Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing

Simple Summary Changes in the gut microbiome are associated with bowel cancers, however, less is known about the microbiome during the pre-cancerous bowel polyp stage. This study compared two DNA sequencing technologies to identify the gut microbiome from mucosa of colonoscopy patients diagnosed with bowel polyps or without bowel polyps. We found that different sequencing technologies and bioinformatic pipelines impact on bacterial taxonomy assignments. Overall, there were only minor differences in gut microbiome communities between participants with bowel polyps and those without. However, Ruminococcus gnavus, a bacteria commonly associated with inflammatory bowel disease (IBD) was shown to be more abundant in participants with polyps, despite participants with IBD being exclude from this study. This paper adds to our knowledge of the gut microbiome associated with bowel neoplasia.Abstract Numerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial taxonomy, and this has led, in part, to inconsistent findings between studies. Here, we examined mucosal microbiota from patients who presented with one or more polyps, compared to patients with no polyps, at the time of colonoscopy. We evaluated the results obtained using both short-read and PacBio long-read 16S rRNA sequencing. Neither sequencing technology identified significant differences in microbial diversity measures between patients with or without bowel polyps. Differential abundance measures showed that amplicon sequence variants (ASVs) associated with Ruminococcus gnavus and Escherichia coli were elevated in mucosa from polyp patients, while ASVs associated with Parabacteroides merdae, Veillonella nakazawae, and Sutterella wadsworthensis were relatively decreased. Only R. gnavus was consistently identified using both sequencing technologies as being altered between patients with polyps compared to patients without polyps, suggesting differences in technologies and bioinformatics processing impact study findings. Several of the differentially abundant bacteria identified using either sequencing technology are associated with inflammatory bowel diseases despite these patients being excluded from the current study, which suggests that early bowel neoplasia may be associated with a local inflammatory niche.