A short abstract of the doctoral research

The small intestinal microbiota plays a key role in human health, yet remains largely unexplored due to invasive and technologically demanding sampling methods. In vitro gastrointestinal models are a promising non-invasive method to study this microbial community, but existing small intestinal models often lack key bacteria known to be abundant in the human small intestine. To obtain a more representative small intestinal in vitro community, the use of the oral community is suggested. Oral microbes continuously enter the small intestine through saliva ingestion and have been shown to partly overlap with the small intestinal microbial community.

This doctoral research evaluated whether oral-to-gut bacterial transfer can result in a more representative small intestinal microbial community in vitro when using human-derived bacterial communities. Short-term dynamics were assessed using the TNO gastro-small intestinal model (TIM-1), and long-term dynamics were explored using a modified Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). Across both models, oral communities successfully contributed to the establishment of small-intestinal-like communities. In TIM-1, short term experiments revealed donor- and region-specific bacterial growth resembling in vivo observations. In the small intestinal M-SHIME (SI-M-SHIME) repeated oral inoculation established characteristic small intestinal bacteria, whereas faecal-derived inoculation enriched for bacteria typical of the distal small intestine.

Although the in vitro communities still differed from in vivo profiles, the overall findings highlight the value of incorporating oral bacteria into in vitro models. Together, the results support the SI-M-SHIME as a promising tool for future mechanistic studies of the small intestinal microbiome.