Collaboratrices et collaborateurs

The spatial organization of bacterial communities along the gastrointestinal tract complicates the analysis of microbiomes. The bacterial composition varies in the different gut compartments, its composition changes as pigs grow. Unless ileal cannulated, it is up to now impossible to collect multiple intestinal content from the same pig. Nowadays, sampling microbiota is limited to faeces or can be done after slaughtering to directly collect intestinal content. A new sampling capsule (CapSa) was developed to perform non-invasive sampling of the small intestinal content on the same individual. This novel capsule is designed to resist acidic pH, therefore it should stay closed in the stomach, but it opens at basic pH allowing collection of microbiota samples in the small intestine. This study assessed the in vitro sampling mechanism of CapSa under various simulated gastrointestinal environments. Three in vitro assays were carried out to test the CapSa at both low (pH≤4.2) and neutral pH (pH=7) to simulate the gastric and the small intestine environment, respectively. In trial 1, the CapSas (n=51) were placed in water at pH2 for 30 min and then moved into water at pH7 until all CapSas had sampled. In trial 2, the CapSas (n=8) were left for 120 min at pH=2 and then moved to pH7. In trial 3, the CapSas (n=5) were kept for 2 h in a solution simulating gastric juices at pH4.2 and then moved to a buffer at pH=7. In all 3 trials, none of the CapSas started sampling under acidic conditions. However, as per design, all CapSas correctly collected samples under neutral conditions. The majority of the CapSas (72.5, 100 and 100%, in trial 1, 2 and 3, respectively) collected a sample within 60 minutes of being moved to the simulated small intestinal environment. The sampling (opening and closing) took less than 10 seconds and sampled volumes ranging from 100 to 250 µl. In conclusion, these preliminary trials revealed that the CapSas performed well in all the simulated environments tested. In the following steps, we will perform in vivo experiments to confirm the efficiency of CapSas to collect small intestine content. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grand agreement no. 955374.