Short summary of content / significance
Functioning of the gastrointestinal tract, and of the bacteria residing therein, is of significance for nutrient digestion and absorption and optimal immune performance. Proper establishment of the gut bacteria, termed the microbiota, is therefore considered essential for healthy development. In early life, the intestinal microbiota is relatively unstable and responsive to perturbations, such as antibiotics. Although gut microbiota development can be negatively impacted during early life, due to for example preterm birth, the developing microbiota also provides an opportunity to be targeted as means of therapeutic strategy to support healthy growth and development. Regarding preterm infants, who commonly experience negative health outcomes like infections and growth retardation, exploration of the gut microbiota and it’s metabolic traits is particularly relevant. In light of this, it is important to understand how the preterm infant gastrointestinal tract is functioning, which bacteria colonise, what the bacteria are doing and how microbiota establishment is affected. Via a metaproteomics approach, we identified the most abundant proteins present in gastric and faecal samples, which served as an indication for functioning of the gastrointestinal tract and its microbiota. We revealed that gestational and postnatal age were associated with quantity of specific markers for gut function and maturation, as well as with composition of the gut microbiota. Our data showed that a Bifidobacterium-dominated bacterial community was associated with increased proteins involved in carbohydrate and energy metabolism, including those involved in the degradation of complex carbohydrates like human milk oligosaccharides. This might aid energy harvest from milk feedings and subsequent growth of the infant. Moreover, we showed that antibiotic treatment during the first week of life impacts microbiota development, particularly by increasing Enterococcus species, while decreasing beneficial Bifidobacterium species. In addition, the longer the treatment with antibiotics, the longer the disturbance of the microbiota. As well as factors acknowledged for their influence on microbiota development, such as antibiotics, delivery mode and feeding strategy, we identified a potential influence of gender, respiratory support and maternal preeclampsia. We believe future studies should implement functional analysis of the microbiota and elucidate the effect of microbiota targeting therapeutic strategies during preterm infant care.