IMPACTT Symposium 2024 Abstracts

Dr. Joongjae Kim (Poster 60)

Chief Technology Officer, Nimble Science Ltd. | Canada

Multi-Omics Mapping of Spatial Differences Along the Gastrointestinal Tract with the SIMBA Capsule: Benchmarking Against Endoscopy and Clinical Applications

Gang Wang, Cedoljub Bundalovic-Torma, Oksana Lukjancenko, Sharanya Menon, Heidi H. Hau, Sabina Bruehlmann, Lynn Wilsack, Renata Rehak, Sahar Bagheri, Mohammad M. Banoei, Lawrence Lou, Yasmin Nasser, Matthew Woo, Ian Lewis, Kathy D. McCoy, Christopher N. Andrews

OBJECTIVE: The small intestine (SI) plays a central role in uptake of nutrients and dysbiosis of its microbiome has been implicated with significant impairments in normal gastro intestinal (GI) function. However, owing to its relative inaccessibility and lack of a widely-applicable standard sampling techonology, the SI microbiome still remains relatively little unexplored.

METHOD: The Small Intestinal MicroBiome Aspiration Capsule (SIMBA) was developed as an effective means for sampling SI luminal content and platform for multi-omic microbiome analysis. SIMBA capsule SI targeting, sampling sealing, and preservation performance was evaluated in a two-visit observational clinical study of healthy and Irritabe Bowel Syndrome (IBS) patients using X-ray tracking. Detailed assessment of SIMBA capsule sample quality was also performed against paired-fecal and ‘gold-standard’ duodenal endoscopy sampling using 16S amplicon and shotgun metagenomic sequencing, and metabolomics.

RESULTS & CONCLUSIONS: X-ray monitoring confirmed all capsules sampled from the distal small intestine with a few (5 of 49) sealing in the proximal colon. 16S amplicon and metabolomics analysis demonstrated that SIMBA capsules were significantly different to fecal samples, and similar to endoscopic aspirate and cytological brush sampling. Shotgun metagenomics demonstrated that despite the low-biomass of SI samples, SIMBA capsules retained a minimal level of host contamination, in comparison to endoscopic aspirate and cytological brush samples (~5 % of vs. ~ 93 – 96% of average total reads per sample). Increased resolution and sequencing depth enabled GI regional-specific differences in known probiotic strains to be traced, as well as functional differences in microbiome-mediated bile acid metabolism and short-chain fatty acid production, demonstrating the great potential for the SIMBA capsule for high-resolution spatial characterization of the GI microbiome with a wide range of applications from disease to nutraceutical research.