Historically the lungs have always been viewed as a sterile organ. This was later supported by bacterial cultures made from lung fluids, that turned out to be negative. When we take into consideration that bacterial based pneumonia has a 75% chance of having a negative lung culture and the fact that 70% of the human bacteria is not able to grow on standard culture media1, with this knowledge in mind it becomes more likely that the lung is not a sterile organ after all and actually contains it's very own microbiome.
Analysis of the microbiome
Rapid development in this subject area was due to the 16S ribosomal RNA exploitation in the lower respiratory tract. Almost every bacteria has rRNA which can be extracted and sequenced with modern techniques. In this rRNA a region is present that is highly specific and conserved in all bacteria. This is the 16S rRNA, which can be amplified by PCR. Samples taken by broncho-alveolar lavage (BAL) are sequenced for the 16S rRNA part and are scanned and compared to bacterial species from different taxonomic databases. Eventually, the bacteria that were present in the BAL will be detected. While most techniques are focused on bacteria, there are similar methods that can analyse fungi and viruses. These microbiota are of large importance in the pathogenesis in chronic and acute respiratory diseases 2. Research discovered that the lung epithelium is one of the least populated surfaces of the human body with 10-100 bacteria per 1000 human cells3. To bring this in perspective; the most densely colonized surface of the human body, the gut, has 1014 bacteria in total4.
Different lung diseases, different microbiomes
It is discovered that chronic obstructive pulmonary disease (COPD) exacerbations are mostly caused by obtaining new microbes in the lungs 3. Also in asthma, the composition is different compared to that in healthy controls. Asthma patients have more Proteobacteria and Haemophilus species in the bronchial tree, while they had a decreased amount of Bacteroidetes in the airways, all compared to controls5. In cystic fibrosis, the diversity of the airway microbiome is highly dependent on the stage of disease. For example, patients with a higher diversity of microbiota are mostly in an better and earlier stage of cystic fibrosis. Moreover, the composition of the microbiome may influence exacerbations in CF 9. Before we go into detail about different lung diseases, we should discuss the healthy lung microbiome and how it is composed. So let's start with the airway microbiome in the fetus.
Microbiome of a healthy lung
The general hypothesis is that in utero, the fetus has sterile lungs. The first microbiota a baby encounters are the vaginal microbiota of the mother which it will be in contact with during labour; these microbiota include Lactobacillus, Prevotella and Sneathia species. In case of a c-section, the baby will be in contact with the microbiota of the mother’s skin at first, such as Staphylococcus, Corynebacterium, Propionibacterium. Dominguez-Bello et al. supports this with his research.5 In the next few weeks of life there is a change of microbiome in the lung of the newborn shifting from Gammaproteobacteria to mostly Bacteriodetes and Firmicutes species. 5
The adapted island model
This change raised the question how the different microbiota evolved and were eliminated. Consequently, researchers created a model which is one of the most well-accepted hypothesis; The adapted island model. This model depicts the lungs as an island, on which there is no stable population. This small island has three main factors that describes the population, just as a real island: the rate of immigration of another community, the elimination of the island community and the rate of reproduction of the community that lives on the island (figure 1). 6
Immigration
The first factor of the model is immigration to the lower respiratory tract. This population largely originate from microbiota that lives in the oral cavity. Furthermore, there is immigration from the nose and esophagus. Microaspiration occurs constantly in every individual without even noticing it. Studies show that more than half of the lower respiratory microbiome is similar to that of the oral cavity. However, it could be discussed what the amount of contamination is, because a bronchoscope has to pass through the oral to take a BAL from the lungs. Morris et al. showed that there were also microorganisms that were only found in the lower respiratory tract and not in the mouth of healthy persons. These organisms include Haemophilus, Enterobacteriaceae and Tropheryma whipplei. The other microorganisms found in the BAL were organisms that were also commonly found in the oral cavity, for example Prevotella, Streptococcus and Veillonella 7. Another immigration factor is the inhalation of air. The air is full of microbiota and the lungs circulate approximately 7000 to 20.000 liters of air per day. 7 There are differences in indoor and outdoor microbiomes of air; indoor environment have relatively more Corynebacterium, Streptococcus, Staphylococcus, Propionibacterium, Lactococcus and Enterobacteriaceae. On the other hand, outdoor environment consists of relatively more Pseudomonas, Acinetobacter and Sphingomonas.8 Probably, there are some differences of the air microbiome in different areas of the world, which can cause different lung microbiomes in different regions. However, this is an area which has not been investigated thoroughly. So, immigration of microbiota starts during birth by acquiring microbes from the mother. In addition, microaspiration occurs constantly, transferring microorganisms from the mouth, nose and esophagus. Lastly, a large immigration stream of microbes from thousands liters of air that circulate through the lungs each day, plays a role. These factors provide the input of the microbiome of the lungs.
Elimination
In the body, there is a certain homeostasis; so by every input, there must be an output. The elimination of the lung "microbe-community" is quite well-known. Cilia are important in the lungs, because they carry the sputum with small microorganism back where it came from. Also, coughing is a mechanical eliminator of the microbiota. On top of that, there are the innate and adaptive immunity which regulate which microbes should be eliminated.6 The innate immune system in CF has already been discussed in another post. Another elimination factor is the use of antibiotics, which has been shown in patients that get a pneumonia as a side effect from antibiotics. Normally, there is a big heterogeneity of microbiota present in the lungs. There are also pathogenic microbes present in healthy lungs, but in such small measures that is not harmful. However, when the healthy microbiota are killed by the antibiotic and the pathogenic microorganisms, certain resistent bacteria, such as Streptococcus pneumoniae, can grow out and cause pneumonia.
Reproduction
The third part of the model contains the reproduction of the community in the lungs. The physiological circumstances determine which microbes thrive and which will eventually die. These circumstances that influence reproduction are pH, blood perfusion, alveolar ventilation, temperature, microbial competition, host epithelial cell interactions with the microbes, nutrient availability and lastly, the concentration and activation of inflammatory cells. These growth conditions keep the elimination and immigration in balance. Pathogenesis erupt when one of these three key elements falls out of balance. 6
In my opinion, the lung microbiome is going to be important in understanding pathogenesis of the lungs. Real conclusions cannot be drawn from the data that are currently available. Coming years, we need to investigate what a healthy lung microbiome exactly is and what goes wrong in different respiratory diseases. For example, in cystic fibrosis, research has shown that having a large variety of microbiota results in a milder disease stage. This can be a point of interest of a new CF treatment, but this has to be researched more. Furthermore, viruses should be studied in the next years, because currently, there is not much information about the role of the virome in health and disease.
Furher reading about Cystic Fibrosis
Written by Tristan Akershoek
References:
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