First-Year Dynamics of the Microbiome in Infantsâ€™ Oral and Gastrointestinal Systems
The development of the infant microbiome is highly influenced by factors like feeding type and introduction of solid foods. In our study, we examined the dynamics of the oral and gut microbiome of healthy infants under one year of age with respect to those factors. We could determine that the oral microbiome especially underwent significant transitions within specific time frames, which were lagged between breastfed (BF, months M04-M06) and non-breastfed (NBF, months M01-M03) infants. BF infants initially had simpler microbial networks that became more complex after six months. At this time, the microbiomes of the two groups became more alike, probably due to the introduction of solid food. Key bacterial genera were Staphylococcus and Streptococcus which showed dynamic changes. Here, Staphylococcus was more transient and Streptococcus decreased in abundance as the microbiome diversified.  We could successfully show that besides bacteria, also archaea were present in the infant oral cavity and gut microbiome from early infancy on. Here, Methanobrevibacter was the predominant archaeal genus. Archaeal colonization seemed to be influenced by environmental factors and breastfeeding and showed a very transient pattern. The stool microbiome exhibited a gradual and extended microbial development. Only for BF infants, we could determine a critical time frame between M03 and M08 with increased microbial diversity and complexity. The maturation of the gut microbiome was reinforced with the establishment of anaerobic microbial networks. NBF infants gut microbiomes complex microbial co-occurrence patterns from the start. For BF infants complexity of the networks just established in the second half of the first year of life. The gut microbiome matured independently from the oral microbiome, marked by decreasing oral contributions and increasing complexity. Using metagenomic data, we could show that specific strains could be tracked within one individual over the time. Additionally, the development of the functional potentials of the gut microbiome is rather driven by time than by presence or absence of breastmilk.  Overall, the infant microbiome differentiates and stabilizes over the first year of life, with breastfeeding playing a crucial role in shaping anaerobic microbial networks.