ABSTRACT
Transit time, fluid intake, diet, and overall gut health all influence stool consistency. However, the relationships between the gut microbiota, metabolome (microbial metabolites), and stool consistency in infants and young children remain poorly understood. In this study, we analyzed the microbiota and metabolome of 618 stool samples from children aged 2.5 months (n = 360), 6 months (n = 229), 14 months (n = 274), and 30 months (n = 169) from the FinnBrain Birth Cohort Study, correlating these data with stool water content and parent-reported stool consistency. We found that breastfeeding had the strongest association with both stool consistency and fecal water content. We observed that the concentrations of newly discovered microbial bile acid amidates were associated with constipation and negatively correlated with stool water content. Partial versus exclusive breastfeeding was further linked to higher levels of specific bile acid amidates through mediation by constipation. Bile salt hydrolase, an enzyme involved in deconjugating primary bile acids and generating novel microbial bile acids, was also predicted to be negatively associated with stool water content. In addition, short-chain fatty acids (SCFAs), particularly acetic acids, were positively associated with stool water content, whereas branched SCFAs showed a negative association. These findings suggest longer transit time appeared to allow more extensive bacterial metabolism of microbial metabolites, including the transformation of bile acid amidates. Here, we also observed that the relative abundances of specific genera such as Clostridium , Hungatella , and Lactobacillus were associated with firmer stool consistency. Overall, our results highlight the importance of documenting stool consistency in fecal metabolomics and microbiome research, and provide new insights into how breastfeeding, microbial metabolism, and gut transit time shape early-life gut development.
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