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  • Writer's pictureJoan Rothchild Hardin

FASCINATING BIOFILMS: The Source of Life on Earth - and Misery When They Take Up Residence in Our Sinuses

You may think you know nothing about biofilms but there's one kind of biofilm we all have experience with: the soft, sticky, white biofilm called plaque that, if not removed by good oral hygiene, combines with minerals in your saliva and turns into the hard yellow tartar (AKA tcalculus) that can only be removed by laborious scraping at your dentist's office.

If you've navigated slippery rocks in a stream or wet area, you were walking on slimey biofilms growing on their surface.

Then there's the variety of icky crud that accumulates inside plumbing pipes. Also biofilms.


An article about bacteria and the biofilms they form may sound really disgusting to you. Granted the three examples of biofilms above are indeed on the icky side.

But did you know that the human body is made up of roughly half human cells and half microbes - thousands of microscopic bacteria, viruses, fungi, yeasts, protozoa and archaea (one-celled organisms similar to but different from bacteria). Together, they are known as the human microbiome, a complex ecosystem of microorganisms that functions as another organ in the body. For the most part, all these miniscule critters perform their various jobs while working together to keep us alive and make us who we are as unique individuals.

I'm mentioning this because this complex ecosystem that is the human body may strike you as similar to the ecosystems of biofilms, the topic of this article.

"Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival. For the first time, a consortium of researchers organized by the National Institutes of Health has mapped the normal microbial makeup of healthy humans, producing numerous insights and even a few surprises.

"Researchers found, for example, that nearly everyone routinely carries pathogens, microorganisms known to cause illnesses. In healthy individuals, however, pathogens cause no disease; they simply coexist with their host and the rest of the human microbiome, the collection of all microorganisms living in the human body." NIH, 2012


Biofilms are groups of bacteria, fungi, viruses, parasites and/or other microbes living cooperatively inside a hard shell composed of polysaccharides they create to protect themselves. Once established, these diverse colonies begin to function more like multicellular organisms.

A biofilm is like a busy crowded city. It starts with a few individuals settling in an area. Over time, more settlers arrive and eventually the colony turns into a large, diverse community.

In the same way, a few bacteria select a suitable place to settle on, reproduce and create a biofilm for themselves and the other organisms attracted to the site. It must contain a good supply of the specific foods they all need to grow. All the organisms inside the biofilm live and work together cooperatively, each type performing a different function for the colony. This cooperation lets the bacteria survive in many environments, including soil, deep in the sea, in foods we eat and even in our bodies!

"Infections and inflammation are rarely caused by a single microorganism in the body.  In fact, microorganisms of different species (bacteria, fungi) can clump together to form a functional matrix called biofilm. 

Biofilm Containing a Variety of Bacteria, Fungi & Viruses

"Within a biofilm, one or more types of bacteria and/or fungi share nutrients and DNA and undergo changes to evade the immune system. Since it requires less oxygen and fewer nutrients and alters the pH at the core, the biofilm is resistant to most antibiotics and antifungals. In addition, the biofilm forms a physical barrier that keeps most immune cells from detecting the pathogenic bacteria. 

"Chronic infections from fungi commonly occur in Chronic Rhinosinusitis (“CRS”) and in the gut, where 80% of the immune system exists as well as the body’s microbiome.  The microbiome is composed of trillions of bacteria, fungi, and viruses.  Both sinus and intestinal passages have a mucosal lining that both keep the pathogen from entering the blood system, but also serve as a medium for inflammation and infection. In fact, mucous production can provide nutrients for the microorganism to reproduce. Inside the safety of a biofilm, microbes share nutrients and DNA and undergo changes to evade the immune system. The biofilm’s hard shell prevents most immune cells from even detecting any pathogenic contents. Since it requires less oxygen and fewer nutrients and alters the pH at the core, the biofilm’s contents are protected from most antibiotics." Collado, 2020

Biofilms Protect Their Contents from Antibiotics & Antifungals


When bacteria, fungi and/or viruses enter the sinuses, the immune system reacts to these pathogens by deploying disease-fighting white blood cells called eosinophils. "The immune system immediately releases eosinophils at levels far exceeding those needed to remove the microorganism. This increased inflammation results in damage to the sinus tissue lining. When a rupture occurs, damage to the smooth lining creates cavities in the sinus, where common bacteria (such as Staphylococcus aureus, locally found on the skin, hair, and in the nose) binds to the mucosal pits. With continuous inhalation and over time, additional Staphylococcus bacteria bind to form a protective matrix around bacteria, called biofilm. This matrix attracts additional bacteria and fungi." Collado, 2020

When this happens, you've got chronic rhinosinusitis - and a whole lot of sinus misery.

Now here's the most interesting part!


When the density of individual bacteria becomes dense enough (ie, there are enough of them to form a quorum), they start communicating with each other in complex interactions called quorum sensing. Quorum sensing is a process of cell-to-cell communication that allows a group of bacteria to act together as a group, sharing information about cell density and adjusting gene expression accordingly.

Bacteria's ability to secrete signal molecules enables quorum sensing. "Quorum sensing allows bacteria populations to communicate and coordinate group behaviour and commonly is used by pathogens (disease-causing organisms) in disease and infection processes." Yen, undated

Quorum sensing also takes place between microscopic species - between different types of bacteria, between bacteria and fungi. This lets all the occupants inside a biofilm make group decisions and assign separate tasks to different groups.

A beautiful use of quorum sensing

Here's a short video about the symbiotic relationship between a marine animal and a biofilm colony of bacteria residing inside its body:

The Hawaiian bobtail squid hosts a biofilm colony of Vibrio fischeri bacteria living inside a small pouch, called a light organ, located on the squid's underside. When the bacterial colony gets large enough to quorum sense, it enables the squid to bioluminesce. Working together as a group, the bacterial colony creates luminescence mimicking moonlight and starlight directed downward, obscuring the animal's shadow and making the squid invisible to potential predators while it's feeding at night near the surface of the ocean.

This symbiotic relationship works well for the bacteria too: The squid provide both a safe home and the nutrients the bacteria need to thrive.

A stunning example of a creature using quorum sensing to create a kind of Klingon cloaking device to protect itself! (You can also find some longer videos on Youtube about these little squid and their bioluminescent bacterial colonies.)

This 6 minute TED Talk by the always interesting Bonnie Bassler (an American molecular biologist; Squibb Professor in Molecular Biology; chair of the Department of Molecular Biology at Princeton University; and a Howard Hughes Medical Institute Investigator) gives insight into how one-celled organisms like bacteria operate together to make decisions:


  • Our planet hosts over 5 million different species of fungi, including molds, yeasts and lichens. Scientists have formally described only 120,000 species so far.

  • Like bacteria, fungi also communicate via quorum sensing.

  • Fungi can form mutually beneficial relationships with other organisms. An example is lichens, which are symbiotic organisms made up of a fungus and a photosynthetic partner, such as algae or cyanobacteria. An even more complex example is mycorrhizal underground mycorrhizal networks which help tree roots with nutrient uptake and allow the trees above the network to communicate with each other. "Scientists call the fungi the Wood Wide Web because ‘adult’ trees can share sugars to younger trees, sick trees can send their remaining resources back into the network for others, and they can communicate with each other about dangers like insect infestations." TKSST, 2024

  • Fungi enable the fermentation process in the making of cheese, bread, beer, wine and other culinary items. Different fungi lend their unique flavors and textures to these foods and beverages.

  • Some fungi have the ability to bioluminesce, creating a magical glow in the forest at night.

  • Fungi are able to break down harmful pollutants and toxins in the environment, a process called bioremediation. They can help clean up oil spills, degrade pesticides and remove heavy metals from contaminated soil, offering a sustainable solution to environment challenges.

On the macroscopic level, communication mechanisms related to quorum sensing are used by larger creatures such as ants and social bees. You likely know that honey bees perform a dance for their hive mates to share information about the location of pollen.

"Quorum-sensing strategies may also be applied to robotics and computer technology in sensors, self-organizing networks, and robot swarms." Yen, undated

All pretty fascinating!


"Most bacteria won't hurt you - less than 1 percent of the different types make people sick. Many are helpful. Some bacteria help to digest food, destroy disease-causing cells, and give the body needed vitamins. Bacteria are also used in making healthy foods like yogurt and cheese.

"But infectious bacteria can make you ill. They reproduce quickly in your body. Many give off chemicals called toxins, which can damage tissue and make you sick. Examples of bacteria that cause infections include Streptococcus, Staphylococcus, and E. coli." Agency for Healthcare Research & Quality, 2022

We've unfortunately been taught to regard all bacteria and the matrices they produce (biofilms) as dangerous, disease causing and generally icky. This is a huge misunderstanding. In fact, most bacteria are beneficial, even essential to humans, other creatures, plants and the planet.

Without bacteria and their ability to form biofilms, life on Earth wouldn't have been possible.

Beneficial Biofilms

Using Bacterial Biofilms to Clean Up Toxic Oil Spills in the Waters

A huge oil leak in a body of water is a major environmental disaster, creating serious pollution and killing marine animals, birds and plant life.

An effective way to contain and clean up an oil spill uses bacteria which form biofilms around the oil droplets. One of these beneficial bacteria is Alcanivorax borkumensis. It's found naturally in many of our oceans and thrives on petrochemicals like petroleum.

How's that for amazing?

"Able to feed on both hydrocarbons and alkanes abundant in oil, A. borkumensis creates a specialized biofilm matrix that works like a glue to allow it to attach to oils in the water. When there is an accidental oil spill, A. borkumensis senses the oily chemical droplets and attaches to their surfaces to eventually form biofilms. A. borkumensis produces compounds called biosurfactants, that make the oil easier for other bacteria to use a food source. In this way, A. borkumensis attracts more helpful bacteria, such as Cycloclasticus species to join the biofilm community and help to clean up toxic chemicals, by eating them and using them for energy.

"In a biofilm community, A. borkumensis grows quickly and produces enzymes, which are tiny machines made from protein that can be used to break down food and other compounds into smaller parts. The enzymes produced by bacterial biofilms help to break down the toxic oil spill droplets into smaller carbon compounds. The broken-down oils are used as food by A. borkumensis and its biofilm neighbors." Gudynaite, 2022 

A short video about bacteria that eat oil spills and plastic:

Healthy Soil Makes Healthy Food

Biofilms are also useful in agriculture—the growth of plants for food. Healthy soil contains many types of bacteria and other microbes. One of the beneficial bacteria found in the soil is Bacillus subtilis, which attaches to plant roots and forms biofilms. "B. subtilis biofilms and the host plant work together to keep the plant healthy. The plant supplies sugars and other foods into the soil for B. subtilis. In return, the biofilm protects the plant from potentially harmful microbes, called phytopathogens, by producing compounds that act as antibiotics or antifungals that kill invading bacteria or fungi. B. subtilis also makes enzymes that change nutrients in the soil to make them more accessible to plants, including the key minerals nitrogen and phosphorus. The bacteria live happily in the soil surrounding the root system and improve the growth of crops and other plants."

Thin biofilms produced by bacteria play a surprising role underground, influencing the movement of water and nutrients and even soil chemistry.

"Think of B. subtilis biofilms as natural fertilizers, if you add a mixture of these helpful bacteria close to the roots of corn plants for example, it increases the chances of having healthier plants. Therefore, bacterial biofilms can be an eco-friendly alternative to chemical fertilizers, that often pollute the air and water and release greenhouse gases, bringing hazards to our health and the environment." Gudynaite, 2022 

B. subtilis, also known as hay bacillus or grass bacillus, is a gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants, humans and marine sponges.

Soil-based probiotics - including B. subtilis - are important strains for gut health, particularly in treating IBS. B. subtilis benefits include improved digestive health and IBS symptoms, immune system function and lipid metabolism.

Some Other Beneficial Biofilms

Beneficial bacterial biofilms are found all around us.

In our homes

We can use them to make foods and drinks like kombucha. In the making of kombucha, a biofilm forms as yeast and several strains of bacteria ferment together, feeding on the sugary tea and each other's leftovers. Over time the biofilm produces carbon dioxide (a gas that we breathe out and makes drinks fizzy) and the acids that give kombucha its tangy flavors.

In agriculture

As mentioned above, biofilms on plant roots help plants grow and be protected from harmful disease-causing microbes.

For wildlife

The microbes in slimy green biofilms growing in mudflats along the seashores release molecules called lipids, which become an excellent food source for birds, crabs and worms.

And in our oceans

Biofilms help keep the water clean.

This short video, made for children, is about beneficial biofilms:

See an earlier post about biofilms:

To read more about how life on earth originated with single celled organisms 3.8 to 3.5 billion years ago, the amazing abilities bacteria possess, quorum sensing & the ubiquity of biofilms, see:

Please rate this post & maybe even leave a comment at the bottom of the page. It would be much appreciated & would help spread the word.

© Copyright 2024 Joan Rothchild Hardin. All Rights Reserved.

DISCLAIMER:  Nothing on this site is intended to provide medical advice, diagnosis or treatment.



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