Rectal swabs in critically-ill patients provide discordant representations of the gut microbiome compared to stool samples

Dysbiosis of gut microbial communities has been proposed to contribute to the evolution and outcome of critical illness, but the actual mechanisms have not been fully characterized. Among critically-ill adults, specific compositional profiles, such as the ratio of Bacteriodetes to Firmicutes phyla (B/F ratio) have been associated with in-hospital mortality. Thus, detailed characterization of gut communities during critical illness may help define new mechanisms and targets for intervention. However, obtaining fecal (stool) samples for research purposes during acute illness is challenging and rectal swabs have been proposed as an alternative that is safe, non-invasive, and easy to perform. In this prospective, observational cohort study, we enrolled mechanically-ventilated patients with acute respiratory failure of any cause and collected stool and rectal swabs. Discordance in alpha and beta diversity and bacterial composition was noted between sample locations, which should raise caution in in the design and analysis of gut microbiome studies in critically-ill patients.