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We are thankful for the letter of Drs Dickson and Cox in response to our paper on the effect of the intestinal microbiota on host responses during pneumococcal pneumonia.1 We do agree that we cannot rule out that the antibiotics we used in our experiments could have influenced the microbiota in the airways and we do underwrite the importance of studying local host–microbe interactions within the respiratory tract during pneumonia. However, some points need to be addressed.
The relative importance of the microbiota of the lower airways, the area where alveolar macrophages reside, is a matter of debate. …