Poster Presentation 14th Lorne Infection and Immunity 2024

A validated study protocol to compare microbiome and mycobiome profilesof Inflammatory Bowel Disease patients in remission and active flare (#101)

Matias Abregu 1
  1. Microbiome Science, DNA Genotek Inc, Ottawa , Ontario , Canada

Several large cohort studies of the gut bacterial composition of patients with Inflammatory Bowel Disease (IBD) have been published in recent years. While these studies have provided intriguing insights into the disease and promising clues for treatment options, they are often challenged by low enrollment and compliance rates. Low rates are largely influenced by donor perception of self-collection of the severe diarrhea samples common for IBD patients in flare. In collaboration with Crohn’s and Colitis Canada we launched a research study with two aims: to adapt and improve current practices for stool collection, preservation, processing and analysis and to use these optimized methods to compare bacterial and fungal profile differences in IBD patients in remission to those in active flare.
To optimize methods for self-collection of IBD stool samples we adapted OMNIgene®•GUT (OMR-200, DNA Genotek), a validated gut microbiome self-collection kit that provides ambient temperature stabilization, to donors with severe diarrhea by pairing OMR-200 with a sampling spoon (OM‑AC2, DNA Genotek). To optimize sample processing, we compared common extraction methodologies, both literature based “home-brew” methods and commercially available extraction kits. 16S and ITS amplicon sequencing was performed on Illumina’s MiSeq platform to interrogate diversity and relative abundance differences for bacterial and fungal taxons. We evaluated donor compliance, ease of use, accuracy of the recovered microbial profile, and sample preservation over time, in addition to investigating microbial and fungal profile differences in a cohort of IBD patients who were either in remission or experiencing flare.
Donors with severe diarrhea reported that OMR-200 when combined with OM-AC2, provided an easy to use method for sample self-collection, with a sample return rate of 92%, 96% of donors reporting the method as easy to very easy and a 100% sample utilization rate. Comparison of extraction methodologies found significant differences in discovery of diversity, particularly in the Blautia and Granulicatella genera, and total nucleic acid yields. Our preliminary profile analysis suggests trends in diversity and abundance of the bacterial and fungal microbiome, between IBD patients in remission or experiencing flare. Future work will expand on these associations between disease state and taxonomic communities in IBD patients.