P143 Evaluating intestinal biopsy preservation and storage methods to facilitate large-scale microbiome research in inflammatory bowel disease (IBD)

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Introduction Large multicentre studies are key to understanding complex relationships between the gut microbiome and outcomes in IBD. Interrogating the mucosal microbiome may identify biological signals not captured by stool, which mostly reflects distal colon. Gold standard tissue cryopreservation by ‘flash freezing’ is likely to limit large study feasibility. We aimed to compare gold standard and pragmatic mucosal biopsy storage vs stool. Methods We collected endoscopic recto-sigmoid biopsies and paired stool (prior to bowel cleansing) from 20 adults with IBD (ethical approval: Wales REC5, ref 21/WA/0228). Biopsy preservation and storage conditions are shown in figure 1. Microbiota was sequenced on the MiSeq (Illumina) platform using the 16S rRNA gene (V4 region). Statistical analyses were performed in R, including decontam package for FFPE analyses. Results Gut microbiome was consistent between proximal and distal biopsies suggesting any within-patient variation observed would be reflective of storage condition, not location. There was no significant difference in alpha diversity (richness, P=0.99; Shannon index, P=0.99) or microbiota profile (P=1.00; R2=0.01) of reagent-preserved vs gold standard tissue. Whilst FFPE community structure was not significantly different to stool, there was significant dissimilarity vs other tissue (P=0.001, R2 0.23). This was driven by differential relative abundance of obligate gut anaerobes; Faecalibacterium, Anaerostipes and Lachnospiraceae. Despite this, tissue microbiota grouped by participant (P=0.001, R2=0.56) regardless of preservation and storage condition. FFPE richness (P=0.11) and Shannon index (P=0.09) was comparable to other tissue conditions. Conclusions Preservative reagents are a convenient alternative to flash freezing tissue in large microbiome studies. Whilst less comparable, FFPE specimens provide potential for microbiome studies using historically banked samples. Access to tissue for microbiome and other omic analysis will evolve mechanistic understanding of IBD.

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