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The changing microflora of bacteria in the lungs

The views expressed are those of the author and are not necessarily those of Scientific American.


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Any part of the human body that is open to the outside world it available for the colonisation of bacteria. While this blog has covered bacteria in the gut, the vagina and the throat, one area I’ve neglected to cover is the bacteria that get into the lungs. As the company I currently work for is involved in respiratory research I was rather excited to find a PLoS One paper that looked at how the population of lung bacteria changes in respiratory disease.

The respiratory disease in question is COPD, which stands for chronic obstructive pulmonary disorder. It’s caused primarily by smoke getting into the lungs, from tobacco or industrial processes, and leads to narrowed airways and overproduction of mucus. It’s not really curable, although many medications exist to help people live with it, and to slow down the progression of the disease.

Healthy lung and a lung with COPD - from the National Heart Lung and Blood Institute, credit below.

In order to explore which bacteria were present in healthy smokers, COPD patients, and people who had never smoked, researchers used massively parallel pyrosequencing. This technique allows the bacteria to be identified by their DNA without the need for producing bacterial cultures, so even ‘unculturable’ bacteria can be identified.

In the smokers, never-smoked, and patients with mild COPD a far wider range of bacterial diversity was found than in patients with severe COPD who tended to have a much smaller number of different bacterial species. There were no specific bacterial species common for each group, the major difference appeared to be in diversity. The most commonly found bacteria in the healthy subjects included PseudomonasStreptococcusPrevotella and Fusobacterium which the researchers suggested may make up a core lung microbiome.

As a secondary analysis, the researchers also looked at bacterial populations in very specific areas of the lung, and found that there was no homology of bacterial species throughout the whole lung. In some cases one small microenvironment in the lung could be exclusively populated by one form of bacteria. Samples from different places in the lungs could therefore result in a very different view of the bacterial microflora in the lungs.

Lung biopsy showing normal lung tissue - from the Columbia University Medical Centre, credit link below

Although this research is fascinating, it is important to note that despite differences seen the microflora cannot be used as a diagnostic for COPD as there were no exclusive differences seen in this small sample size between diseased and healthy lung flora. The small patches of different microflora may suggest areas that are more prone to developing COPD and other respiratory diseases, in the same way that patches of different skin bacterial flora can be more prone to dermatitis and skin diseases.

Credit link for image 1

Credit link for image 2

Reference: Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, et al. (2011) Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD. PLoS ONE 6(2): e16384. doi:10.1371/journal.pone.0016384

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. greenhome123 6:10 pm 10/30/2012

    I accidentally inhaled a little piece of spinach when I was eating a salad the other day, and it made me have bad breath for a few days afterward. I was thinking that there was probably some sort of bacteria growing on the piece of spinach in my lungs that was making my breath smell. It seems to have gone away, but it is nice to see that research is being done on different types of bacteria in the lungs. I would like to see more research on this to see if there are any types of bacteria that are beneficial to have in the lungs. Also, I would like to see if there are any types of fungus that live in the lungs.

    Link to this
  2. 2. ironjustice 10:33 pm 10/30/2012

    I’ve always wondered whether the lungs wouldn’t be just like any other ‘surface’ exposed to smoke , in which it gets covered with a bit of tar and therefore could , in theory , be ‘degreased’ by a good soaking in ‘natural orange degreaser’ and a rinse and flush . The citrus would be a good anti-bacterial at the same time.

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  3. 3. S.E. Gould in reply to S.E. Gould 3:48 am 11/5/2012

    @greenhome: these bacteria may not be strictly beneficial, but they certainly aren’t harmful as they exist in healthy lungs. They may even help to keep out more harmful strains.
    Not to
    @iron: lungs do indeed get covered with tar, however the inner surface of the lungs is fairly delicate and would not respond well to harsh cleaning treatments. Not to mention the logistical problems of ‘cleaning out ‘ the lungs!

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  4. 4. BeneficialB 11:07 am 08/28/2013

    This is an interesting topic, and it was one that my research colleagues speculated about for quite awhile. The reason for their interest was that probiotic treatment was really effective in models of lung diseases. @greenhome123: Yes, it does appear that some bacteria can be more helpful than others in the lung.

    Link to this

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