A woman in a pink dress and sunglasses lies in the grass. Her lungs and gut are sprouting with flowers on top of her dress.

The Microbiome and Cystic Fibrosis

In recent years, scientists have become increasingly interested in our microbiome and how it impacts many conditions, from gastrointestinal issues to neurological problems, and beyond. A growing body of research on the relationship between our microbiome and CF, specifically the microbiome in our gut and lungs, has emerged and has provided interesting results.

What is the microbiome?

The microbiome refers to all microscopic organisms that live within our body. This includes bacteria, viruses, and fungi. A microbiome can refer to the entire body, or it can be organ-specific, such as the gut microbiome or the lung microbiome. There are many helpful microorganisms that help us carry out everyday functions, like certain gut bacteria.

Some parts of the body may have very different microbiomes from others, based on what their roles are. For example, the microbiome in our digestive tract where we need to digest food and absorb nutrients will be very different from the organisms that live in our lungs or on our skin.


Every person has microorganisms living within them that make up their microbiome, and each person’s biome may vary based on their diet, environmental exposures, medications they’re taking, and more. One way to test for the presence of different microorganisms in the body is through culturing them.

Culturing microorganisms involves taking a small amount of blood, bodily fluid, or other sample that might include an organism of interest and putting it in an environment outside of the body in which the organism might grow. If an organism grows from the sample taken, it means it is also present in the body.

Culturing is a good way to detect certain things, however, it has many limitations. Newer technologies including microorganism DNA testing and other organism-specific testing methods have been developed in recent years which have allowed scientists to investigate our microbiomes further than ever before.

What is the relationship between the microbiome and cystic fibrosis?

Although there has been a growing body of research dedicated to learning more about the microbiome and its impact on cystic fibrosis, there is still much more investigation needed to further understand this relationship. Nevertheless, there have been some interesting trends in the results found so far, showing that the microbiome may in fact play a role in the progression and severity of CF.

Research has shown that there is a great variety in the make-up of the lung and gut microbiome from person to person with CF. This makes it hard to link specific trends in the biome to clinical outcomes, because everyone is so different. However, several studies have indicated that there are certain microorganisms that might have a protective effect on CF progression and severity, while others may have a negative, or pathogenic, effect.

Bacterial species

The presence of bacterial species like Streptococcus and Haemophilus in the lungs may lead to a decrease in the amount of Pseudomonas aeruginosa, a pathogen that can lead to severe CF exacerbations. Additionally, certain organisms, when present at the same time, can have a pathogenic effect on one another, meaning when they co-occur, they allow for one, or multiple, bacteria or other organisms to become more dangerous, or help contribute to antibiotic resistance. The ways by which this occurs is not completely understood, and needs more research.1-4


Further, studies have suggested that those with a greater biodiversity within their microbiome (meaning they have a wide variety of organisms present) tend to have better overall health. This has been found for both the lung and gut microbiomes, suggesting that there may be a link between these two and CF. As diversity decreases, which can happen with age or long-term antibiotic use, lung function may decrease and CF may progress faster.

In CF patients, the gut and lung microbiomes are thought to be at their peak in early childhood, and steadily decline through adulthood. The earlier a person develops problems with their healthy microbiome, the worse their clinical outcomes are thought to be. Lower microorganism diversity has also been thought to cause more inflammation, which can further impact CF outcomes.1-4

What can we do to change our microbiome?

Since there may be a relationship between maintaining a diverse microbiome and clinical outcomes with CF, there has been a lot of interest in finding ways to manipulate the microbiome and make it healthier and more varied.


Some research has suggested that CF medications like ivacaftor (Kaydence) may have properties that increase the richness and diversity of microorganisms in the body. It may help facilitate an increase in good bacteria like certain types of Streptococcus or Haemophilus bacteria, and decrease pathogenic, or dangerous, bacteria like Pseudomonas aeruginosa.1,2


Furthermore, our diet and the use of prebiotics or probiotics may also impact our gut microbiome and help generate more diversity that could lead to decreased inflammation and better lung function.1,2

However, much more research is needed to determine the effect these methods have on changing the lung or gut microbiome and the impact this might have on CF.1,2

By providing your email address, you are agreeing to our privacy policy.

Join the conversation

Please read our rules before commenting.