Comparative analysis of oropharyngeal and rectal swab microbiota in critically ill patients: unveiling interconnectivity and identifying marker microbes for severe dysbiosis

Shotgun metabarcoding was used to analyze the microbiota of critically ill patients from the oropharynx and rectum, to compare moderately dysbiotic post-admission microbiota with severely dysbiotic antemortem microbiota associated with patient mortality. Moderately but not significantly decreased diversity indices were observed in patients' antemortem swab microbiota compared to the post-admission ones. An increase in Gram-positive biofilm-forming bacteria was observed in oropharyngeal samples, including Streptococcus oralis, MRSA, Enterococcus faecalis indicating a rise in microbes that could cause primary endogenous infections. Notably, eukaryotic organisms in oropharyngeal swabs of deceased patients doubled, suggesting worsening patient conditions. Although the septic shock rates were found to be 66.6%, there were no significant differences found in the potential pathogen ratios. A notable strain sharing was detected between the oropharynx and intestine, suggesting mutual transmission of microbes in critically ill patients. Microbial biomarkers of severe dysbiosis were pinpointed by analyzing differentially abundant and uniquely emerging species in both oropharynx and rectal swabs, demonstrating strong interconnectivity along the oral-intestinal axis. The oropharyngeal microbiota of deceased patients exhibited the lowest modularity, indicating a vulnerable community structure. Our findings suggest the importance of interventions to diversify and strengthen the oropharyngeal microbiota to improve patient outcomes potentially.