Enrichment of oral-associated microbiota in bronchoalveolar lavage fluid is associated with altered immune markers in aspiration pneumonia, with Gemella linked to in-hospital mortality

Background Aspiration pneumonia (AP) is common and life-threatening among hospitalized patients, particularly older adults. However, the lower respiratory tract microbiome in AP and its clinical relevance remain incompletely understood. Methods We conducted a single-center retrospective study of intensive care unit patients and profiled bronchoalveolar lavage fluid (BALF) microbiota using metagenomic next-generation sequencing (mNGS). BALF samples were obtained from 49 patients with AP and 23 patients with community-acquired pneumonia (CAP). Alpha diversity (Shannon/Simpson) and beta diversity (Bray–Curtis; PERMANOVA) were compared between groups. Differentially abundant taxa were identified and correlated with inflammatory and immune markers using Spearman correlation with false discovery rate (FDR) correction. Within AP, associations between Gemella detection and in-hospital mortality were assessed using logistic regression adjusted for age, APACHE II score, and CD3 ⁺ percentage. Results Alpha diversity was significantly higher in AP than in CAP (Shannon p = 0.008; Simpson p = 0.0068). In contrast, the overall community structure showed no significant difference between the groups (PERMANOVA R² = 0.022, p = 0.066). AP samples were enriched in oral-associated genera including Streptococcus and Rothia and depleted in Acinetobacter and Stenotrophomonas . Streptococcus abundance correlated positively with lactate, procalcitonin, and NK cell percentage, and negatively with CD3 ⁺ and CD8 ⁺ T-cell proportions. Within AP, overall microbiome profiles were broadly similar between survivors and non-survivors; however, non-survivors had higher Gemella abundance and a higher detection rate (30.8% vs 4.3%, Fisher’s exact p = 0.026). Gemella detection was associated with in-hospital mortality in univariate analysis and showed a non-significant trend after multivariable adjustment (adjusted OR 6.81, 95% CI 0.67–69.58; p = 0.106). Conclusions AP was characterized by enrichment of oral-associated taxa in BALF that were associated with inflammatory and cellular immune alterations. Gemella abundance and detection may be linked to in-hospital mortality in AP, warranting validation in larger prospective cohorts.