Dynamics of the gut microbiome and metabolome in children during and after an infectious diarrheal episode.

INTRODUCTION: Acute diarrhea is associated with significant alterations in the gut microbiota and metabolome. Despite several studies documenting increased levels of histamine and short-chain fatty acids (SCFAs) during diarrheal episodes, the dynamics of these metabolites and microbiota following clinical recovery remain poorly understood, especially in children. METHODS: We evaluated the composition of the intestinal microbiota and the levels of histamine and SCFAs in stool samples from children under five years old with acute diarrhea and after clinical recovery. Additionally, a comparison with a sample of healthy children was included. RESULTS: Our results revealed significant differences in the community structure of the intestinal microbiota among the three conditions. The recovery samples exhibited a greater abundance of genera associated with diarrhea, such as Escherichia-Shigella, Streptococcus, Veillonella, and Akkermansia, as well as genera associated with healthy microbiota, such as Bifidobacterium. Regarding metabolites, butyrate levels decreased following clinical recovery, reaching values comparable to those found in the healthy samples, whereas histamine levels did not differ significantly among the conditions. DISCUSSION: Our findings suggest that, after clinical resolution of diarrhea, the gut microbiota and its metabolites remain significantly different from those observed in healthy children, possibly representing an intermediate stage between diarrhea and a healthy condition. These findings suggest that recovery of the gut microbiota to a healthy condition may take longer and does not necessarily coincide with clinical recovery from diarrhea.