ICU Oral Care Cuts Bacterial Counts and Reveals Microbiome Disruption During Intubation

Ventilator-associated pneumonia (VAP) affects 8–28% of mechanically ventilated ICU patients and dramatically increases mortality, ICU length of stay, and healthcare costs. The oral cavity is a known reservoir for VAP-associated pathogens, and deterioration of oral hygiene during intubation may tip the balance from commensal-dominated microbiota toward pathogen colonization. This study examined whether structured oral care could reduce bacterial burden and explored how intubation itself alters the oral microbiome.

Fifteen ICU patients (mean age 68.9 years, average 11.4 days intubated) were enrolled in a single-arm longitudinal intervention study. Oral swabs were collected from the tongue surface at four time points: before and after oral care, both pre- and post-extubation. Bacterial counts were measured using dielectrophoretic impedance measurement (DEPIM), a validated method correlating well with culture and fluorescence microscopy. Microbiome profiling via 16S rRNA gene sequencing (V3–V4 region) was performed before oral care at both the pre- and post-extubation phases. Oral care was delivered four times daily per Japanese Society of Critical Care Nursing guidelines, using moisturizing gel, toothbrushing, and mucosal cleaning with sponge brushes — without chlorhexidine.

Oral care significantly reduced bacterial counts at both time points (pre-extubation: p < 0.001; post-extubation: p = 0.011). Notably, bacterial counts before oral care were significantly higher during intubation than after extubation (p = 0.009), suggesting ongoing bacterial accumulation while the endotracheal tube is in place. After oral care, counts were similar regardless of intubation status, implying oral care normalizes bacterial burden effectively.

Microbiome analysis revealed that alpha diversity — measured by both the Shannon index (p = 0.0479) and the Chao1 index (p = 0.0054) — was significantly higher pre-extubation than post-extubation, meaning the oral ecosystem becomes less diverse following extubation. Beta diversity analysis (UniFrac-based PCoA) showed no significant difference in overall community composition between groups (p = 0.68). LEfSe analysis identified seven bacterial taxa significantly reduced post-extubation, including the commensal Streptococcus sinensis, suggesting that commensal species that may help resist pathogen colonization are depleted after intubation exposure. Importantly, no patient developed VAP during the study period.

These findings suggest two distinct mechanisms: intubation creates conditions for bacterial accumulation (higher pre-care counts during intubation), while the intubation period itself depletes commensal diversity, potentially leaving the oral cavity more vulnerable to pathogen establishment after extubation. The study supports a role for structured, professional oral care as part of VAP prevention bundles — even without chlorhexidine — and raises important questions about microbiome recovery trajectories following extubation.