P668. Interspace microbiome profiling (IS-pro) enables to differentiate IBD subclasses and disease activity by specific loss of bacterial diversity
M. Grasman1, R. van der Borden1, A. Budding2, A. Eck Hauer2, P. Savelkoul2, A. van Bodegraven3, 1VU University Medical Centre, Gastroenterology and Hepatology, Amsterdam, Netherlands, 2VU University Medical Centre, Medical Microbiology and Infection control, Amsterdam, Netherlands, 3ORBIS Medical Centre, Gastroenterology and Hepatology, Sittard, Netherlands
Supposedly, intestinal microbiota plays a major role in IBD pathogenesis. Differences in its composition have been observed between and within patients with Crohn's disease (CD) and ulcerative colitis (UC), varying with disease activity. This opens diagnostic potential in IBD. To date no standard laboratory techniques for microbiota analysis, suitable for daily clinical practice, are available, the more when using sample types like faeces and mucosal biopsies. As sampling method, storage and processing of samples have been shown to affect microbiota analysis, limitations in standardisation and accessibility arise. Therefore, we aimed to collect rectal swabs from IBD patients during consultation in an outpatient clinical setting and analyse these with IS-pro.
Rectal swabs were collected from consecutive IBD patients at a referral, third-line IBD outpatient clinic. Disease activity was determined with clinical indices. Total DNA was isolated by standard laboratory isolation procedures. Subsequently, microbial DNA was analysed with IS-pro, a within 8 hours performed, automated, high-throughput molecular fingerprinting method identifying composition of intestinal microbiota based on the ribosomal DNA (rDNA) interspace (IS) region combined with phylum specific sequence variation of the 16S rDNA. Combined with the proprietary IS-pro software suite, final output consists of profiles giving relative quantification of bacterial species within the most prominent phyla, Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria and Verrucomicrobia. From these data, Shannon diversity indices were calculated for all samples.
In total 144 rectal swabs were collected (CD n = 85; UC n = 59). Lower species diversity in the Firmicutes/Actinobacteria phyla was observed in CD as compared to UC (p 0.02).
Species diversity in the Proteobacteria phylum was lower in active disease, both for CD (p 0.02) and UC (p 0.05). Loss of species in Bacteroidetes phylum in active CD versus quiescent CD was observed (p < 0.01).
Total species diversity was lower in active disease, both in CD and UC (p 0.05 and p 0.05, respectively). Within each phylum no specific species was typically associated with disease type or degree of activity.
Rectal swabs analysed with IS-pro is a feasible means of microbiota determination in an outpatient clinical setting. Differences in species diversity were observed in IBD; disease subtype differed when analysing diversity in the Firmicutes/Actinobacteria phyla whereas disease activity was associated with lower diversity in Proteobacteria (in IBD) and in Bacteroidetes (in CD). These data suggest that diagnosis and stratification of IBD by microbial profiling (IS-pro) may be feasible.