Natural lung bacteria offer clues on treating airway infections, says expert

January 9, 2018 by Francesca Davenport, Caroline Brogan, Imperial College London
Credit: Imperial College London

Further research on the lung microbiome could uncover new, more effective approaches to managing lung infections, according to an Imperial researcher.

An Imperial College London expert has highlighted the importance of studying microorganisms, known as the lung microbiome, in helping us to understand and manage airway infections.

Professor William Cookson, from Imperial's National Heart and Lung Institute, spoke to Francesca Davenport about his Nature Reviews Microbiology paper, to explain how further studying the microbiome could help to improve the management of lung infections and avoid problems associated with antimicrobial resistance (AMR).

What were your reasons for writing the review paper?

Lung infections are amongst the most important causes of death and disability in the world, but progress in diagnosing and treating them has lagged far behind infections of other organs such as the gut and skin. In particular, we have only just begun to use DNA sequencing to identify the bacteria and funguses that we all carry in our airways.

Our article highlights the size of this problem, and shows how modern microbiome research has the potential to improve the prevention and treatment of common lung diseases.

How much do we currently know about the lung microbiome?

Until recently, scientists incorrectly believed that the lungs and airways were sterile, and so the Human Microbiome Project and similar research ventures almost completely ignored the lungs.

Now we know the surfaces of the airways have a resident population of microbes, known as the microbiome, which is similar in density to that of the skin and upper intestines. We also know these microbial communities are disturbed in common lung diseases like chronic obstructive pulmonary disease (COPD), which is common in smokers, and asthma.

However, other than the few organisms that commonly cause lung infections, we know surprisingly little about the different bacteria that live there. We don't yet know how members of the microbial community interact with each other, and how they might control inflammation and protect the airway linings from disease.

What are the specific challenges to researching the lung microbiome?

It is more difficult to get samples from the airways than easier to access areas like the skin and bowel. Subjects can cough up mucus for testing, or clinicians can introduce a fine tube, or bronchoscope, into the airways.

Difficulties arise because lung samples contain many human cells, and the presence of high concentrations of human DNA means special techniques are necessary for the bacterial signals to be seen.

The resident microorganisms in the lungs might provide important clues. Credit: Imperial College London

How do we develop and maintain a balanced and healthy lung microbiome?

There are one or two hundred different kinds of bacteria in the lungs of healthy individuals. Taken across the population there are several thousand different bacterial strains.

Normal colonisation of the airways likely begins after birth, and many of the organisms may initially come from the mother. Over the first two years of life, the microbiome becomes more complex and species-diverse. As with other natural ecosystems, it is likely that it is the diversity of the microbiota in the lungs protects them against with harmful miroorganisms.

A rural lifestyle, for example living on farms, encourages diversity for the microbiome in the lungs as well as the bowel and skin. We have known for some time that rural living protects against asthma and allergies. Living in cities decreases the species-diversity, and also provides many more opportunities for harmful bacteria to spread in the community.

What are the problems with traditional diagnostics and treatments of lung infections?

In our society, lung infections most often arise in people with pre-existing lung diseases such as COPD and diseases such as asthma also show marked abnormalities in their airway microbiome. Infections are usually diagnosed by culturing the bacteria, where specimens from patients are spread on agar plates and incubated for one or more days until the bacteria can be seen as colonies on the plate. However, it is important to treat more quickly than the timeframe allowed by culturing.

Because culturing takes so long, doctors often have to guess at the cause of infections and prescribe broad spectrum antibiotics that wipe out both good and harmful bacteria. As a result, there are approximately 16 million antibiotic prescriptions for respiratory infections each year in the UK; equivalent to a quarter of the population. Thus the timing issue is a major cause of AMR in our society.

What improvements have there been in diagnostics with modern sequencing? How can these improve treatments and avoid problems with AMR?

Once we are sure exactly which organisms cause lung disease, we can use rapid sequencing methods to find if these bacteria are present.

We will also be able to estimate their numbers, tell how dangerous they are, and to which antibiotics they will respond. With improved diagnosis, we can target antibiotics towards the bad bacteria and do less damage to good bacteria. We can also make antibiotics for inhaling directly into the lungs, which will protect against any side effects on other body systems.

Another new approach is to use bacteriophages, which are very small viruses that can infect and destroy bacteria. They may be used to treat infections in conditions such as cystic fibrosis, where almost continuous antibiotic therapy has led to the emergence of 'super-pathogens' that are resistant to almost all existing antibiotics.

We will eventually be able to to replace abnormal airway bacteria with a healthy population of good bacteria, similar to planting a meadow in a field that has previously been stripped of vegetation. Using to recolonise the is hugely effective in treating bowel conditions, and the same is likely to be true for lung and diseases.

In the paper you suggest developing an international lung microbiome project – can you describe how this would work?

Only a few of the thousands of organisms that can be found in normal airways have been isolated and studied in any detail. For sequence-based diagnostics to be effective, we need to know as much as possible about the good and bad in the lungs. International collaborations to isolate and sequence bacterial DNA have hugely improved the diagnosis and treatment of infections in the mouth, skin and bowel. A concerted project will speed up the development of all the potential advances in diagnosis and therapy described in our review.

Explore further: How the microbiome could tackle antibiotic resistant infections in the lungs

More information: William O. C. M. Cookson et al. New opportunities for managing acute and chronic lung infections, Nature Reviews Microbiology (2017). DOI: 10.1038/nrmicro.2017.122

Related Stories

How the microbiome could tackle antibiotic resistant infections in the lungs

August 10, 2017
Understanding how microbes contribute to respiratory health and immunity could help tackle drug resistant infections in the lungs, say scientists.

Glucose in the airways could increase infections in lung disease patients

January 5, 2018
People with the lung disease COPD have higher levels of glucose in their airways, researchers have shown for the first time.

New asthma biomarkers identified from lung bacteria

October 24, 2017
While the microbiome has gained significant attention for its impact on digestive health in recent years, its effect on lung disease has largely remained unstudied.

COPD – changes in the lungs, changes in the microbiome

July 14, 2017
Chronic obstructive pulmonary disease (COPD) can result in structural changes within the lungs over time. Scientists at the Helmholtz Zentrum München have now been able to show that these changes not only affect the organ ...

No consensus on how the microbiome affects tuberculosis, review finds

September 7, 2016
Inconsistencies across studies and sampling errors remain major barriers to understanding how the lung microbiome changes with tuberculosis, according to a review published Wednesday in Clinical Microbiology Reviews.

What's lurking in your lungs? Surprising findings emerge from microbiome research

August 17, 2015
With every breath you take, microbes have a chance of making it into your lungs. But what happens when they get there? And why do dangerous lung infections like pneumonia happen in some people, but not others?

Recommended for you

Breakthrough treatment for crippling jaw disease created

June 20, 2018
A first-ever tissue implant to safely treat a common jaw defect, known as temporomandibular joint dysfunction, has been successfully tested by UCI-led researchers in a large animal model, according to new findings.

Cell-free DNA profiling informative way to monitor urinary tract infections

June 20, 2018
Using shotgun DNA sequencing, Cornell University researchers have demonstrated a new method for monitoring urinary tract infections (UTIs) that surpasses traditional methods in providing valuable information about the dynamics ...

New flu vaccine only a little better than traditional shot

June 20, 2018
A newer kind of flu vaccine only worked a little bit better in seniors this past winter than traditional shots, the government reported Wednesday.

Blood signature could improve early tuberculosis diagnosis

June 19, 2018
A gene signature in the bloodstream could reveal whether someone is going to develop active tuberculosis (TB) disease months before symptoms begin. Such a signature has now been developed by a team led by the Francis Crick ...

Scientists uncover a factor important for Zika virus host species restriction

June 19, 2018
Princeton University researchers Qiang Ding, Alexander Ploss, and colleagues have identified one of the mechanisms by which Zika virus (ZIKV) circumvents immune control to replicate in human cells. The paper detailing this ...

Toothpaste and hand wash may contribute to antibiotic resistance

June 19, 2018
A common ingredient in toothpaste and hand wash could be contributing to antibiotic resistance, according to University of Queensland research.

1 comment

Adjust slider to filter visible comments by rank

Display comments: newest first

AnneGallen
not rated yet Jan 12, 2018
lung microbiome, I really enjoyed learning about this fascinating thing as I never knew that in airways such unknown species are working. Besides that, I am hoping for the best solution to treat Asthma and COPD. though there are some basic treatments available in medical in medical science to control the Asthma. Some other natural treatments like Salt therapy which gaining popularity among the users due to its natural effctiveness, in fact, some stores like "Saltair.fi" are selling a device to use this therapy at home. But still, I wish Scientist could discover the best treatment for COPD.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.