Spatially and Temporally Precise Microbiome Profiling in the Small Intestine using the SIMBA Capsule with X-ray tracking

Abstract

Few minimally invasive options for sampling the small intestinal (SI) luminal fluid exist to study the SI microbiota in health and disease. To address the lack of tools and methods to study GI regions that are difficult to access, Nimble Science developed a fully autonomous and passive sampling method, the Small Intestine MicroBiome Aspiration (SIMBATM) capsule, for convenient, high-quality, and reliable sampling to study the diet-microbiota interactions in the SI. The sealing efficacy and microbial DNA preservation capacity of the SIMBA capsules was first validated through in vitro simulation assays. Then, a clinical study was conducted with 20 healthy participants to validate the in vivo use of SIMBA capsules to reliably capture samples for SI microbiome analysis before and after an intervention (NCT04489329). Briefly, participants ingested the capsules at baseline and 7 days later, with a probiotic capsule containing a blend of L. rhamnosus R0011 and B. longum R0175. Following baseline SIMBA capsule ingestion, multiple low-dosage x-ray scans were performed to track the sampling location. Fecal samples corresponding with the baseline and intervention capsule were analyzed for comparison. The SIMBA capsules performance in vitro demonstrated the potential for contamination-free sampling with preservation of the microbial communities. Within the clinical study, the capsules performed safely and reliably for collection of SI content. X-ray tracking confirmed that 97.2% of the capsules completed sample collection in the SI regions before reaching the colon. Importantly, our data showed that the capsules sampled in the right area of the intestines and that baseline SIMBA microbiome profile is significantly different from fecal microbiome profile. SIMBA successfully detected a concurrent probiotic intervention in the small intestine, which was not detectable using stool samples. The high accuracy of sampling location and sealing efficacy of the SIMBA capsules makes them potentially useful research tools in clinical trials for studying diet microbiota interactions in health and disease, and perhaps eventually for the clinical diagnosis of GI tract conditions affecting the SI such as SIBO.

Clinical Sampling of Small Intestine Luminal Content for Microbiome Multi-Omics Analysis: A Performance Analysis of the Small Intestine Microbiome Aspiration (Simba) Capsule and Benchmarking Against Endoscopy

“…Indeed, SIMBA capsules were effective in collecting SI samples with variability on par with endoscopy, and high reproducibility across study visits (at least 1 week apart) with no significant differences observed in both 16S and metabolomics profiling compared to feces. Compared to a previous study [7], we did note an unexpected increase in SIMBA capsule samples with low total sequencing depth (< 1000 reads), reflected by a decrease in 16S profile microbiome diversity, which was attributed to suboptimal 16S primer selection. For example, previously using a V3-V4 primer for 16S amplicon sequencing resulted in a sequencing depth of 7 x 10 4 for SIMBA capsule samples, which was roughly equivalent to the sequencing depth obtained from corresponding fecal samples, despite an over 100 average fold difference in DNA concentration.…”

“…Further investigation determined that the most likely cause was the choice of a suboptimal primer for PCR amplification, as a previous study using a primer spanning the V3-V4 region generated an overall 10-fold increase in read depth (i.e. a minimum depth of 3 x 10 4 total reads across 80 capsule samples) [7]. No significant difference in microbiome composition was observed between capsules which finished sampling in the jejunum vs. Ileum vs. colon (PERMANOVA p-value ~ 0.344, R 2 ~ 0.1) nor by participant IBS status (PERMANOVA p-value ~ 0.2, R 2 ~ 0.13), and did not substantially change with the inclusion of samples with lower sequencing depth.…”

“…The Small Intestine MicroBiome Aspiration (SIMBA) capsule is a pH-based autonomous sampling capsule designed to open and close while transiting the small intestine [7]. The SIMBA capsule has a pH-dependent coating, which keeps it sterile through the oral and gastric regions, and then sloughs off; large sampling ports for content collection of varying consistencies in the SI; effective timed non-electronic sealing performance to avoid colonic contamination; and embedded microbial DNA preserving agents to maintain sample quality during the capsule passage and collection process.…”

“…There is a critical need for minimally invasive and cost-effective devices that allow direct high-quality sampling in the small intestine. Over the past few years, a few capsulebased sampling systems have been introduced to target the small intestine using passive sampling technologies [5][6][7]. While early studies in humans have demonstrated luminal fluid collection with multi-omics profiles differing from stool, reference data regarding SI localization and endoscopic sampling has been lacking.…”

“…The Small Intestine MicroBiome Aspiration (SIMBA) capsule is a pH-based autonomous sampling capsule designed to open and close while transiting the small intestine [7].…”