Respiratory infections alter the composition of the murine gut microbiota

Alterations in the composition of the gut microbiota have profound effects on human health. Consequently there is great interest in identifying, characterising and understanding factors which initiate these changes. Despite their high prevalence, little is known about how lung infections impact the gut microbiota. The aim of this study was to investigate the effect of respiratory viral infection on the gut microbiota. Mice were infected intranasally with the common respiratory pathogen Respiratory Syncytial Virus (RSV) and the gut microbiota assessed by 16S rRNA gene sequencing. Lung infection significantly altered gut microbiota diversity, with an increase in Bacteroidetes and a concomitant decrease in Firmicutes. Although the increase in Bacteroidetes was consistent across several experiments, differences were observed at the family and operational taxonomic unit (OTU) level. This suggests there is a change in gut conditions after lung infection that favours Bacteroidetes outgrowth but no specific effect on individual families. Similar microbiota changes were seen after influenza virus infection suggesting that the effects were not virus specific. The changes in the gut microbiota do not appear to be immune mediated as no increase in gut inflammation or change in colonic cytokine levels was observed. However viral infection did cause an increase in airway and colonic Muc5ac levels which, owing to the important role mucus plays in the competitive gut environment, may explain the changes in microbiota composition observed. In conclusion this study demonstrates that lung infections may influence the gut microbiota and that the “gut-lung axis” may in fact be bidirectional.