Fecal microbiome profiling of children with diarrhea from low- and middle-income countries.

is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of . Our results showed that qPCR positive cases were characterized by a significantly higher abundance of and other , alongside a lower abundance of the probiotic genus . This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to infection. While no significant difference in abundance was found between the culture positive and culture negative groups, genera and were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with infection and a possible correlation between increased pathogenicity and the culturability. These findings might contribute to a more comprehensive understanding of pathogenicity and improving diagnostic methods for .IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with and to investigate the factors affecting culturability. We identified a distinct intestinal microbial profile associated with -infected diarrheal children, observed a correlation between increased pathogenicity and the culturability, and also proposed some potential factors that might promote the growth of strains. These findings might provide evidence for improving diagnostic methods for .