| Summary: | Infectious diarrhoeal diseases remain a substantial health burden in young children in low- and middleincome countries. The disease and its variable treatment options significantly alter the gut
microbiome, which may affect clinical outcomes and overall gut health. Antibiotics are often
prescribed, but their impact on the gut microbiome during recovery is unclear. Here, we used 16S
rRNA sequencing to investigate changes in the gut microbiota in Vietnamese children with acute
watery diarrhoea, and highlight the impact of antibiotic treatment on these changes. Our analyses
identified that, regardless of treatment, recovery was characterised by reductions in Streptococcus
and Rothia species and expansion of Bacteroides/Phocaeicola, Lachnospiraceae and
Ruminococcacae taxa. Antibiotic treatment significantly delayed the temporal increases in alpha- and
beta-diversity within patients, resulting in distinctive patterns of taxonomic change. These changes
included a pronounced, transient overabundance of Enterococcus species and depletion of
Bifidobacterium pseudocatenulatum. Our findings demonstrate that antibiotic treatment slows gut
microbiota recovery in children following watery diarrhoea.
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