When an older adult develops fever, cough, and sore throat, the first battleground of the infection is not the lung but a narrow passage behind the nose. A new study published in iScience by Jolanda Kool of the Dutch National Institute for Public Health and the Environment (RIVM) and colleagues shows that this nasopharyngeal niche, rather than the nearby oropharynx, carries the clearest microbial and immunological fingerprints of influenza-like illness in people aged 60 to 88. The findings suggest that the two upper-airway compartments, though anatomically connected, behave as fundamentally different ecosystems during respiratory infection, with consequences for how scientists monitor and protect aging populations.
Respiratory viral infections remain a leading global cause of illness and death, with influenza virus alone responsible for an estimated 3 to 5 million severe cases and up to 650,000 deaths each year. Older adults bear a disproportionate share of this burden, experiencing substantially higher mortality than younger populations. Vaccination remains the main strategy to reduce influenza disease, but its effectiveness in people aged 60 and older is markedly lower than in younger adults, with most studies reporting protection of roughly 20 to 50 percent in older individuals compared with 60 to 90 percent in younger groups. This gap has created an urgent need for approaches that safeguard aging populations against influenza and other respiratory infections, and the upper respiratory tract microbiota has emerged as a promising target.
The human respiratory tract is divided into upper and lower compartments. The upper tract includes the anterior nares, nasal passages, paranasal sinuses, nasopharynx, and oropharynx, while the lower tract comprises the larynx, trachea, bronchi, and alveoli. Because the upper tract is the primary entry point for inhaled air and hosts the highest microbial density, it acts as a gatekeeper to the lower airways. Within it, the nasopharynx and oropharynx provide distinct environments shaped by immune activity, mucus flow, temperature, tissue architecture, and cell composition. Bacterial biomass varies dramatically by site, with around 1,000 bacteria in the nasopharynx and up to 1 million in the oropharynx. Disruption of these ecosystems by viral infection can reduce colonization resistance, worsen local inflammatory responses, and facilitate the spread of pathogens into the lower respiratory tract, leading to more severe disease.
Although the role of the upper-airway microbiome in respiratory health is increasingly recognized, evidence on how aging shapes these communities remains limited. Studies in older adults have shown reduced oropharyngeal diversity, changes in community composition, and a loss of niche distinctness compared with younger individuals. These age-related shifts are discussed in relation to immunosenescence and chronic low-grade inflammation and may contribute to the higher burden of respiratory infections in older adults. However, little has been known about upper-airway microbiota dynamics during acute respiratory illness in this population and its interaction with the host, leaving an important gap in understanding infection risk and resilience.
To address this gap, Kool and colleagues analyzed nasopharyngeal and oropharyngeal swabs from 221 participants aged 60 to 88, including 136 who experienced influenza-like illness during the 2014-2015 season and 85 who reported no symptoms and had no detectable respiratory pathogens at the time of sampling. The researchers characterized microbial composition, bacterial load, and cytokine patterns in a healthy state and determined the impact of acute infection. Influenza-like illness was defined according to the Dutch Pel criteria, which categorize individuals as having the condition based on the presence of fever of at least 37.8 degrees Celsius and at least one additional symptom such as headache, myalgia, sore throat, coughing, rhinitis, or chest pain. Swabs were collected within 72 hours of reported symptoms, and the causative viruses and bacteria were identified using multiplex ligation-dependent probe amplification and conventional bacterial culture.
Cluster analyses of the nasopharyngeal samples revealed three distinct community state types based on their dominant genera. The first was dominated by Moraxella, the second was characterized by Haemophilus, Staphylococcus, and Streptococcus, and the third was dominated by Corynebacterium and Dolosigranulum. The Moraxella-dominated cluster had the lowest diversity and evenness, while the other two were the most diverse. Beta-diversity analysis based on Bray-Curtis dissimilarity demonstrated clear separation between the three clusters, confirmed by permutational analysis of variance with an R-squared of 0.41 and a p value of 0.001. In contrast, no meaningful clustering structure was identified in the oropharyngeal samples, suggesting that the two niches have fundamentally different microbial ecosystems.
When the researchers compared healthy and infected individuals, they found that nasopharyngeal microbiome composition differed significantly between the two groups, with a PERMANOVA R-squared of 0.025 and a p value of 0.002, while no differences were observed in the oropharyngeal microbiome. Infected individuals were significantly more frequently found in the Moraxella-dominated and mixed clusters, with 73 percent and 69 percent infected samples respectively, whereas the Corynebacterium and Dolosigranulum-dominated cluster contained an equal mix of healthy and infected individuals. Genus-level differential-abundance analysis revealed that Corynebacterium and Dolosigranulum were more abundant in healthy individuals, while Streptococcus and Haemophilus were more abundant in infected individuals. Together, these findings suggest that the nasopharynx, rather than the oropharynx, is the most reflective niche for compositional change during acute infection.
The immune response mirrored this site specificity. In nasopharyngeal samples, infection was associated with a broad local response, with pro-inflammatory and innate immune markers such as IL-6, CXCL8, CCL2, and CXCL5, antiviral and interferon-associated markers including CXCL9, CXCL10, IFN-lambda1, and granzyme A, the tissue remodeling marker CRP, and the B cell survival factor APRIL all higher in infected individuals. In contrast, the oropharyngeal niche showed only limited changes, with only B-cell activating factor and CRP increased in infected individuals. Systemically, infected individuals had higher levels of pro-inflammatory markers, antiviral and interferon-associated chemokines, and the regulatory cytokine IL-10, while eotaxin, a chemokine associated with eosinophil recruitment and allergic inflammation, was higher in healthy individuals.
To probe the host-microbe interaction, the researchers constructed a network of cytokines identified as increased in infected individuals and the bacterial genera significantly associated with them. Among the genera enriched in infected participants, Haemophilus was positively associated with IL-6 and CXCL10, Streptococcus was positively linked to CXCL9, IL-6, and CXCL10, and Moraxella showed a positive link with CXCL10. In contrast, genera enriched in healthy participants showed only negative associations. Corynebacterium was negatively associated with IL-6, CXCL9, and CXCL10, while Staphylococcus was negatively linked to granzyme A, CXCL9, and CXCL10. This negative association suggests that Corynebacterium is linked to lower local inflammation, consistent with its association with the healthy, Corynebacterium and Dolosigranulum-dominated microbiome.
The nasopharyngeal community composition was also associated with clinical features and symptom burden. The Corynebacterium and Dolosigranulum-dominated cluster was associated with significantly lower odds of several respiratory symptoms, including influenza-like illness symptoms and fever, cough, sore throat, and nasal symptoms. In contrast, the Moraxella-dominated cluster was associated with significantly higher odds of nasal symptoms only, and the mixed cluster showed no significant associations with any symptom. These findings suggest that community membership is more consistently related to local, nasal symptoms than to systemic symptoms. At the genus level, a higher number of cumulative bacterial pathogens detected was positively associated with Haemophilus, while a higher number of total and viral pathogens detected was negatively associated with Corynebacterium. Smoking was positively associated with Porphyromonas and negatively associated with Corynebacterium, aligning with previous reports that Corynebacterium is underrepresented in the nasopharyngeal microbiota of smokers.
Perhaps most strikingly, the researchers found that nasopharyngeal immune responses remained elevated 7 to 9 weeks after infection. Several markers, including IL-6, CRP, IP-10, IL-1Ra, IFN-gamma, and IL-10, remained elevated when compared with healthy controls, indicating ongoing immune activation. Although effect sizes were smaller than in the acute phase and fewer markers reached statistical significance after adjustment, immune levels had not returned to those observed in healthy individuals. A distance-to-healthy centroid analysis showed that most participants moved closer to healthy immune profiles between the acute and recovery visits, but recovery samples remained distinct from healthy controls, indicating that immune normalization was partial rather than complete. This suggests that local immune recovery in the nasopharynx is slower than symptom resolution after acute infection.
The study’s authors note that persistent immune activation at mucosal sites may reflect several biological processes. Epithelial repair and restoration of barrier integrity can require sustained chemokine signaling, residual viral RNA or antigen may continue to stimulate low-level innate responses even after symptoms decline, and immune cell populations recruited during acute infection may remain locally active during resolution. Prolonged but declining interferon and chemokine signaling in the upper airway has been described in both experimental and natural human influenza infection. Such prolonged, microbiome-associated immune activation may delay full recovery of mucosal balance and thereby increase the risk of secondary bacterial infections, particularly in older adults and other vulnerable groups.
These findings show that influenza-like illness in older adults is associated with site-specific immune and microbiome responses in the upper respiratory tract. The nasopharynx emerged as the primary site of biological change, characterized by strong local innate immune activation and associations between specific genera and inflammatory mediators. Communities enriched in infected individuals, including those characterized by Moraxella, Haemophilus, and Streptococcus, were linked to higher levels of pro-inflammatory and interferon-related cytokines, while Corynebacterium and Dolosigranulum-associated communities were linked to lower inflammatory signatures and reduced symptom burden. The oropharyngeal niche showed comparatively limited immune and microbiome changes during infection, suggesting functional specialization between upper airway niches. While the nasopharynx reflected early antiviral immune activation, the oropharynx appeared more stable at both the microbial and immune level, possibly attributed to daily influences such as saliva flow, food intake, and oral hygiene practices that promote resilience and prevent dysbiosis.
More broadly, these results highlight the importance of considering anatomical niche when studying respiratory infections in aging populations, as immune responses and microbial associations differ between the nasopharynx and oropharynx. The results also emphasize the need to monitor mucosal immune responses beyond the acute phase, as prolonged immune activation may delay the restoration of immune and microbial homeostasis and increase susceptibility to secondary infections, particularly in older individuals. Ultimately, identifying microbiome-immune patterns may help enable early risk stratification and more effective preventive strategies in older adults, a population for whom current vaccination approaches leave substantial room for improvement.
Subject of Research: Immunology
Article Title: Linking nasopharyngeal and oropharyngeal microbiota to immune responses during influenza-like illness in an aging population
Article References: Kool, J., Konstanti, P., van Dijken, H., Chu, M. L. J. N., Nanlohy, N. M., Bijvank, E., van Woudenbergh, E., van Beek, J., van Baarle, D., & Fuentes, S. (2026). Linking nasopharyngeal and oropharyngeal microbiota to immune responses during influenza-like illness in an aging population. iScience, 29(11), Article 117929. https://doi.org/10.1016/j.isci.2026.117929
Image Credits: AI Generated
DOI: 10.1016/j.isci.2026.117929
Keywords: microbiome, influenza, aging, nasopharynx, oropharynx, immune response, respiratory infection, immunosenescence, Corynebacterium, Dolosigranulum, Linking, nasopharyngeal
News Source: Morgan Morrow. (October 17, 2026). Nasopharyngeal microbiome reveals immune fingerprints of flu-like illness in older adults. Scienmag.
