Dynamics of the gut microbiome in Shigella-infected children during the first two years of life

Shigella continues to be a major contributor to diarrheal illness and dysentery in children less than 5 years of age in low- and middle-income countries. However, the effects of this invasive pathogen on the developing gastrointestinal microbiome that may predispose children to subsequent infections and illnesses is unknown. In this study, we used 16S rRNA amplicon sequencing to characterize the gastrointestinal microbiota of infants enrolled in a longitudinal birth cohort in Malawi. Children who had at least one Shigella qPCR positive sample during the first 2 years of life (cases) were compared to non-infected controls matched on sex and age. Overall, the species diversity, as measured by the Shannon Diversity Index, increased over time regardless of case status. The microbial community was dominated by Bifidobacterium longum and Escherichia/Shigella at early time points, both decreasing over time, accompanied by higher abundances of Prevotella 9 and Bifidobacterium kashiwanohense by 2 years of age. While no single species was associated with susceptibility to Shigella infection, a significant increase in two species, Lachnospiraceae NK4A136 and Fusicatenibacter saccharivorans, was observed following Shigella infection, when comparing cases to controls, and in Shigella-associated diarrheal samples. Both taxa are in the family Lachnospiraceae, known short-chain fatty acid producers that are associated with improvements in gut health, suggesting a return to gut microbiota homeostasis following Shigella infection. Our findings expand our current understanding of the temporal dynamics of the gastrointestinal microbiota associated with Shigella infection in young children in Malawi and highlight avenues for further exploration to identify protective elements.