Design and characterization of synthetic model communities for the human neonatal gut microbiota

The mammalian gut is colonized by diverse microbial communities that provide its host with different functions, e.g. nutrition or protection against invading pathogens. These microbiota functions are dependent on the microbial community composition (who is there?) and inter- and intraspecies interaction networks (what do they do?).

Profound understanding of individual species interactions and their consequences for the mammalian host is often hindered by the microbiome´s diversity and difficulty in conducting experimental manipulations. Here, synthetic communities (Syncoms) can serve as tool to analyze bacterial ecology in detail by reducing complexity and increasing experimental manipulability. We previously used Syncoms to gain a mechanistic understanding of microbiome-mediated colonization resistance against pathogens (Eberl et al. 2021), bacterial interactions networks (Weiss et al. 2022) and the systematic investigation of bacterial keystone species (Weiss et al. 2023).

Building on our expertise, we now aim to generate a synthetic community to model the human neonatal gut microbiota (NeoSyn). The microbiota plays a crucial role in various aspects of early development and health. NeoSyn is intended to mimic the highly variable neonatal gut microbiome both functionally and taxonomically.

The variations in the neonatal gut microbiome are driven by many different factors, such as the mode of delivery, the type of feeding or the use of medication (especially antibiotics).

Using MiMiC (Kumar et al. 2021), a tool which aids the design of minimal microbial consortia based on the functional potential identified in a given metagenomic sample, we designed different variants of NeoSyn consisting of 12 members to mimic an infant's microbiota of vaginally-born (NeoVaSyn) and caesarean-born (NeoCeSyn) infants. This core composition can be complemented with additional species of interest to perform research specific experiments. Using NeoSyns, we plan to investigate and understand e.g. differences in microbial ecology and microbiome functions or apply them for studying different antimicrobial compounds.