Understanding the nasal microbiome

Electron micrography of Staphylococcus aureus.

The nasal microbiome remains largely unstudied despite its potential importance to many diseases, such as rhinosinusitis, allergies, and staph infection (incuding MRSA).  Staphylococcus aureus is probably the most well-known nasal resident, but simple questions, such as which species of bacteria are most prevalent in the nose, are still not answered.  Understanding all the residents of the nasal microbiome, the influence of our genetics and the environment on defining their populations, and the influence each one has on others may be critically important to preventing diseases such as staph infection, and more research is needed.  Fortunately, a new study out of Johns Hopkins that investigated sets of twins shed light on many of these questions, and was published in Science Advances last week.

The scientists sequenced the nasal microbiomes of 46 identical and 43 fraternal pairs of twins.  First, thy learned that these people’s nasal microbiomes could be classified into 7 different phenotypes or community state types (CST) which broadly described their nasal microbiomes.  These 7 types are defined by their most abundant bacteria, and are as follows: CST1 – S. aureus, CST2 - Escherichia spp., Proteus spp., and Klebsiella spp., CST3 - Staphylococcus epidermidis, CST4 - Propionibacterium spp., CST5 - Corynebacterium spp., CST6 - Moraxella spp., and CST7 - Dolosigranulum spp.   The most common CTS was CTS4 with 29% of the sampled population having that CTS, whereas CTS4 was the least popular, coming in at 6% of the individuals tested.  The researchers noted that many of these bacteria, such as Proteus, were not considered to be important to the nasal microbiome at all, so their dominance in some noses was surprising.  The scientists learned that genetics plays nearly no role in the microbiome community composition, but does influence the overall microbiome population.  In addition, gender influenced the overall population, with women having about half as many total bacteria in their noses as men.

With regards to S. aureus, while it existed in 56% of the individuals studied, it was associated with other bacterial.   For example, the researchers discovered that Dolosigranulum, and Propionibacterium granulosum were negatively correlated to the existence of S. aureus, whereas S. epidermidis was positively correlated with S. aureus abundance.  This lends itself to the idea that specific bacteria can create colonization resistance against S. aureus, and thus could be used to prevent the disease.  The researchers suggest a probiotic should be tested for its therapeutic value in preventing S. aureus colonization, and hopefully they move forward with those trials.

Bacteria in the back of our nose can cause pneumonia

I can tell you from first hand experience, getting pneumonia is not a fun experience. It can actually be quite deadly and results in approximately 1.3 million childhood deaths each year worldwide.  One of the causes of pneumonia is invasive pneumococcal disease, or a fancy way of saying a bacterial infection caused by a specific bacterium, Streptococcus pneumonia (or the pneumococcus). This bacterium often resides in the place where your mouth and nose connect called the nasopharynx. A better understanding of the relationship between this bacteria and the nasal microbiome will allow for a better ability to modulate the bacteria and prevent or treat diseases like pneumonia or meningitis.

Scientists recently published a study in the journal Microbiome that compared the nasopharyngeal microbiome of individuals who were natural carriers of this bacterium and those who were not.  In a study of 40 individuals, 10 were natural carriers of the pneumococcus and 30 were not. Those who were not were inoculated (vaccinated) through their nose with one of two strains of the bacteria.

They found that the natural carriers had greater phylogenetic distances (PD) between the bacteria in their nasopharyngeal microbiome. Phylogenetic distance is a measure of how common the ancestors of specific bacteria are. Those with a greater PD had bacteria that had common ancestors a longer time ago than those with a lower PD.  In individuals who were not carriers and were inoculated with the bacterial strains, those who had a more diverse microbiome resulted in pneumococcal carriage being established, meaning the presence of S. pneumonia, was identified in the nasopharynx.

This study provided a model for studying the interaction between the microbiome of our nose and specific bacteria that are important for disease onset. We often see that in an environment like the gut with a more diverse microbiome, bacteria are unable to colonize and establish a presence, but the opposite is true in this case. Those with a more diverse microbiome often had pneumococcus in their nose after inoculation.  It is proposed that carriage of pneumococcus results in an immunizing event and therefore the ability for the bacteria to become established is beneficial and helps establish better immunity.  Better understanding of this relationship will be important for better immunizations and preventing invasive pneumococcal disease.