How Does the Preterm Gut Microbiota Develop?

Preterm birth occurs during a period of rapid gastrointestinal and immune development. At the same time, microbial colonisation begins under conditions that differ considerably from those experienced by term-born infants.

During the first weeks of life, the gut microbiota of preterm infants is typically less diverse and more variable between infants, with delayed establishment of obligate anaerobic bacteria³^– ⁴. These differences reflect both biological immaturity and the clinical environment in which colonisation takes place.

Longitudinal studies have moved the field beyond these early snapshots, showing that the microbiota changes continuously after birth, with recurring patterns of ecological succession but considerable variation in pace and pattern between infants ^1-3,5.

How does the microbiota develop?

A different starting point

During the first weeks after birth, the gut microbiota of preterm infants typically differs from that of term-born infants. Studies in very preterm (<32 weeks of gestation) and extremely preterm (<28 weeks of gestation) infants receiving neonatal intensive care³, ⁴ report lower alpha diversity and considerable variability in composition between infants.

Early microbial communities are frequently enriched with taxa common in hospitalised preterm populations, including Staphylococcus, Enterococcus and members of the Enterobacteriaceae family, with delayed establishment of obligate anaerobes such as Bifidobacterium and Bacteroides.²⁻⁵

These are recurring patterns across preterm cohorts, not a profile shared by every infant. Differences are apparent from early life, and composition continues to change throughout hospitalisation and beyond.³⁻⁵

Development through ecological succession

The microbiota does not simply accumulate microorganisms over time. Longitudinal studies indicate that microbial communities change through ecological succession, with different community structures appearing as infants develop.

La Rosa et al. followed 58 premature infants weighing ≤1,500 g at birth in a single NICU and analysed 922 stool samples, describing a patterned progression in dominant bacterial classes, from Bacilli to Gammaproteobacteria and then Clostridia. This progression was not always continuous, and abrupt changes in microbial populations were also observed; gestational age was strongly associated with the pace of progression, whereas antibiotics, mode of delivery and diet influenced the pace but not the sequence of progression. ¹

Korpela et al. later described four phases characterised by predominance of Staphylococcus, Enterococcus, Enterobacter and, later, Bifidobacterium, in a relatively small cohort of 45 breastfed very-low-birth-weight infants (birth weight <1,500 g; 262 stool samples) originally recruited for a nutritional intervention study; the Enterococcus phase was observed only in the extremely preterm infants and appeared to delay succession.² These phases illustrate microbial succession but should not be read as a sequence followed by every preterm infant.

More recent longitudinal data reinforce this variability Toubon et al. followed 596 very preterm infants (<32 weeks of gestation) from 24 NICUs of the French EPIPAGE-2/EPIFLORE cohort, with 1,307 stool samples collected at four time points from the first week of life to 3.5 years of age. During hospitalisation, infants moved between multiple microbial community states rather than following one fixed sequence, as inferred from cluster assignments at three sampling points during hospitalisation; diversity generally increased over time, while differences between infants decreased as the microbiota matured. ³

Taken together, these studies identify recurring patterns of succession alongside considerable variation between infants.

KEY MESSAGE

Recurring patterns of microbial succession can be observed in preterm infants, but no single developmental sequence applies to all.

Why do developmental trajectories differ?

No single factor explains microbiota development. Biological maturity and postnatal experience are both associated with the microbial patterns observed over time.

Biological maturity

Microbial colonisation begins while the gastrointestinal tract and immune system are still developing. Gestational age at birth and postmenstrual age have repeatedly been associated with differences in the pace and composition of microbiota development.

La Rosa et al. found a strong association between gestational age and the pace of microbial succession; ¹ Korpela et al. found microbiota development to be driven mainly by postmenstrual age, with gestational age at birth having little additional influence once postmenstrual age was taken into account. ²
Gestational age does not act in isolation, however. It provides the biological context in which colonisation occurs, alongside the exposures associated with neonatal care.

The clinical environment

For many preterm infants, microbiota development takes place during a prolonged NICU stay, with exposure to antibiotics and other medications, varying feeding practices, and the hospital environment itself. These exposures are closely linked to maturity: an infant born at 25 weeks typically has a very different clinical course from one [AW7.1]born at 31 weeks, which makes separating the effect of gestational age from what follows it difficult.

Thänert et al. examined microbiome development in 236 hospitalised preterm infants across three NICUs. using shotgun metagenomics of 2,512 stool samples and metatranscriptomics of 1,381 stool samples over the first three months of life. Medication exposures, including antibiotics and non-antibiotic drugs, were strongly associated with microbiome composition. ⁵

The relationship between individual exposures and microbial composition may also shift over time, depending on when an infant was exposed, when a sample was collected, and the infant’s developmental stage. In practice, a microbial profile at any given time reflects both developmental stage and cumulative postnatal history.

KEY MESSAGE

Differences in developmental trajectories rarely trace to a single factor. Biological maturity and postnatal experience need to be considered together.

A note on the evidence

Most of the detailed longitudinal evidence comes from very preterm (<32 weeks) and extremely preterm (<28 weeks) infants in neonatal intensive care, and from cohorts restricted to very low birth weight (<1,500 g).

While Korpela et al. classified “extremely premature as <28 weeks, with a birthweight below 1,500 g, La Rosa only enrolled infants weighing ≤1,500 g. Toubon et al. enrolled infants below 32 weeks’ gestation, Thänert et al. used eligible infants born ≤37 weeks and ≤1,500 g. Finally, the systematic review of Agilar-Lopez et al. defined preterm as 37 weeks, but included studies used very different populations.

Moderate and late preterm infants remain comparatively underrepresented, and findings from very preterm NICU cohorts should not be extrapolated across the full spectrum of prematurity without caution. No single microbial profile serves as a reference point across all preterm infants; results from different populations and clinical settings often diverge without necessarily conflicting.

Cross-study comparisons also warrant attention to sequencing method. [AW9.1]La Rosa, Korpela and Toubon relied on 16S rRNA gene profiling; Aguilar-Lopez et al. pooled 60 studies with heterogeneous methods in a systematic review; Thänert’s group used shotgun metagenomics paired with metatranscriptomics, resolving composition and gene expression rather than composition alone. Differences in gestational age, clinical practice, nutrition, medication exposure, sampling schedule and sequencing approach can all produce apparently divergent results without reflecting genuinely contradictory biology.

One distinction worth keeping in mind: detecting a gene indicates functional potential, not that the function is active. Thänert’s transcriptomic data captured expression directly; none of the other cited studies did.

CONCLUSION

Longitudinal studies have changed how the preterm gut microbiota is understood, from a description of which microorganisms are present at a given time to a view of microbial communities changing continuously as infants develop.

Recurring patterns of succession have been identified, but infants do not all follow the same sequence or progress at the same pace. Biological maturity, neonatal care and prior exposures are all associated with the trajectories observed. Reading microbiome research with this context in mind, including the population studied, sampling timing and sequencing method, helps explain why findings across studies and clinical settings are not always directly comparable.

The preterm gut microbiota is best understood as a developing ecosystem rather than a fixed profile.

REFERENCES

IMPORTANT INFORMATION

This article is provided for general scientific and educational information only. It discusses published research on the development of the preterm gut microbiota and is not intended to promote any product or to provide medical advice. The information should be considered in the context of the populations, methods and limitations of the cited studies.