Lung Microbiome: The essential to know

Yousser Mohammad1*

1Department of Internal Medicine, Section Pulmonary, Syrian Private University, Syria

• The microbiota , is defined as all microorganisms that inhabit a particular site or place, eg, the gastrointestinal (GI) tract, skin, or airways.(mostly bacteria, but also virus, protozoa and fungi)

• The term microbiome consists of the genes these cells harbor. This term was coined by Joshua Lederberg in 2001.

how ever the two terms are used interchangeably1.

The Human microbiome project(HMP), had been launched in the 21st century, as an outcome of the Genome Wide Survey. Beside human genes, the new generations gene sequencing methods, surprisingly demonstrated the presence of huge number of other genes characterizing commensal microbes living in symbios with human genes2.

- First sequencing of gene 16s rRNA was performed in the gut(GI). Then Skin, and oropharynx .

- Lungs were not initially selected for the HMP , They were originally believed to be sterile because germs were not discovered by traditional methods of culture of Broncho -Alveolar Lavage(BAL) , or brushing or lung tissue. But Genotyping and sequencing of 16s rRNA in BAL &Brushing during endoscopy, surprisingly discovered a huge microbiota.

- Microbiome projects for lungs have been launched with the goal of understanding the roles that these symbionts play and their impacts on human health2,3.

- In a state of the art article of the ATS 2014: Authors highlighted that: Characterization of the microbiome can be done by sequencing regions of a conserved gene, such as the hypervariable regions of the 16S r RNA gene. This lead to different sequences in different microbes. The unit for research is the taxon, each microbe has taxons , characterized by operational taxonomic unit (OTU)3. The microbiota plays a particularly important role in the development and functional integrity of the immune system. Shifts or perturbations in the microbiota can lead to disease4. The lung microbiome varies in health and disease . And there is daily interaction between lung microbiome and environmental microbiome2,3,4.

1) Asthma and allergies : Interaction of lung microbiome with the environmental microbiome, has now been shown to be associated with the development of asthma and other allergic respiratory disorders, the diversity and abundance of microbial exposure correlates inversely with the development of childhood asthma3,5; This could explain the hygiene hypothesis: hypothesizing that individuals with a higher number of older siblings and thus living under “less hygienic” conditions have less asthma.

- Microbiome could also have a protective role: Maternal exposure to Acinetobacter lwoffii also protected offspring from asthma .

- Antibiotic overuse:

In the ISAAC study , antibiotic use during the first year of life is correlated with higher incidence of asthma onset6, Antibiotic are shown to alter the GI microbiome which plays a role in immunity and inflammation,leading to more atopy and asthma7.

2- COPD, may be associated with perturbations of the lung microbiome4:

COPD is in part mediated by dysregulated immune responses to cigarette smoke and other environmental insults. Recent reports have identified diverse bacterial communities in the human lung that may change in COPD. And that perturbation in microbiome explains why inflammation persists after stopping smoking

3) Cystic fibrosis: Microbiome alteration plays a role in cystic fibrosis4.

Microbiome studies are expected to help to develop markers for diseases diagnosis and follow up, and new therapeutic options , helping on personalized medicine5.

The limitation is: It is challenging to have 100% contaminant free DNA, in BAL-Brushing and tissue of the lung during fibroscopy3,4.

Conclusion: Sequencing of 16 s rRNA gene surprisingly showed that Lungs are not sterile. The lung microbiome as well as environmental microbiome may all be important in lung health and disease. The microbiota plays a particularly important role in the development and functional integrity of the immune system. Shifts or perturbations in the microbiota can lead to disease. Microbiome manipulation is expected to play important role in personalized medicine: new biomarkers for diagnosis, But also Targeted therapy (like for IPF), and for asthma and allergies treatment and prevention.

  1. Luke K Ursell, Jessica L Metcalf, Laura Wegener Parfrey, et al. Defining the Human Microbiome. Nutr Rev. 2012 August ; 70(Suppl 1): S38–S44. doi:10.1111/j.1753-4887.2012.00493.x.
  2. Peter J Turnbaugh, Ruth E Ley, Micah Hamady, et al. The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature. 2007 October 18; 449(7164): 804–810. doi:10.1038/nature06244
  3. Lijia Cui, Alison Morris, Laurence Huang, et al. Twigg III, Erika von Mutius9,Elodie Ghedin. PITTSBURGH LUNG CONFERENCE. The Microbiome and the Lung. Ann Am Thorac Soc. 2014; Vol 11 Supplement 4: pp S227–S232, DOI: 10.1513/AnnalsATS.201402-052PL Internet address:
  4. Marc A Sze, James C Hogg, Don D Sin. Bacterial microbiome of lungs in COPD. International Journal of COPD. 2014; 9: 229–238.
  5. Cope EK. Host-microbe interactions in airway disease: toward disease mechanisms and novel therapeutic strategies. mSystems. 2018; 3: e00158-17. .1128/mSystems.00158-17.
  6. Ellwood P, Asher I, Ellwood E, and the Global Asthma Network Steering Group. Global Asthma Network Phase I Manual. Global Surveillance: Prevalence, Severity, Management and Risk Factors. Auckland, New Zealand. 2015.
  7. Stefan A.Unger,DebbyBogaert,. The respiratory microbiome and respiratory infections. Journal of Infection.Volume. 2017; 74, Supplement 1: Pages S84-S88(Below)

Article Info

Article Notes

  • Published on: June 13, 2018


  • Microbiota

  • Gastrointestinal
  • Human microbiome project


Professor Yousser Mohammad
Department of Internal Medicine, Section Pulmonary, Syrian Private University, Syria