Stool Dynamics and the Developing Gut Microbiome During Infancy

Al-Andoli, M.; Schoch, S.; Markovic, A.; Muhlematter, C.; Beaugrand, M.; Jenni, O.; Liamlahi, R.; Walser, J.-C.; Nielsen, D. S.; Kurth, S.

doi:10.1101/2025.06.30.662361

bioRxiv · 10.1101/2025.06.30.662361

Stool Dynamics and the Developing Gut Microbiome During Infancy

Al-Andoli, M.·Schoch, S.·Markovic, A.·Muhlematter, C.·Beaugrand, M.·Jenni, O.·Liamlahi, R.·Walser, J.-C.·Nielsen, D. S.·Kurth, S.

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Abstract

The infant gut microbiome is a dynamic ecosystem that plays a crucial role in early development, influences immune system maturation, and overall health. Recent insights reveal that the gut microbiota undergoes changes across the 24-h day, raising the possibility that it may act as "zeitgeber", helping to regulate the hosts sleep-wake organisation. Despite its importance, timing factors influencing microbiome composition are poorly understood, limiting its use as a health predictor. This study investigates the relationship between stool dynamics (interval since last defecation, collection time of the sample), sleep pressure (interval since last sleep), meal timing and the composition of the gut microbiome. Stool samples from 198 healthy infants, aged 3 to 31 months, were analysed to assess microbial diversity, richness evenness, and abundance. Our findings reveal that longer intervals since the last bowel movement are associated with increased microbial diversity, evenness, and richness. Stool timing is associated with shifts in microbial composition, especially in younger infants, indicating that diurnal microbial fluctuations may become more stable as infants mature. We found that longer periods of wakefulness were associated with increased microbial diversity in early infancy, although this effect appeared to diminish with age. Feeding schedules appeared to have a limited effect on the gut microbiome. Longer fasting before sampling showed no significant associations with most microbial parameters, except for a positive association with microbial richness. At the phylum level, results indicate that infant gut microbial composition is influenced by behaviour and physiology. Longer intervals between bowel movements were associated with shifts in bacterial abundance, with Proteobacteria decreasing and Actinobacteria increasing. Stool timing and meal timing also affected microbial diversity: later sampling times showed higher Actinobacteria levels, and longer fasting was associated with reduced Bacteroidetes. Sleep pressure showed a trend effect with Firmicutes displaying a slight decrease in infants who had been awake longer. Our findings underscore the importance of time-based factors on infant gut microbiome composition.

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Al-Andoli, M., Schoch, S., Markovic, A., Muhlematter, C., Beaugrand, M., Jenni, O., Liamlahi, R., Walser, J.-C., Nielsen, D. S., Kurth, S.. 2025-07-04. Stool Dynamics and the Developing Gut Microbiome During Infancy. https://doi.org/10.1101/2025.06.30.662361

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