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Children presenting for the first time with inflammatory bowel disease (IBD) offer a unique opportunity to study aetiological agents before the confounders of treatment. Microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium;  Helicobacter  and  Campylobacter  are previously implicated in IBD pathogenesis. We set out to study these and other microaerophilic bacteria in  de-novo  paediatric IBD.    Patients and Methods  100 children undergoing colonoscopy were recruited including 44 treatment naïve  de-novo  IBD patients and 42 with normal colons. Colonic biopsies were subjected to microaerophilic culture with Gram-negative isolates then identified by sequencing. Biopsies were also PCR screened for the specific microaerophilic bacterial groups: Helicobacteraceae, Campylobacteraceae and  Sutterella wadsworthensis.Results  129 Gram-negative microaerophilic bacterial isolates were identified from 10 genera. The most frequently cultured was  S. wadsworthensis  (32 distinct isolates). Unusual  Campylobacter  were isolated from 8 subjects (including 3  C. concisus , 1  C. curvus , 1  C. lari , 1  C. rectus , 3  C. showae ). No  Helicobacter  were cultured. When comparing IBD vs. normal colon control by PCR the prevalence figures were not significantly different ( Helicobacter  11% vs. 12%, p = 1.00;  Campylobacter  75% vs. 76%, p = 1.00;  S. wadsworthensis  82% vs. 71%, p = 0.312).    Conclusions  This study offers a comprehensive overview of the microaerophilic microbiota of the paediatric colon including at IBD onset.  Campylobacter  appear to be surprisingly common, are not more strongly associated with IBD and can be isolated from around 8% of paediatric colonic biopsies.  S. wadsworthensis  appears to be a common commensal.  Helicobacter  species are relatively rare in the paediatric colon.    Trial Registration  This study is publically registered on the United Kingdom Clinical Research Network Portfolio (9633).

The Microaerophilic Microbiota of De-Novo Paediatric Inflammatory Bowel Disease: The BISCUIT Study