Alterations in the Duodenal Fluid Microbiome of Patients With Pancreatic Cancer

Abstract

Background & aims: The tumor microbiome of patients with pancreas ductal adenocarcinoma (PDAC) includes bacteria normally present in the upper gastrointestinal tract. If the predominant source of intratumoral bacteria in patients with PDAC is retrograde migration from the duodenum, duodenal fluid could be a representative biospecimen for determining microbiome profiles of patients with PDAC or at risk of developing PDAC.

Methods: We performed a case-control study comparing bacterial and fungal (16S and 18S rRNA) profiles of secretin-stimulated duodenal fluid collections from 308 patients undergoing duodenal endoscopy including 134 normal pancreas control subjects, 98 patients with pancreatic cyst(s) and 74 patients with PDAC.

Results: Alterations in duodenal fluid microbiomes with diminished alpha diversity were significantly associated with age >70 and proton pump inhibitor use. Patients with PDAC had significantly decreased duodenal microbial alpha diversity compared with age-matched control subjects with normal pancreata and those with pancreatic cyst(s). There was evidence of enrichment of Bifidobacterium genera in the duodenal fluid of patients with PDAC compared with control subjects and those with pancreatic cyst(s). There were also enrichment of duodenal fluid Fusobacteria and Rothia bacteria among patients with PDAC with short-term survival. Duodenal fluid microbiome profiles were not significantly different between control subjects and patients with pancreatic cyst(s).

Conclusion: Patients with PDAC have alterations in their duodenal fluid microbiome profiles compared with patients with pancreatic cysts and those with normal pancreata. ClinicalTrials.gov, Number: NCT02000089.

Keywords: Duodenal Fluid; Microbiome; Mycobiome; Pancreatic Cancer.

Figure 1. Duodenal fluid microbiomes of PPI users and non-users:

(A) The duodenal microbiomes of regular PPI users and non-users in normal pancreas controls were analyzed for alpha-diversity measures. (B) The relative abundance of genera between the two groups. (C) LDA score computed from features differentially abundant between regular-PPI users and non-users.

Figure 2. Duodenal fluid bacterial microbiomes in patients with PDAC vs. Normal pancreas:

(A) Duodenal fluid bacterial concentrations. (B) The duodenal microbiomes of PDAC vs. normal pancreas controls were analyzed for alpha diversity measures. The beta diversity among these groups were compared by (C) Unweighted Unifrac plot. P values were determined by pairwise PERMANOVA. The relative abundance of (D) phylum and (E) genera between PDAC vs. normal pancreas controls. (F) Taxonomic cladogram from LEfSe analysis. The criteria for feature selection is log LDA score >3.0.

Figure 3. Duodenal fluid bacterial microbiomes in patients with PDAC vs pancreatic cyst(s):

(A) Duodenal fluid bacterial concentrations PDAC subjects vs. age-matched subjects with a pancreas cyst. (B) The duodenal microbiomes of PDAC and pancreas cyst subjects were analyzed for alpha-diversity measures. Beta diversity compared by (C) unweighted, and weighted Unifrac plot. The relative abundance of phylum (D) and genera (E) between the two groups. (F) Taxonomic cladogram from LEfSe analysis. The criteria for feature selection is log LDA score >3.0.

Figure 4. Duodenal fluid mycobiomes in patients with PDAC vs. those with normal Pancreata:

(A) Duodenal mycobiome alpha-diversity measures. The beta diversity compared by (B) Unweighted, and (C) Weighted Unifrac plot. Relative phylum (D) and genera (E) abundance between groups. (F) Taxonomic cladogram from LEfSe analysis. The criteria for feature selection is log LDA score >3.0.