial biofilms from forming in clean water pipes, granting the water a safe trip to your faucet [source: Sturman].

Biofilms and Invasive Species

Researchers have found that ballast water, water that ships store in their bows for balance, houses biofilms, too [source: Drake et al.]. Organisms ranging from shellfish to bacteria can be transported in ballast tanks. But when ships gather ballast water at one port and release it in another, that's when things get sticky.

Emptying ballast water in a new environment gives these non-native organisms an advantage, allowing them to outcompete native species for food and resources. Just like on other submerged surfaces, biofilms can colonize on the inside of these tanks. Once in a ballast tank, microbes from biofilms can either detach from the colony or be scraped off into the new environment.

Researchers say we should treat invasive microorganisms in these biofilms and ballast water with the same caution as other invasive organisms, because they may spread certain pathogens or disease-causing microbes.


Benefits of Biofilms

Microorganisms can cause imbalance in an environment if the conditions are right. Ironically, that's why microbes can be beneficial, too. For instance, it turns out that the same nutrient-hungry bacteria that break down carbon in treated water can also restore balance to an area by eating excess carbon when the situation arises.

Recovering From Oil Spills

When oil accidentally winds up in nature (as seen in oil spills), microbes slowly break down oil particles. Oil is primarily made of carbon, and there are a variety of bacteria that break down small oil molecules for food. Biofilms then, can potentially help clean up environmental messes.


Using biofilms in this way is an example of bioremediation, or returning an environment from an altered state back to its natural one with the help of microorganisms. Though collecting oil and running it through a biofilm filter of some sort isn't a common method to clean up oil spills today, it may be an interesting option to explore in the future.

Responsible Mining

Biofilms even have their place in the mining industry. Quite often, valuable ore is separated from normal rock in mining settings. But in the presence of water and oxygen, certain types of leftover crushed rock can create a sulfuric acid solution if left alone.

Once the reaction takes place, this acid and other runoff are hard to clean up and can pollute nearby water sources. But if you take out a part of the equation, the rock material won't become acidic and can be disposed of differently. It turns out that placing biofilm-forming bacteria that need oxygen on these rocks will strip the element from its surface and disable this acid runoff from forming [source: Sturman].

Wastewater Treatment

In addition to bioremediation, biofilms can be used in biofilm trickling filters to treat wastewater [source: Sturman]. In this process, biofilms are grown on rocks or pieces of plastic to clean wastes out of the water slowly trickling through.

On a small scale, this process is efficient enough, but most municipal water treatment centers still rely on larger quantities of bacteria to treat wastewater.

Friendly Flora

Biofilms also benefit other organisms in nature. Underground, microorganisms will form a biofilm around the rhizosphere, or the area between roots and soil, in plants. Chemical interactions in this symbiotic relationship grant both parties access to nutrients that would otherwise not be available. Biofilm formation on plant roots is one of many examples of why biofilms are ecologically important.

Black Death, Ticks and — Biofilms?

It's hard to tell which organism was really responsible for the bubonic plague, a disease that caused millions of deaths in the 14th century. Ticks were responsible for spreading the disease from rats to humans, but researchers are taking a closer look at the bacteria itself — one species called Yersinia pestis.

Modern studies show that these bacteria form a biofilm in the area between the tick's esophagus structure and stomach, blocking its food intake and starving the animal [source: Darby]. So why did the plague still spread if ticks carrying the bacteria starved to death? Well, since the ticks were constantly hungry, they tried to eat more often, and humans, unfortunately, were on the receiving end of these attempts.


Lots More Information

Related HowStuffWorks Articles

More Great Links


  • Bowen, R. "Lactose Intolerance (Lactase Non-Persistence)." The Small Intestine: Introduction and Index, Colorado State Hypertexts for Biomedical Sciences. April 25, 2009. (June 12, 2010).
  • Christenson, B.E. & Characklis, W.G. "Physical and Chemical Properties of Biofilms." In Characklis, W.G. & Marshall, K.C. (eds.). "Biofilms." John Wiley & Sons Inc. 1990.
  • Costerton, W. J. & Wilson, M. "Introducing Biofilms." Biofilms. Vol. 1, no. 1. May 4, 2004.
  • Cromie, William. "Discovering Who Lives in Your Mouth: Bacteria Give Clues to Cancer and Gum Disease." Harvard University Gazette. 2002. (June 12, 2010).
  • Cunningham, Alfred B.; Lennox, John E.; & Ross, Rockford J., (eds.). "The Biofilms Hypertextbook." Aug. 12, 2008. (June 3, 2010).
  • Darby, Creg. "Uniquely Insidious: Yersinia pestis biofilms." Trends in Microbiology. Vol. 16, no. 4. 2008. (June 12, 2010).
  • Davies, David G. & Marques, Cláudia, N. H. "A Fatty Acid Messenger is Responsible for Inducing Dispersion in Microbial Biofilms." Journal of Bacteriology. Vol. 191, no. 5. 1393-1403. March 2009. (June 12, 2010).
  • Donlan, Rodney. "Biofilms and device-associated infections." Emerging Infectious Diseases. Vol. 7, no. 7. March 2001. (June 4, 2010).
  • Donlan, Rodney. "Biofilms: Microbial Life on Surfaces." Emerging Infectious Diseases. Vol. 8, no. 9. September 2002. (June 9, 2010). (June 12, 2010).
  • Donlan, Rodney. "Biofilm Development and Public Health." Personal interview. June 9, 2010.
  • Drake, Lisa A.; Doblin, Martina A.; & Dobbs, Fred C. "Potential Microbial Bioinvasions Via Ships' Ballast Water, Sediment and Biofilm." Marine Pollution Bulletin. Vol. 55. 2007.
  • Eberl, Leo; von Bodman, Susanne B.; & Fuqua, Clay. "Biofilms on Plant Surfaces." In Kjelleberg, Staffan & Givskov, Michael (Eds.). "The Biofilm Mode of Life." Horizon Bioscience. 2007.
  • Lemon, K. P..; Earl, A. M.; Vlamakis, H. C.; Aguilar, C; & Kolter, R. "Biofilm development with an emphasis on Bacillus subtilis." In T. Romeo (ed.) Bacterial Biofilms: Current Topics in Microbiology and Immunology. Springer-Verlag Berlin Heidelberg. 2008.
  • Montana State University Center for Biofilm Engineering. "Biofilm Basics." 2008. (June 3, 2010).
  • "Otitis Media (Ear Infection)." National Institute on Deafness and Other Communication Disorders, National Institutes of Health. June 7, 2010. (June 12, 2010).
  • "Periodontitis." no date. (June 7, 2010).
  • Prince, Roger. "Bioremediation of Marine Oil Spills." Trends of Biotechnology. Vol. 15, issue 5. May 1997. (June 12, 2010).
  • Stewart, Philip S. & Costerton, William J. "Antibiotic Resistance of Bacteria in Biofilms." The Lancet. Vol. 358. 135-38. July 14, 2001. (June 12, 2010).
  • Sturman, Paul. "Biofilm Development in Industrial and Natural Environments." Personal interview. June 8, 2010.
  • Waldman, Scott. "One Small Step Toward Helping Astronauts." May 13, 2010. (June 3, 2010).
  • Watnick, Paula & Kolter, Roberto. "Minireview: Biofilm, City of Microbes." Journal of Bacteriology. Vol. 182, no. 10. 2675-2679. May 2000. (June 2, 2010).
  • "What is Cystic Fibrosis?" National Heart, Lung and Blood Institute, National Institutes of Health. June 23, 2009 (June 6, 2010).
  • Zona, Kathleen (Ed.). "What is Microgravity?" National Aeronautics and Space Administration. Feb.13, 2009. (June 13, 2010).