Analysis of the oral bacteriome and mycobiome in children with inflammatory bowel disease compared to healthy children by 16S and ITS2 profiling

Abstract

Abstract

Aims: This study aimed to analyse the oral mucosal microbiota (bacteria and fungi) in paediatric IBD patients. The mucosa was selected rather than the saliva as this is the region where tissue and immune cells directly interact with the microbiome Methods: The oral microbiome and mycobiome were examined in a cohort of children diagnosed with Crohn s disease (n=38, CD), and ulcerative colitis (n=21, UC). Children were treatment naïve at the time of sampling. A cohort of 36 children who were attending DDUH were grouped as a healthy control (HC) group. DNA was extracted from tongue and buccal swabs and the V1-V2 region of the 16S gene and ITS2 barcode of fungal DNA were amplified and sequenced using the Illumina MiSeq. Sequences were analysed with the Mothur and DADA2 pipelines. Additionally, IBD children following therapy were also analysed. Results: The tongue and buccal microbiota of CD children exhibted reduced biodiversity and lower species richness compared to healthy children. Our finding shows a reduction in the levels of several major oral bacterial genera, including Veillonella, and H. parinfluenza, and increased levels of oral Enterobacteriaceae and Actinobacteria in patients with severe IBD. Previous studies have implicated these taxa in the pathogenesis of IBD. In our follow up studies, remission from IBD symptoms was associated with loss of Enterobacteriaceae from the oral microbiome. We observed an increase in C. albicans and S. cerevisiae in the oral mycobiota in IBD. Interestingly, C. krusei and C. dubliniensis were also observed in the oral cavity in IBD. Overall, the mycobiome changes observed were more related to IBD disease activity compared to microbiome changes. Shifting of the oral microbial community was noted in follow up samples from patients after therapy, returning some taxa (Veillonella, Enterobacteriaceae) to levels close to the normal oral community. Conclusion: Children with IBD have an altered microbiota that may contribute to their oral health problems and may be linked to the pathogenesis of IBD. These data could potentially important to understand the aetiology of IBD and could be used in practical applications in diagnosis and monitoring disease progression.