Upper respiratory microbiome shows age, sex, and lifestyle impacts, study finds

By Dr. Chinta SidharthanReviewed by Susha Cheriyedath, M.Sc.Aug 5 2024

In a recent study published in the journal Cell, a team of researchers in the Netherlands analyzed nasopharyngeal, oropharyngeal, and saliva samples across various age groups and analyzed the microbial composition of these samples to determine the association between the microbiota in the upper respiratory tract and the health of the host and environmental factors.

Study: Host and environmental factors shape upper airway microbiota and respiratory health across the human lifespan. Image Credit: Kateryna Kon / Shutterstock

Background

A large body of evidence now proves that the microbial communities within the human body play a vital role in human health and disease. However, a substantial portion of the research on the role of microbiota in health has focused on the gut microbiome. Studies have shown that the microbiome of the upper respiratory tract is strongly linked to respiratory health and plays an important role in determining susceptibility to respiratory infections.

The upper respiratory tract microbiota also influences susceptibility to chronic respiratory conditions, including chronic obstructive pulmonary disease, asthma, and cardiovascular diseases. The diverse environments within the respiratory tract provide a variety of ecological niches for microbial communities, which in turn act as a barrier to pathogens and interact with the immune system in the mucosal membranes to protect the respiratory system.

About the study

In the present study, the researchers analyzed the microbiome composition and diversity from nasopharyngeal, oropharyngeal, and saliva samples from a cross-section of the Dutch population to characterize upper respiratory tract microbiome changes across a lifespan and study its associations with the host and the environment.

Saliva and oropharynx samples, representing the oral niche of the upper respiratory tract, were collected from children below and above 10 years of age, respectively, while nasopharyngeal samples were obtained from all the study participants. The researchers ensured that the study population was a true representation of the Dutch population and adequately covered communities that resided in areas where the vaccine coverage was sparse.

Questionnaires were administered to collect socio-demographic data and information on disease status, vaccine coverage, diet, and behavior. Deoxyribonucleic acid (DNA) was extracted from all the samples and processed using polymerase chain reaction (PCR) to amplify the hypervariable region 4 of the 16S ribosomal ribonucleic acid (rRNA) gene.

Additionally, quantitative PCR was used to determine the bacterial load in the samples. A bioinformatics pipeline was employed to infer the amplicon sequence variants and to assign taxonomy. Furthermore, single-plex quantitative PCR was conducted to detect the presence of Streptococcus pneumoniae. This process used primers targeting the pneumococcal iron uptake adenosine triphosphate (ATP) synthase-binding cassette (ABC) transporter lipoprotein and pneumococcal autolysin.

A principal coordinate analysis was performed to assess the overall microbial community composition variation across a lifespan and to observe the differences in microbial community between upper respiratory tract niches. The researchers also calculated the alpha diversity, which is the microbial diversity within the oral and nasopharynx niches.

The study also included a complete linkage hierarchical clustering to examine the community structures within the oral and nasopharynx niches. Additionally, the researchers examined the association between variations in the upper respiratory tract microbiome and environmental characteristics such as sampling season, socioeconomic factors, lifestyle, antibiotic use, diet, household composition, and contact with animals, children, older people, or patients during work.

Results

The study found that the microbiome composition in the upper respiratory tract, especially in the nasopharyngeal niche, was strongly correlated with and underwent maturation with age. The upper respiratory tract microbiota also exhibited distinct patterns within different niches.

The microbiome in the nasopharynx of younger individuals had a higher density of total bacteria but lower diversity. In comparison, the nasopharynx niche exhibited the opposite pattern, with higher diversity and lower overall bacterial density in older individuals. The abundance of commensal bacteria such as Dolosigranulum pigrum and Corynebacterium species in the nasopharynx was also seen to vary with age.

Furthermore, the density and diversity of bacteria in the nasopharyngeal niche stabilized between 15 and 24 years of age, indicating that the development and maturation of the microbiome in the nasopharynx continued into early adulthood. This finding was surprising considering the fact that the gut microbiome stabilizes by the age of 5 years.

Sex-related differences in the microbiome diversity within the upper respiratory tract were also observed, with a higher abundance of bacteria such as Lawsonella clevelandensis, Finegoldia magna, and Corynebacterium and Peptoniphilus species being more abundant in males than females.

In contrast, the composition and diversity in the oral niche showed stronger associations with tobacco smoking, alcohol consumption, and antibiotic use. Past and active smokers showed low microbial diversity in the oral niche.

Conclusions

To summarize, the study examined the microbial composition and diversity within the upper respiratory tract's oral and nasopharyngeal niches. The results suggested that the upper respiratory tract microbiome showed development and maturation patterns associated with age and sex in the nasopharyngeal niche, while in the oral niche, the associations were with lifestyle factors such as tobacco, antibiotics, and alcohol use.