The first months of life are marked by rapid changes — not only in babies’ behavior, but also in barely visible biological systems. Four current, not yet peer-reviewed preprints from our research provide insights into how sleep, the gut microbiome, and circadian rhythms are intertwined.
#1 Rhythms in the gut – rhythms in sleep
Mühlematter et al. analyzed stool samples from 162 babies in their first year of life and compared them with objective sleep data. Our results show that certain types of bacteria fluctuate on a daily rhythm – similar to the children’s sleep-wake cycles. With increasing age, this synchronization became more pronounced: more bacteria showed rhythmic patterns that were closely linked to the maturation of circadian organization (Circadian Function Index). This suggests a genuine “clock coupling” between the gut and sleep in the first year of life.
#2 Microbiota rhythms and sleep: Initial longitudinal findings
The study by Kerff et al. went one step further: Babies ages 2, 4, and 6 months were closely observed over a period of 48 hours — using actigraphy, parent diaries, and stool samples. The study showed that some children exhibited a diurnal pattern in bacterial diversity. Particularly exciting: babies with a higher overall diversity of gut bacteria had more robust sleep rhythms. Even though no clear causality can yet be proven, this suggests a connection between the microbiome and sleep maturation, even on a 24-hour scale.
#3 Stool dynamics and the microbiome
A study by Al-Andoli et al. investigated how stool frequency, time of bowel movements, eating and sleeping patterns influence the microbiome. The result: the longer the interval since the last bowel movement, the more diverse the intestinal community. The time of day also plays a role, especially in younger infants. Later in the day, the composition changed measurably. This makes it clear that not only what babies eat, but also when they sleep, eat, and excrete shapes the microbiome.
#4 Melatonin in stool: A new biomarker?
Another study by Al-Andoli et al. shows for the first time that melatonin can be measured not only in blood or saliva, but also in the stool of infants. This finding is more than just a technical novelty: Stool melatonin increases with age, but varies greatly from person to person. It is noteworthy that higher levels are associated with a lower diversity of intestinal bacteria. In addition, correlations with the time of day and the stability of the sleep-wake cycle can be observed. Thus, stool melatonin could become a new marker for the maturation of the circadian system and the interaction between sleep and the intestine.
A review by Zimmermann et al. summarizes how bacteria themselves can produce melatonin or influence its levels. This process could be relevant not only for the gut, but also for the circadian rhythm of the entire body — with potential therapeutic implications for sleep and metabolic disorders.
#5 From the womb to the crib – and the role of breast milk
The study by Markovic et al. provides a unique perspective: over 20,000 hours of movement data from fetuses in the third trimester show that even unborn children develop day-night patterns – closely linked to their mothers’ rhythms. These prenatal patterns continue after birth: fetuses that tended to sleep at night while in the womb also did so as infants.
Another highlight of the study: immediately after birth, breast milk and stool samples were collected to investigate the role of melatonin. Breast milk follows a circadian rhythm – it contains hardly any melatonin during the day, but significantly more at night. This gives the newborn a “time cue” with every meal. Together with the melatonin in the babies’ stool (as a reflection of their intake and own production), the picture emerges that the transition from maternal to child rhythms is hormonally supported.
This research thus rounds out the concept: maternal rhythms already affect the child during pregnancy, and after birth, melatonin in breast milk helps to stabilize the baby’s sleep-wake organization.
References
Rhythms of early life: Gut microbiota rhythmicity and circadian maturation in infants
Mühlematter C, Nielsen DS, Castro-Mejía JL, Walser JC, Schoch SF, Kurth S, in revision, preprint at bioRxiv
The gut microbiota and sleep in infants: a focus on diurnal rhythmicity patterns
Kerff F, Mühlematter C, Adamov A, Fast D, Plüss S, Zimmermann P, Kurth S*, Bokulich NA*, *Shared last authorship, preprint at bioRxiv
Fecal melatonin as a biomarker of emerging circadian maturity and gut microbiota in infancy
Al-Andoli M, Zimmermann P, Schoch S, Markovic A, Mühlematter C, Beaugrand M, Jenni O, Liamlahi R, Walser JC, Nielsen D, Kurth S, preprint at Research Square
Stool Dynamics and the Developing Gut Microbiome During Infancy
Al-Andoli M, Schoch S, Markovic A, Mühlematter C, Beaugrand M, Jenni OG, Liamlahi R, Walser JC, Nielsen D, Kurth S, preprint at bioRxiv
Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders Zimmermann P, Kurth S, Pugin B, Bokulich N, 2024, npj Biofilms and Microbiomes
From womb to crib: How fetal activity patterns in utero reveal postnatal sleep behavior
Markovic A, Mühlematter C, Blume C, Zimmermann P, Kurth S, in revision (at Nature Communications), preprint at bioRxiv
Image: DALLE