  In Nature Microbiology, Palleja and colleagues studied the changes in gut
microbiome composition in twelve healthy men over a period of six months
following an antibiotic intervention. The authors argued that the 'gut
microbiota of the subjects recovered to near-baseline composition within 1.5
months' and only exhibited a 'mild yet long-lasting imprint following
antibiotics exposure.' We here present a series of re-analyses of their
original data which demonstrate a significant loss of microbial taxa even after
the complete study period of 180 days. Additionally we show that the
composition of the microbiomes after the complete study period only moderately
correlates with the initial baseline states. Taken together with the lack of
significant compositional differences between day 42 and day 180, we think that
these findings suggest the convergence of the microbiomes to another stable
composition, which is different from the pre-treatment states, instead of a
recovery of the baseline state. Given the accumulating evidence of the role of
microbiome perturbations in a variety of infectious and non-infectious
diseases, as well as the crucial role antibiotics play in modern medicine, we
consider these differences in compositional states worthy of further
investigation.
