Introduction Paediatric Inflammatory bowel disease (IBD) incidence is rising worldwide. Recently the role of the gut microbiota has been recognised as pivotal in disease pathogenesis. IBD microbial studies to date have focused on bacterial diversity assessment in established disease cohorts, with limited studies in treatment naive patients. In contrast to bacteria, the exact role of the colonising fungi and their pathogenic potential has not been fully explored. The aim of the study was to examine candidate fungal triggers at disease onset in children with IBD using pyrosequencing, utilising the Bacteria in Inflammatory bowel disease in Scottish Children Undergoing Investigation before Treatment (BISCUIT) study cohort.
Methods 128 children undergoing colonoscopy were approached from three Scottish paediatric centres (Aberdeen, Glasgow and Dundee) with 100 ultimately recruited and biopsied; 44 IBD (comprising Crohn’s disease (CD; 29), ulcerative colitis (UC; 13) and IBD-type unspecified (2)), 42 normal colon controls (NCC) and 14 “others”. All IBD patient samples were taken from inflamed tissue. Fungal DNA was amplified on a reduced cohort of 37 recruits (13 CD, 12 UC, 12 NCC) using 18S rDNA primers. Roche 454 Titanium sequencing was conducted by NewGene (Newcastle, UK). Data analysis was performed using QIIME version 1.3.0 workflow. Taxonomy assignment of operational taxonomic units (OTUs) was performed according to ribosomal database project taxonomy. OTU tables were rarefied at 3,000 reads.
Results Fungal DNA was amplifiable from 7 patient samples, 6 children with a diagnosis of IBD – 4 with CD (BISCUIT1, 31, 62 and 89), 2 children with UC (BISCUIT33 and 104) and 1 NCC (BISCUIT 27). Fungal diversity was assessed in all paediatric samples alongside three adult samples to act as comparison. The adult samples comprised 1 patient with UC (2UC21Aa) and 2 NCC (GH4 and GH9). Phylum level analysis indicated that all fungal sequences belonged to the Ascomycota and Basidiomycota phyla. Control patients contained predominantly Ascomycota sequences ( > 80% of sequences in all patients) whilst 6/7 IBD patients contained exclusively Basidiomycota species. Genus level analysis was undertaken and there was no similarity between fungal profiles from the paediatric and adult samples.
Conclusion By using robust methodology we have characterised the IBD “fungal microbiota” at diagnosis in children. Based on the current study, it would appear that a distinctly altered fungal species profile is present at IBD disease presentation. Further work should now focus on expanding this study and identifying how to beneficially modify the microbiota using established and novel IBD treatments.
Disclosure of Interest None Declared
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