Paving the way : Exploring glycan-driven formation of the infant gut microbiota using synthetic communities

Summary

Upon birth, the infant gut is quickly seeded with microorganisms. During the first year of life, the infant gut microbiota forms through ecological succession and utilizes glycans from human milk, solid food, but also endogenous sources such as mucins. However, it is still not clear how these glycans, and their combinations, affect the formation of the infant gut microbiota as a complex community. This thesis harnessed the potential of synthetic communities – selections of bacteria naturally found in the infant gut – to study this in all its complexity.---This thesis dives into existing literature and cohort-derived information on the ability of the infant gut microbiota to utilize human milk oligosaccharides (HMOs) and common infant formula additives through the analysis of publicly available Metagenome Assembled Genomes (MAGs). It was found that withdrawal from breastfeeding as well as age contribute towards the enrichment of the gut microbiota with glycoside hydrolases from different phyla.---Moreover, querying of the aforementioned MAGs, showed that formula-fed infants had a higher prevalence of putative fructoselysine degrading genes. In vitro experiments also showed that feces from formula-fed infants degraded fructoselysine more efficiently and with a distinct composition trajectory.---To better understand the ecological relationships created in the presence of human milk, we created BIG-Syc, a 13-strain synthetic community. BIG-Syc grown on different HMO mixes proved to be an accurate model for the representation of the pre-weaned infant gut microbiota. Bacteria that cannot utilize HMOs, relied on HMO degraders, which led to a fully sustainable community. Moreover, bifidobacteria reclaimed their niche in a deletion experiment with HMOs.---Using BIG-Syc grown on HMOs, this thesis explored the effects of a simplified sequential batch method on community dynamics. This method favored cross-feeders, and the production of intermediate metabolites and gases, but allowed for a reproducible growth of all trophic levels. Assessing the effect of in vitro fermentation methods helps with critically extrapolating experiments on gut microbial communities.---Here the biology, adaptation, and health effects of A. muciniphila are also reviewed. A. muciniphila is found in infants from the first month of life, and its relative abundance increases as infants age. Its abilities to utilize both HMOs and mucin and to train the immune system imply a pivotal role in the maturation of the infant gut microbiota.---Additionally, the interplay between dietary glycans, such as HMOs, and mucin on the maturing infant gut microbiota was investigated using the BabyBac synthetic community. The experiments showed that the presence and ratio of HMOs and mucin affected the composition and metabolism of BabyBac. Despite the ability of A. muciniphila to utilize HMOs, in BabyBac, it is restricted to mucolytic activity.---In summary, this thesis touches upon the succession of the infant gut microbiota and the ecological processes that govern it, the resource pressure posed by HMOs and mucin for community formation, the importance of assessing the effects of different in vitro fermentation methods, and the future perspectives on the utilization of synthetic communities as supplements or as research models.