Colonization and succession of the human gastrointestinal microbiome in neonates and infants at high risk of metabolic disease in adulthood

Recent studies have highlighted that the human gastrointestinal microbiome not only maintains important functions for the human host, but is also intimately linked to the development of the neonatal immune system. Therefore, earliest perturbations to the initial colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. While the rate of caesarean section deliveries is increasing worldwide, it still remains unclear to what extent a caesarean section delivery (CSD) or other perturbations affect the colonization and succession of the gastrointestinal microbiome and might eventually impact the immune development of a neonate. Although much research has been performed on bacterial colonization and succession to date, far less is known about the other two domains of life, archaea and eukaryotes. Furthermore, it remains unclear whether a delivery by caesarean section causes a disruption of mother-to-infant transmission of microbiota and whether this affects human physiology early on, with potentially persistent effects in later life.

Over the course of this thesis, a multitude of objectives was tackled. First of all, the description of microbial communities and trends over time within the neonatal and infant gut microbiome, and the study of the early colonization and succession by members of the three domains of life. Second, the careful application of high-throughput approaches on earliest low biomass samples, the detection of functional repertoires and strains transferred from mothers to neonates, and the analysis of the immunostimulatory potential of neonatal gut microbiomes in relation to delivery mode with likely effects on the later health status.

In a first study based on 15 infants and using a combination of 16S and 18S rRNA gene amplicon sequencing and quantitative real-time PCR, earliest differences among the three domains of life according to delivery mode were detected as early as three days postpartum. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The findings complement previous observations of a delay in colonization and succession of CSD infants, which likely affects not only bacteria but also archaea and microeukaryotes. Based on the observation that the first 5 days postpartum showed significant differing trends between delivery modes and considering the fact that the very first days postpartum are generally under-studied, this highlighted the importance to perform more in-depth analyses of these microbiome samples. In a next step, based on 12 mother-neonate pairs, high-resolution, metagenomic analysis of the gut microbiomes of mothers and neonates was performed to resolve the earliest colonizing microbiome. After data curation and in accordance with the observed changes in community composition for both cohorts, differences with respect to encoded metabolic functions between the microbiomes of vaginally delivered (VD) or CSD neonates as early as day 3 were observed. Several functional pathways were over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. Genes encoding proteins involved in these functions were linked to specific strains, which were vertically transmitted from the respective mothers. Based on the candidate’s work, more follow-up work on LPS was done by a colleague with a background in immunology. Isolated LPS from faecal samples collected at day 3 had a higher immunostimulatory potential in VD neonates and cytokines measured in plasma collected at the same day presented an increased immune reaction in VD neonates. Collectively, these results suggest that vaginal delivery favours vertical transmission of specific gastrointestinal strains from mother to neonate, while caesarean section may impede this process and thereby decrease linked functional repertoires and immunostimulatory potential with potential effects on human physiology later in life.

Taken together, the results obtained from both cohorts strongly indicate that maternal and neonatal factors, such as antibiotics intake or milk diet, but most importantly the delivery mode, have the potential to influence the initial neonatal bacterial, archaeal and microeukaryotic colonization of the gut microbiome shortly postpartum, with the potential to impact the neonatal immune development, which could thereby affect the later health status.