Endoscopic ultrasound (EUS)-guided fine needle biopsy (FNB) formalin fixed paraffin-embedded (FFPE) pancreatic tissue samples are a potential resource for microbiota analysis

We read with great interest the study by Gaiser et al 1; their finding of enrichment of oral bacterial taxa, including Fusobacterium nucleatum , in intraductal papillary mucinous neoplasms with high-grade dysplasia adds to the growing literature on the pancreatic microbiome in pancreatic ductal adenocarcinoma (PDAC).2–4 Previous PDAC microbiome studies have an inherent bias as they are restricted to samples from patients undergoing surgical resection. Less than 20% of patients with PDAC undergo surgery and such cases are not representative of the full gamut of the disease. Additionally there is uncertainty regarding the extent of exogenous bacterial DNA contamination of samples used. Endoscopic ultrasound (EUS) fine needle biopsy (FNB) is often utilised to make a histological diagnosis in patients with suspected PDAC. Novel needles which provide samples better suited to DNA extraction and gene sequencing5 are available. However, the relatively low biomass of the samples and nature of sample collection present challenges with contamination and technical noise. Recently computational approaches have been developed to remove contaminants in such low biomass …