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Updated: Jan 16, 2026
High-throughput Measurement of Gut Transit Time Using Larval Zebrafish
Published on: October 23, 2018
Early life gut microbial and metabolic shifts reflected in stool consistency- a gut transit time proxy
Anna-Katariina Aatsinki1,2, Matilda Kråkström3, Katja Salonen3
1Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.
Insights
Breastfeeding significantly impacts infant stool consistency and water content. Microbial metabolites like bile acid amidates and short-chain fatty acids (SCFAs) also play key roles in infant gut health.
Area of Science:
- Microbiology
- Metabolomics
- Pediatric Gastroenterology
Background:
- Gut microbiota and metabolome influence stool consistency, but relationships in early childhood are unclear.
- Stool consistency is affected by transit time, diet, fluid intake, and overall gut health.
Purpose of the Study:
- To investigate the associations between gut microbiota, metabolome, and stool consistency in infants and young children.
- To explore the impact of breastfeeding on infant gut microbial composition and metabolite profiles.
Main Methods:
- Analysis of 618 stool samples from children aged 2.5 to 30 months.
- Correlation of microbiota and metabolome data with stool water content and parent-reported consistency.
- Utilized data from the FinnBrain Birth Cohort Study.
Main Results:
- Breastfeeding showed the strongest association with stool consistency and fecal water content.
- Microbial bile acid amidates were linked to constipation and reduced stool water, while SCFAs showed mixed associations.
- Specific bacterial genera (e.g., Clostridium, Lactobacillus) were associated with firmer stools.
Conclusions:
- Stool consistency documentation is crucial in fecal metabolomics and microbiome research.
- Findings offer insights into how breastfeeding, microbial metabolism, and gut transit time influence early-life gut development.
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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