. 2024 Jun 14;110(10):6771–6799. doi: 10.1097/JS9.0000000000001762

Table 3.

Summary of included studies.

Article	Methodology	Sequencing and annotation	PDAC Signatures	Healthy and positive control signatures	Conclusions	Available Bio-data
Serum Plasma
Microbiome Markers of Pancreatic Cancer Based on Bacteria-Derived Extracellular Vesicles Acquired from Blood Samples: A Retrospective Propensity Score Matching Analysis. Kim JR et al.³³ 2021. South Korea	PDAC (n=38) Healthy controls (n=52) Microbial EVs via blood plasma.	16S rRNA gene analysis performed. V3-V4 hypervariable regions of the 16SrRNA gene. Taxonomic assignment was performed using UCLUST and QIIME against the GREENGENES reference database.	At the phylum level, most abundant: Verrucomicrobia Deferribacteres Bacteroidetes At the genus level, most abundant: Akkermansia Ruminococcaceae UCG-014/Ruminiclostridium	Most abundant in the control group Sphingomonas Propionibacterium Corynebacterium	These microbiome markers, which altered microbial compositions, are therefore candidate biomarkers for early diagnosis of PDAC.	Not available
Oral saliva
Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study. Nagata N et al.⁴² 2022. Japan	Japan cohort PDAC (n=47) Controls (n=235) Spanish cohort: PDAC (n=43) Controls (n=45) Saliva samples collected from patients with treatment-naïve PDAC and non-PDAC controls in Japan and Spain	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. The reads in the generated clusters were sorted by redundancy, and clustered with 97% identity using UCLUST. The 16S database was reconstructed from three publicly available databases: Ribosomal Database Project v.10.27 and a reference genome sequence database obtained from the NCBI FTP site.	Significantly enriched in the phylum of PDAC patients were: Firmicutes (unknown Firmicutes, Dialister, and Solobacterium spp.) Prevotella spp. (P. pallens and P. sp. C561)	Moreover, no oral species or genes were significantly different between patients with PDAC and controls. However, the following bacteria were depleted in PDAC cases: Streptococcus. salivarius S. thermophilus S. australis	The significant depletion of S. salivarius, which has been reported to have anti-inflammatory effects, was the most prominent signature in the PDAC oral microbiome.	Yes, available. https://www.sciencedirect.com/science/article/pii/S0016508522003547
A faecal microbiota signature with high specificity for pancreatic cancer. Kartal E et al.³⁹ 2022 Germany, Spain	Spanish case–control PDAC (n=59) Controls (n=55) Oral Saliva, tissue and faecal samples were collected To account for potential bacterial contamination of extraction, negative controls (extraction blanks) were included.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Raw reads were quality trimmed and filtered against chimeric PCR artefacts using DADA2.	Data showed overall 27 enhanced levels of oral-intestinal transmission. Veillonella spp, were highly prevalent in both salivary (100% of subjects) and faecal (87.5%) samples across the entire study population.	Not mentioned	Faecal metagenomic classifiers performed much better than saliva-based classifiers and identified patients with PDAC based on a set of 27 microbial species. Significantly increased levels of oral-intestinal strain transmission in patients with PDAC.	Yes, available. PRJEB38625. PRJEB42013.
Comparisons of oral, intestinal, and pancreatic bacterial microbiomes in patients with pancreatic cancer and other gastrointestinal diseases. Chung, M et al.⁴⁵ 2021. USA	PDAC (n=24) Ampullary adenocarcinoma (n=8) Cholangiocarcinoma (n=4) Benign controls (n=16) 316 oral samples (52 tongue swab, 46 buccal swab, 35 supragingival swab, 48 saliva samples) 6 normal pancreatic tissues 33 pancreatic tumour samples 22 Duodenum tissue 34 jejunum swab, 19 bile duct swab samples, 21 pancreatic ducts,	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Sequence quality checking and denoising were performed using the DADA2 Illumina sequence denoising process. Taxonomic classification, alignment, and phylogenetic tree building were completed using QIIME2.	Bacterial communities from tongue and saliva samples clustered together, while those from buccal and supragingival samples formed another cluster. The saliva bacteria samples were: Capnocytophaga gingivali Fusobacterium nucleatum Streptococcus ASVs. Matched bacteria present between saliva and any pancreatic tissue were: Fusobacterium Rothia Saccharibacteria Oribacterium Streptococcus	Not mentioned	Findings indicate that oral, intestinal, and pancreatic bacterial microbiomes overlap but exhibit distinct co-abundance patterns in patients with pancreatic cancer and other gastrointestinal diseases.	Yes, available. PRJNA558364.
Dysbiotic gut microbiota in pancreatic cancer patients form correlation networks with the oral microbiota and prognostic factors. Matsukawa, H et al.³⁵ 2021. Japan	PDAC (n=24) Healthy controls (n=18) 15 PDAC salivary samples were obtained.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Downstream sequences were processed using MacQIIME v1.9.1. Representative sequence taxonomies were assigned using the Greengenes reference database.	Multiple salivary microbes were present in the co-occurrence network. Microbacterium Stenotrophomonas These bacteria formed a network with faecal microbes in PDAC tissues.	Not mentioned	The dysbiotic gut microbiota in the pancreatic cancer patients forms a complex network with the oral and cancerous microbiota, and gut microbes abundant in these patients are related to poor overall survival.	Yes, available. PRJNA665854. PRJNA665618.
Characterization of Oral Microbiome and Exploration of Potential Biomarkers in Patients with Pancreatic Cancer. Sun, HY et al.²⁹ 2020. China	PDAC (n=10) Benign pancreatic disease (BPD) (n=17) Healthy controls (HC) (n=10) 37 saliva samples	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Paired-end reads into a single sequence by means of using FLASH software v.1.2.10. Then, 16S rRNA operational taxonomic units (OTUs) were selected from the combined reads via QIIME toolkit v.1.9.1.	The dominant bacteria in the PDAC group were: Fusobacterium Megasphaera Prevotella Spirochaeta Treponema	The dominant bacteria in the HC group (45.60%) and the BPD group (29.40%) were Proteobacteria. The dominant bacteria in the HC group were Neisseriaceae.	High concentrations of Fusobacterium periodonticum and low concentrations of Neisseria mucosa as specific risk factors for PDAC.	Yes, available. SRP237984.
Oral microbiome and pancreatic cancer. Wei, AL et al.³¹2020. China	PDAC (n=41) Healthy controls (n=69) Prior to surgery saliva samples were collected.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Raw sequences were denoised via FLASH. Quality filtering was performed on raw sequences using QIIME (v1.9.1) then high-quality clean tags were obtained. Tags were compared with gold database and chimeras were removed with the UCHIME algorithm (v11.0).	Compared with the healthy control group, carriage of Streptococcus and Leptotrichina was associated with a higher risk of PDAC. Among the patients with PDAC, patients reporting bloating have a higher abundance of: Porphyromonas Fusobacterium Alloprevotella While patients reporting jaundice had a higher amount of Prevotella.	Veillonella and Neisseria were considered a protective microbe that decreased the risk of PDAC and abundant in the healthy control group	Saliva microbiome was able to distinguish patients with PDAC and healthy individuals. Higher Streptococcus and Leptotrichia abundances were associated with increased risk of PDAC.	Yes, available. PMC7789059.
Oral microbial community composition is associated with pancreatic cancer: A case-control study in Iran. Vogtmann, E et al.³⁰ 2020. USA, Iran	PDAC (n=273) Controls (n=285)	16S rRNA gene analysis performed V4 region of the 16SrRNA gene Sequence data processing was performed with QIIME 2 2017.2. Sequences quality control was performed with DADA2. Taxonomy was assigned to the Human Oral Microbiome Database version 14.51.	Increased risk of PDAC were associated with: Enterobacteriaceae Lachnospiraceae G7 Bacteroidaceae Staphylococcaceae Aggregatibacter actinomycetemcomitans	An increased relative abundance of Haemophilus and Proteobacteria, were associated with decreased odds of PDAC.	The overall microbial community appeared to differ between pancreatic cancer cases and controls.	Yes, available. PRJNA549488.
Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study. Fan, XZ et al. 2016. USA	PDAC (n=361) Controls (n=371) Population-based nested case–control study	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Multiplexed and barcoded sequences were deconvoluted using the default parameters of the QIIME script split_libraries.py. Taxonomy was assigned to the Human Oral Microbiome Database version 14.51.	Oral pathogens associated with increased risk of PDAC: Porphyromonas gingivalis Aggregatibacter actinomycetemcomitans Alloprevotella	Fusobacteria and its genus Leptotrichia were associated with decreased risk of PDAC and common in the controls.	This study provides supportive evidence that oral microbiota may play a role in the aetiology of pancreatic cancer.	Not available
Characterization of the salivary microbiome in patients with pancreatic cancer. Torres, PJ et al.²⁵ 2015. USA	PDAC (n=8) Positive controls (n=78) Healthy controls (n=22) Identified as contaminants were removed from all subsequent analyses.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. 16S rRNA sequences were de-multiplexed using QIIME (v.1.8.0) pipeline. Sequences were grouped into OTUs at 97% sequence similarity using the Greengenes reference database.	At the phylum level, PDAC patients had higher proportions of Firmicutes and lower proportions of Proteobacteria At finer taxonomic levels, there was a higher proportion of Leptotrichia in PDAC patients.	Porphyromonas and Neisseria were lower in PDAC patients compared to the controls.	Bacteria abundance profiles in saliva are useful biomarkers for pancreatic cancer though much larger patient studies are needed to verify their predictive utility.	Yes, available. DNA Deposition file
Biofluid (Bile, Pancreas, and Duodenal Fluid)
Bile Microbiome Signatures Associated with Pancreatic Ductal Adenocarcinoma Compared to Benign Disease: A UK Pilot Study. Merali N et al.¹⁵ 2023. UK	PDAC (n=12) Benign control group (n=17) ERCP performed to obtain bile samples.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. The reads were quality checked by DADA2 (v1.25.2) R package [27214047]. Next, by using the “assignTaxonomy” function of DADA2, the reads were mapped to the formatted GTDB database.	In the same samples, the genus Streptococcus (FDR = 0.033) had increased abundance in the PDAC group.	Authors found three genera to be of significantly lower abundance among PDAC samples compared to benign group: Escherichia Proteobacteria Enterobacteriaceae	This study has demonstrated that patients with obstructive jaundice caused by PDAC have an altered microbiome in the bile compared to those with benign disease	Yes, available. PRJNA1018343.
Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease. Shyam K et al. 2023. USA	PDAC (n=25) Cholangiocarcinoma (n=6) Gallbladder cancer (n=1) Benign control group (n=14) ERCP performed to obtain bile samples.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. After the sequencing, the paired-end sequences were processed with QIIME2 package (version 2019.7). The DADA2 pipeline within QIIME2 was used to trim the sequences, dereplicate, filter chimeric sequences and finally merge the paired end reads.	PDAC patients exhibited a predominance of genus Rothia. At the genus level, most abundant in PDAC were: Dickeya Eubacterium hallii group Bacteroides Faecalibacterium Escherichia-Shigella Ruminococcus	Cholangiocarcinoma showed a predominance of genera of: Akkermansia Achromobacter	Microbiome analyses of bile may differentiate malignant from benign samples in pancreaticobiliary diseases.	Yes, available. https://github.com/poudelmd/BileMicrobiome.
Biliary tract microbiota similarities in pancreatic ductal adenocarcinoma. Arteta.A et al. 2022. Colombia	PDAC (n=11) Benign control (n=3) Bile collected from the gallbladder as well as brushings from the intrapancreatic bile duct in PDAC cases.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Fastq files were analysed using Qiime2-2019. The analysis pipeline includes Dada2 for sequence quality control and an in-house trained classifier based on the Greengenes database for taxonomic analysis using a Qiime2 feature-classifier.	In both PDAC groups (GB and PD samples) predominant phylum were: Proteobacteria (64-76%) Firmicutes (14-25%) Bacteroidetes (5-6%) At class taxonomic level, Gammaproteobacteria represents 73% in PDAC.	Not mentioned	Compares microbiota using 16S rRNA in two anatomic locations of the biliary tract in PDAC patients (bile and biliary tract brush over pancreatic tumour.	Not available
Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis. Kirishima M et al.⁴⁰ 2022. Japan	PDAC (n=77) Cholangiocarcinoma (n=99) Gallbladder cancer (n=12) Pancreatic cyst (n=27) Benign other (n=29) Microbiome-derived DNA from the bile juice in surgically resected gallbladders.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Raw reads obtained from the sequencer were filtered according to the barcode and primer sequences using the MiSeq system. Then, the reads were imported into QIIME2 v2019.4 in Linux. Quality assessment, filtering, and chimera detection were performed using the DADA2 pipeline. Taxonomic classification was assigned to amplicon sequence variants using 99% clustering in SILVA 132 database.	Following bacteria showed a significant difference between with and without lymph node metastasis in PDAC: Enterobacter Hungatella Mycolicibacterium Phyllobacterium Sphingomonas Good prognosis factors for PDAC were: Enterococcus Staphylococcus Bacteroides	In the bile duct lesions, high relative abundance and poor prognosis were: Enterococcus, Corynebacterium Haemophilus Lawsonella Staphylococcus The microbiota in the normal gallbladder consists of main phyla: Proteobacteria Firmicutes Bacteroidetes	This study shows a link between gallbladder microbiota and pancreaticobiliary cancer prognosis.	Not available
Characteristics of bile microbiota in cholelithiasis, perihilar cholangiocarcinoma, distal cholangiocarcinoma, and pancreatic cancer. Li Z et al.⁴¹ 2022. China	PDAC (n=8) Cholangiocarcinoma (CCA) (n=23) Benign cholelithiasis (n=22) ERCP performed to obtain bile samples.	16S rRNA gene analysis performed V4 region of the 16SrRNA gene Amplified and processed using the QIIME2 platform and silva138.1 database was used to annotate species.	The significant 10 microbial biomarkers results for the PDAC group were: Pseudomonas Chloroplast Acinetobacter Allorhizobium Neorhizobium Pararhizobium Rhizobium Exiguobacterium Halomonas Staphylococcus	At genus level the biomarkers for proximal CCA were: Pseudomonas Sphingomonas Halomonas Acinetobacter Prevotella For distal CCA they were: Streptococcus Prevotella Halomonas Helicobacter Rikenellaceae	We found an increase in α diversity of the dCCA and PDAC groups compared to the benign group. As this pilot study identified specific microbial bile markers.	Not available
Alterations in the Duodenal Fluid Microbiome of Patients with Pancreatic Cancer. Kohi S et al.¹¹ 2022. USA	PDAC (n=74) Pancreatic Cysts (n=98) Healthy controls (n=134) All patients underwent duodenal endoscopy	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Raw sequences were analysed with QIIME2 2019.1. Raw sequence data were demultiplexed and quality filtered using DADA2. Taxonomy was assigned to ASVs using the SILVA (v132) database.	Duodenal fluid samples from patients with PDAC has higher levels of: Escherichia-Shigella Enterococcus Clostridium sensustricto 1 Bifidobacterium PDAC with short-term survival patients had enrichment of: Fusobacteria Rothia	Duodenal fluid microbiome profiles were not significantly different between control subjects.	Patients with PDAC have alterations in their duodenal fluid microbiome profiles compared with patients with pancreatic cysts.	Yes, available. Bacterial PCR amplification sequencing with the supplementary file
Enterococcus spp. have higher fitness for survival, in a pH-dependent manner, in pancreatic juice among duodenal bacterial flora. Itoyama, S et al. 2021. Japan	PDAC (n=34). Duodenal or Bile duct cancer (BDC) (n=28) Pancreatic juice was collected after pancreatectomy from the drainage tube Only clear colourless pancreatic juice was used.	16S rRNA gene analysis performed V1-V2 hypervariable regions of the 16SrRNA gene. The paired‐end sequences obtained were merged, filtered, and denoised using DADA2. The taxonomic assignment was performed using the QIIME2 feature‐classifier plugin with the Greengenes 13_8 database.	Enterococcus spp. have a higher potential to survive and colonize in pancreatic juice than other bacteria in PDAC cases. The pancreatic juice of patients with PDAC and BDC has a highly heterogeneous bacterial composition.	Not mentioned	Alkalinity is one of the important factors for the selective survival of E. faecalis among microbiota.	Not available
Microbiome Patterns in Matched Bile, Duodenal, Pancreatic Tumour Tissue, Drainage, and Stool Samples: Association with Preoperative Stenting and Postoperative Pancreatic Fistula Development. Langheinrich, M et al.⁴⁴ 2020. Germany	PDAC (N=10) Bile collected intra-operatively Tissue collected intraoperatively Preoperative collected faecal samples	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Reads were demultiplexed and trimmed using Cutadapt, 16S the Uparse, and Sintax algorithms within Usearch using the silva 16S rRNA database (v123).	At genus level the most dominant genera within the bile fluid were: Enterococcus Streptococcus Escherichia Shigella Veilonella Enterobacter	Not mentioned	The microbiome is altered in patients undergoing preoperative stent placement. This cohort of patients have relatively more Enterococci in their bile, tumours, and duodenum.	Not available
Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer. Gaiser RA et al.⁴³ 2019. Sweden	PDAC (n=14) IPMN low grade (n=14) IPMN high grade (n=8) Paired cyst and plasma patients Plasma samples excluded due to low quality results.	16S rRNA gene analysis performed V1-V8 region (1381 bp) of the 16SrRNA gene These libraries were used as input for PacBio Single Molecule, Real-Time (SMRT) amplicon sequencing. Chimera sequences were filtered with UCHIME using a full length, good quality, and non-chimeric 16S rRNA gene reference database. To increase the granularity of the taxonomic assignment, sequences were also mapped to the HOMD 15.1 database.	Highly enriched in the PDAC group: Methylobacterium Sphingomonas	Cyst fluid from IPMN with high-grade dysplasia: Granulicatella Serratia Fusobacterium Cyst fluid from IPMN with low-grade dysplasia: Propionibacterium	The authors identified a co-occurrence and enrichment of oral bacterial taxa within the pancreatic cyst fluid samples. These findings warrant further investigation into the role of oral bacteria in cystic precursors to PDAC.	Not available
Formalin-fixed, paraffin-embedded (FFPE) tissue
Intratumor Microbiome Analysis Identifies Positive Association Between Megasphaera and Survival of Chinese Patients with Pancreatic Ductal Adenocarcinomas. Huang, Y et al.³⁸ 2022. China	PDAC (n=30) 13 short term survivors (OS <300 days) 17 long term survivors (OS>600 days) 16S rRNA gene analysis performed To eliminate any potential effect of contamination, same extraction, and sequencing procedures on margins of the paraffin blocks.	16S rRNA gene analysis performed V4 hypervariable regions of the 16SrRNA gene Each unique ASV was assigned to a high-resolution taxonomy using the Ribosomal Database Project classifiers (implemented in DADA2 pipeline) and SILVA Database v132.	Megasphaera specifically enriched in the LTS samples had a better inhibitory effect on tumour growth. LTS samples exhibited higher abundances of: Sphingomonas Megasphaera Bradyrhizobium hgcI_clade Desulfovibrio Flavobacterium Enhydrobacter Megamonas STS samples exhibited higher abundances of: Clostridium-sensu stricto 1 Actinomyces Porphyromonas Aggregatibacter Neisseria	n/a	Patients with high relative abundances of Sphingomonas and Megasphaera were associated with significantly prolonged overall survival. High abundance of Clostridium were associated with shortened survival time.	Yes. Available PRJNA764032.
Dysbiotic gut microbiota in pancreatic cancer patients form correlation networks with the oral microbiota and prognostic factors. Matsukawa, H et al.³⁵ 2021. Japan	PDAC (n=24) Healthy controls (n=18) FFPE tissue for PDAC patients Faecal samples: PDAC (n=24) Healthy controls (n=18)	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Downstream sequences were processed using MacQIIME v1.9.1. Representative sequence taxonomies were assigned using the Greengenes reference database.	Genera were significantly abundant in PDAC tissues: Sediminibacterium Microbacterium Ralstonia Stenotrophomonas Cupriavidus Microbacterium and Stenotrophomonas were detected in PDAC tissues.	Not mentioned	The dysbiotic gut microbiota in the PDAC patients forms a complex network with the oral and cancerous microbiota, and gut microbes abundant in these patients are related to poor overall survival	Yes. Available PRJNA665854. PRJNA665618.
Endoscopic ultrasound (EUS)-guided fine needle biopsy (FNB) formalin fixed paraffin-embedded (FFPE) pancreatic tissue samples are a potential resource for microbiota analysis. Masi AC et al.³⁴ 2021. UK	PDAC (n=8) Healthy controls (n=8) FFPE EUS-FNB samples were performed.	16S rRNA gene analysis performed V4 hypervariable regions of the 16SrRNA gene. Sequencing annotations not described.	Increase relative abundance of bacteria within PDAC: Cloacibacterium Pseudomonas Corynebacterium Bacteroides	There was an increase of relative abundance of the following bacteria within the healthy controls: Streptococcus Tepidimonas Haemophilus Rothia	There is potential of EUS-FNB FFPE samples to study the pancreas microbiome.	Not available
Tumour Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes. Riquelme, EM et al.²⁰ 2019. USA	LTS PDAC, median survival 10.14 years (n=22) STS PDAC, median survival 1.62 years (n=21) FFPE of PDAC tissue were aseptically collected and bacterial genomic DNA was extracted.	16S rRNA gene analysis performed V4 hypervariable regions of the 16SrRNA gene. Raw paired-end 16S rRNA reads (V4 region) were merged into consensus fragments by FLASH and subsequently filtered for quality using QIIME. High-quality passing 16S rRNA sequences were assigned to a high-resolution taxonomic lineage using Resphera Insight and SILVA Database v128.	A higher alpha-diversity in the tumour microbiome of LTS patients. Intra-tumoral microbiome signature (Pseudoxanthomonas/Streptomyces/Saccharopolyspora/Bacillus clausii) highly predictive of long-term survivorship	n/a	PDAC microbiome composition can cross-talk with the gut microbiome, influences the host immune response and natural history of the disease.	Yes. Available PRJNA542615.
Duodenal mucosa tissue
Comparisons of oral, intestinal, and pancreatic bacterial microbiomes in patients with pancreatic cancer and other gastrointestinal diseases. Chung, M et al.⁴⁵ 2021. USA	PDAC (n=24) Ampullary adenocarcinoma (n=8) Cholangiocarcinoma (n=4) Benign controls (n=16) 22 Duodenum tissue 316 oral samples 34 jejunum swabs, 19 bile duct swab samples, 21 pancreatic ducts, 6 normal pancreatic tissues 33 pancreatic tumour samples.	16S rRNA gene analysis performed V4 hypervariable regions of the 16SrRNA gene. Sequence quality checking performed using DADA2. Taxonomic classification, alignment, and phylogenetic tree building were completed using the QIIME2 database.	Following bacteria were shown to be present between saliva, pancreatic or intestinal tissues of PDAC were: Fusobacterium Rothia Saccharibacteria Oribacterium Streptococcus	Not mentioned	Oral, intestinal, and pancreatic bacterial microbiomes overlap but exhibit distinct co-abundance patterns in patients with pancreatic cancer and other gastrointestinal diseases.	Yes, available. PRJNA558364.
Dysbiosis of the duodenal microbiota as a diagnostic marker for pancreaticobiliary cancer. Sugimoto, M et al.³⁶ 2021. Japan	PDAC (n=12) Benign group (n=22) Endoscopic ultrasound-guided fine needle aspiration.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Bacterial classification was performed according to the OTUs, which were identified by correspondence to a database of human intestinal flora.	Useful biomarkers in PDAC and significantly different from the benign group were: Clostridium cluster XVIII Bifidobacterium Prevotella	The duodenal microbiota is more relevant to the pancreas and bile duct than is the salivary microbiota.	It was possible to investigate the microbiota of duodenal juice. Duodenal microbiota evaluation may contribute to the diagnosis of PDAC.	Not available
Microbiome Patterns in Matched Bile, Duodenal, Pancreatic Tumour Tissue, Drainage, and Stool Samples: Association with Preoperative Stenting and Postoperative Pancreatic Fistula Development. Langheinrich, M et al.⁴⁴ 2020. Germany	PDAC (n=10) Bile collected intra-operatively Tissue collected intra-operatively Pre-operative collected faecal samples	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Reads were demultiplexed and trimmed using Cutadapt, 16S the Uparse, and Sintax algorithms within Usearch using the silva 16S rRNA database (v123).	At genus level the most dominant genera within PDAC duodenal tissue group were: Enterococcus Enterobacter Fusobacterium Akkermansia Veilonella	n/a	The microbiome is altered in patients undergoing preoperative stent placement. This cohort of patients have relatively more Enterococciin their bile, tumours, and duodenum.	Not available
The Microbiomes of Pancreatic and Duodenum Tissue Overlap and Are Highly Subject Specific but Differ between Pancreatic Cancer and Noncancer Subjects. Del Castillo et al.¹⁰ 2019.USA	PDAC (n=51) Benign (chronic pancreatitis. Cysts)n=18 NDRI Organ donation (n=34) 189 tissue samples (pancreatic duct, duodenum, pancreas) 57 swabs (bile duct, jejunum, stomach) 12 stool samples To remove additional contamination, we removed a thin tissue layer around each sample prior to extracting DNA.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Sequences were BLASTN-searched against a combined set of 16S rRNA reference sequences that consist of the HOMD (version 14.5), Greengenes Gold, and the NCBI 16S rRNA reference sequence set. All assigned reads were subject to several down-stream bioinformatics analyses, including alpha and beta diversity assessments, provided in the QIIME software package version 1.9.1.	Significantly increased abundance in PDAC patients: Fusobacterium spp. Within the duodenal tissue of PDAC patients, Selenomonas was also elevated.	Lactobacillus spp. was significantly reduced in PDAC cancers compared with non-cancer patients	Bacterial DNA profiles in the pancreas were like those in the duodenum tissue of the same subjects. Suggesting that bacteria may be migrating from the gut into the pancreas.	Yes, available. PRJNA421501.
Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls. Mei, QX et al.²⁷ 2018. China	PDAC (n=14) Healthy controls (n=14) Endoscopic duodenal mucosal biopsies.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. OTUs were clustered with a 97% similarity cutoff using UPARSE (version 7.1) and chimeric sequences were identified and removed using UCHIME. The taxonomy of each 16S rRNA gene sequence was analysed using the RDP Classifier against the SILVA 119 16S rRNA database.	The most abundant bacteria at genus level were: Acinetobacter Aquabacterium Oceanobacillus Rahnella Massilia Delftia Deinococcus Sphingobium	Duodenal microbiotas of healthy controls were enriched with: Porphyromonas Paenibacillus Enhydrobacter Escherichia Shigella Pseudomonas	These results reveal a picture of duodenal microbiota in PDAC patients	Yes, available. SRP097254.
Intratumoural pancreatic tissue
Bacterial and fungal characterization of pancreatic adenocarcinoma from Endoscopic Ultrasound guided Biopsies. Wright et al.⁵⁰ 2023. USA	PDAC (n=15) 5 EUS FNA biopsies 10 unmatched surgical specimens	16S rRNA gene analysis performed V4 hypervariable regions of the 16SrRNA gene. High-quality passing 16S rRNA sequences were assigned to a high-resolution taxonomic lineage using Resphera Insight. High-quality passing ITS sequences were clustered into OTUs by UCLUST (de novo mode) and assigned a taxonomic lineage using the RDP classifier with the UNITE database.	EUS FNA identified PDAC bacteria: Actinomyces Campylobacter Fusobacterium Granulicatella Haemophilus Prevotella Veilonella Prevotella was the most abundant.	n/a	The Venn diagram and bar plot of genera composition observed at least 35 genera in common with 54% similarity between these two sample types.	Yes. Available. PRJNA1008674.
Endoscopic ultrasound-guided fine-needle biopsy as a tool for studying the intra-tumoral microbiome in pancreatic ductal adenocarcinoma: a pilot study. Chu CS et al.⁴⁷ 2022. China	PDAC (n=9) 6 patients had EUS-FNB biopsy 4 patients had intraoperative biopsy (NB: 1 patient has both EUS FNB and open biopsy)	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Quality-filtered and non-chimeric reads were analysed (UPARSE pipeline) to generate OTUs per sample (at 97% identity level). The OTU representative sequences were searched against the Greengenes 13_5 database by using USEARCH global alignment to identify the corresponding taxonomy.	The following bacteria were found to play a role in the development of PDAC: Porphyromonas Fusobacterium Aggregatibacter Prevotella Capnocytophaga	n/a	The intra-tumoral microbiome profile in tissues obtained by EUS-FNB had similar alpha-diversity and taxonomic profiles with those obtained by surgical biopsy.	Not available
Composition, diversity, and potential utility of intervention-naïve pancreatic cancer intratumoural microbiome signature profiling via endoscopic ultrasound. Gleeson FC et al.¹⁹ 2022. USA	PDAC (n=18) PNET (n=2) Acinar neuroendocrine carcinoma (n=1) Tissues were obtained via EUS fine needle biopsy.	16S rRNA gene analysis performed The hypervariable regions of the 16SrRNA gene were not mentioned. Sequencing annotations not described.	The predominant phyla were: Proteobacteria Bacteroidetes Firmicutes Actinobacteria Gammaproteobacteria (91%) and Fusobacteriota (38%) were the predominant genera	Three positive control tumours had relatively high Helicobacter content, specifically H. pylori.	Proteobacteria dominated the microbiome in PDAC. No difference in either α-diversity or β-diversity metrics between anatomical locations or between the predominant phyla or genera were noted.	Not available
Analysis of the Pancreatic Cancer Microbiome Using Endoscopic Ultrasound–Guided Fine-Needle Aspiration–Derived Samples. Nakano S et al.⁴⁸ 2022. Japan.	PDAC (n=30) Tissues were collected from patients who undergo EUS-FNA. 30 PDAC tissues matched with 30 duodenal and 30 stomach tissues (n=90)	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Amplicon sequence analysis was performed using QIIME2 v.2020.8. Paired-end sequences were imported into QIIME2 and denoised using the DADA2 pipeline. Amplicon sequence variants were selected by aligning the sequences with those in the latest Silva 16S database (v.138).	There was a predominance of Acinetobacter and Pseudomonas in PDAC tissue. Proteobacteria were significantly more abundant in PDAC samples. Delftia was more abundant in resectable PDAC.	Firmicutes, Bacteroidetes, and Fusobacteria were significantly less abundant in PDAC tissues than in GI tissues.	PDAC tissues obtained by EUS-FNA were useful for analysing intratumor microbiome.	Not available
A faecal microbiota signature with high specificity for pancreatic cancer. Kartal E et al.³⁹ 2022 Germany, Spain	Spanish case–control PDAC (n=23) Adjacent healthy tissue (n=20) Intraoperative tumour biopsies were taken To account for potential bacterial contamination of extraction, negative controls (extraction blanks) were included.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Raw reads were quality trimmed and filtered against chimeric PCR artefacts using DADA2.	Enriched in PDAC tissue were: Lactobacillus spp Akkermansia muciniphila Bacteroides spp FISH assays verified the prevalence of genus-specific primers in PDAC tissues: Akkermansia spp Lactobacillus spp Bifidobacterium spp Veillonella spp Bacteroides spp	Not mentioned	Several taxa could be traced between the gut and pancreas, with univariate enrichment in tumours relative to adjacent healthy tissue. Indicating direct associations of PDAC with the gut microbiome.	Yes, available. PRJEB38625. PRJEB42013.
Tumour microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer. Guo W et al.¹² 2021. China	PDAC (n=62) PDAC tumour and adjacent tissues were collected intraoperatively	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. After sequence trimming and duplicate filtering, the passing reads were aligned to the human reference (GRCh38) using Bowtie2 to preliminarily remove the host DNA sequences. A customized database, which consists of reference libraries of bacteria, viruses, fungi, archaea, plasmids, UniVec and human from the NCBI database, was constructed for taxonomic classification in Kraken2.	Basal-like tumours had a distinct microbial community. Increasing abundance of: Acinetobacter Pseudomonas Sphingopyxis	n/a	These findings indicated that the tumour microbiome is closely related to PDAC oncogenesis and the induction of inflammation.	Yes, available. PRJNA719915
Role of biliary stent and neoadjuvant chemotherapy in the pancreatic tumour microbiome. Nalluri et al.⁴⁶ 2021. USA	PDAC (n=27) PDAC tumour and adjacent tissues were collected intra-operatively	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Amplicon sequence data were processed and analysed using Mothur software version 1.41.1. Reads were paired end joined, quality trimmed, and aligned against the SILVA database version.	Among both malignant and normal adjacent tissue samples, the most abundant families of bacteria include: Ruminococcaceae Staphylococcaceae Bacillaceae Enterobacteriaceae Pseudomonadaceae.	n/a	Preoperative biliary stent placement and neoadjuvant chemotherapy can encourage bacterial colonization of PDAC tissue.	Yes, available. SRP197553.
Comparisons of oral, intestinal, and pancreatic bacterial microbiomes in patients with pancreatic cancer and other gastrointestinal diseases. Chung M et al.⁴⁵ 2021. USA	PDAC (n=24) Ampullary adenocarcinoma (n=8) Cholangiocarcinoma (n=4) Benign controls (n=16) 6 normal pancreatic tissues 33 pancreatic tumour samples 22 Duodenum tissue 316 oral samples (52 tongue swab, 46 buccal swab, 35 supragingival swab, 48 saliva samples) 34 jejunum swab, 19 bile duct swab samples, 21 pancreatic ducts,	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Sequence quality checking and denoising were performed using the DADA2 Illumina sequence denoising process. Taxonomic classification, alignment, and phylogenetic tree building were completed using QIIME2.	Fusobacterium nucleatum was among the top shared species based on the taxonomic annotations between oral and intestinal or pancreatic samples. ASV (Amplicon Sequence Variants) that were present in PDAC were: Fusobacterium Rothia Saccharibacteria Oribacterium Streptococcus	Not mentioned	Oral, intestinal, and pancreatic bacterial microbiomes overlap but exhibit distinct co-abundance patterns in patients with PDAC and other gastrointestinal diseases.	Yes, available. PRJNA558364.
Microbiome Patterns in Matched Bile, Duodenal, Pancreatic Tumour Tissue, Drainage, and Stool Samples: Association with Preoperative Stenting and Postoperative Pancreatic Fistula Development. Langheinrich, M et al.⁴⁴ 2020. Germany	PDAC (N=10) Bile collected intra-operatively Tissue collected intra-operatively Pre-operative collected faecal samples	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Reads were demultiplexed and trimmed using Cutadapt, 16S the Uparse, and Sintax algorithms within Usearch using the silva 16S rRNA database (v123).	At genus level the most dominant genera within PDAC tissue group were: Enterococcus Enterobacter Fusobacterium Barnesiella Akkermansia	n/a	This study demonstrates that there is a distinct microbiome in the different compartments adjacent to the pancreas.	Not available
Faecal
Gut Streptococcus is a microbial marker for the occurrence and liver metastasis of pancreatic cancer. Yang J et al.⁵¹ 2023. China	PDAC (n=44) Liver metastasis (LMn=27) Nonliver metastasis (non-LM,n=17) Healthy patients (n=50)	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. The data reads were filtered by the DADA2 method of QIIME2 software (v2019.4) and used to cross compare with the Greengenes database (release 13.8) for species annotation.	Significantly increased bacteria in PDAC were: Streptococcus Lactobacillus Bifidobacterium Linear discriminant analysis (LDA) was conducted to estimate the effect size (LEfSe) of each differential flora and found 16 significantly different microorganisms in the PDAC group.	11 significantly microbes in healthy group: p_Bacteroidetes, c_Bacteroidia, o_Bacteroidales, f_Bacteroidaceae, g_Bacteroides, c_Clostridia, o_Clostridiales, f_Lachnospiraceae, g_Roseburia, g_Faecalibacterium, f_Veillonellaceae	The study found that the intestinal microbial richness of PDAC patients was higher. The Streptococcus content was a predictive microbiota marker of PDAC (AUC of 0.927 (p < 0.001). As well as playing a key role in identifying liver metastases (AUC = 0.796, p < 0.001).	Yes. Available. PRJNA977486.
Impact of neoadjuvant therapy on gut microbiome in patients with resectable/borderline resectable pancreatic ductal adenocarcinoma. Takaori A et al.⁴⁹ 2023. Japan	PDAC (n=20) Stool samples were collected from patients before and after neoadjuvant chemotherapy treatment (NAC). Faecal microbiota profiles before and after NAC were analysed using bacterial 16S rRNA gene sequences in patients with R/BR-PDAC.	16S rRNA gene analysis performed The hypervariable regions of the 16SrRNA gene were not mentioned. The sequence reads were imported into QIIME2 software and analysed for bacterial identification and diversity.	At the phylum level, Firmicutes was the most abundant bacteria before and after NAC. The next most common bacteria were: Bacteroidota Actinocabteriota Proteobacteriota	n/a	This study is the first to compare the gut microbiota before and after NAC for PDAC. Lower incidence of Bifidobacterium genus before NAC associated with a lower pathological response to NAC.	Not available
Changes in intestinal bacteria and imbalances of metabolites induced in the intestines of pancreatic ductal adenocarcinoma patients in a Japanese population: a preliminary result. Hashimoto S et al. 2022.Japan	Unresectable PDAC (n=5) Healthy controls (n=68)	16S rRNA gene analysis performed The hypervariable regions of the 16SrRNA gene were not mentioned. Sequencing annotations not described.	A significant increase in oral-associated bacteria were noted in PDAC cases: Actinomyces Streptococcus Veillonella Lactobacillus	A significant decrease of Anaerostipes was demonstrated in the faeces of PDAC patients compared with the control.	Showing the intestinal environment of PDAC patients is characterized by an increase in oral-associated bacteria.	Not available
Integrative analysis of metabolome and gut microbiota in patients with pancreatic ductal adenocarcinoma. Guo X et al. 2022³⁷. China	Resectable PDAC (n=36) Unresectable PDAC (n=36)	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. The data was analysed with QIIME (version 1.9.1).	Resectable PDAC patients were: Alistipes Anaerostipes Faecalibacterium Parvimonas Unresectable PDAC patients were: Pseudonocardia Cloacibacterium Mucispirillum Anaerotruncus	n/a	There are metabolic and microbiome differences between resectable and unresectable PDAC patients.	Not available
A faecal microbiota signature with high specificity for pancreatic cancer. Kartal E et al.³⁹ 2022 Germany, Spain	Spanish case–control faecal samples PDAC (n=51) Controls (n=46) Chronic pancreatitis (n=23) German case-control faecal samples PDAC (n=44) Controls (n=32)	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Raw reads were quality trimmed and filtered against chimeric PCR artefacts using DADA2.	Enriched in faeces of patients with PDAC were: Veillonella atypica, Fusobacterium nucleatum/hwasookii Alloscardovia omnicolens	Whereas following bacteria species were depleted in PDAC: Romboutsia timonensis Faecalibacterium prausnitzii Bacteroides coprocola Bifidobacterium bifidum	The presented PDAC-specific microbiome signatures, including links between microbial populations across tissues, provide novel microbiome-related hypotheses.	Yes, available. PRJEB38625. PRJEB42013.
Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study. Nagata N et al.⁴² 2022. Japan	Japan cohort: PDAC (n=47), Controls (n=235) Spanish cohort: PDAC (n=57), Controls (n=50) German cohort: 44 PDAC (n=44), Controls (n=32) Multinational shotgun metagenomic analysis of faecal samples collected from patients with treatment-naïve PDAC and non-PDAC controls in Japan, Spain, and Germany.	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. The 16S database was reconstructed from three publicly available databases: Ribosomal Database Project v.10.27 and a reference genome sequence database obtained from the NCBI FTP site.	Significant enrichments of gut signatures for PDAC in all the 3 cohorts: Streptococcus Veillonella spp	Faecalibacterium prausnitzii was consistently decreased in the gut microbiome of patients with PDAC in all the 3 cohorts.	The identification of shared gut microbial signatures for PDAC in Asian and European cohorts indicates the presence of robust and global gut microbial biomarkers	Yes, available. https://www.sciencedirect.com/science/article/pii/S0016508522003547
Dysbiotic gut microbiota in pancreatic cancer patients form correlation networks with the oral microbiota and prognostic factors. Matsukawa, H et al.³⁵ 2021. Japan	PDAC (n=24) Healthy controls (n=18) Faecal samples: PDAC (n=24) Healthy controls (n=18) 16S rRNA gene analysis performed	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Downstream sequences were processed using MacQIIME v1.9.1. Representative sequence taxonomies were assigned using the Greengenes reference database.	Four faecal microbes associated with poor survival in PDAC: S. thermophiles, Bifidobacterium animalis Eubacterium ventriosum Collinsella aerofaciens	Not mentioned	The dysbiotic gut microbiota in the PDAC patients forms a complex network with the oral and cancerous microbiota. Gut microbes abundant in these patients are related to poor overall survival	Yes, available. PRJNA665854. PRJNA665618.
Metataxonomic and Metabolic Impact of Faecal Microbiota Transplantation from Patients with Pancreatic Cancer into Germ-Free Mice: A Pilot Study. Genton, L et al.³² 2021. Switzerland.	Faecal microbiome transplant treatment PDAC (n=5) Healthy controls (n=5) Faecal samples collected within 7 days of recruitment	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. For the sequence analysis, paired reads were quality filtered using PEAR v0.9.11. Merged sequence reads were clustered using UNOISE3 from the USEARCH v10.0.240 pipeline and OTUs were classified using EzBioCloud 16S database.	PDAC was associated with: Escherichia coli Streptococcus salivarius Enterobacteriaceae Proteobacteria	These species were lower in PDAC patients and in mice transplanted with the faeces from these patients: Alistipes obesi Lachnospiraceae Coriobacteriaceae	The strengths of this study are its translational and innovative design, using the faeces of PDAC patients naïve of oncologic treatments and healthy volunteers.	Yes, available. PRJEB43581.
Microbiome Patterns in Matched Bile, Duodenal, Pancreatic Tumour Tissue, Drainage, and Stool Samples: Association with Preoperative Stenting and Postoperative Pancreatic Fistula Development. Langheinrich, M et al.⁴⁴ 2020. Germany	PDAC (N=10) preoperative faecal sample Bile collected intra-operatively Tissue collected intra-operatively 16S rRNA gene analysis performed	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Reads were demultiplexed and trimmed using Cutadapt, 16S the Uparse, and Sintax algorithms within Usearch using the silva 16S rRNA database (v123).	The predominant genera in the gut were: Bacteroides Escherichia_Shigella Clostridium_XlVa Faecalibacterium Enterobacter	n/a	This study demonstrates that there is a distinct microbiome in the different compartments adjacent to the pancreas.	Not available
Faecal microbiome signatures of pancreatic cancer patients. Half, E et al.²⁸ 2019. Israel	PDAC (n=30) Nonalcoholic fatty-liver disease (NAFLD) (n=16) Precancerous lesions (PCL) (n=6) Healthy cohort (n=13) faecal samples collected after diagnosis and before treatment	16S rRNA gene analysis performed V3-V4 hypervariable regions of the 16SrRNA gene. Demultiplexed raw sequences were quality and merged using PEAR. Data was then processed with the QIIME package and VSEARCH, and according to the strategy described in the UPARSE pipeline. Taxonomy assignment used the UCLUST algorithm against Silva v128 database.	In this study we find a distinct PDAC-associated gut microbiome signature in an Israeli cohort: Veillonellaceae Akkermansia Odoribacter	Prevalent in the healthy control: Clostridiacea Lachnospiraceae Ruminococcaceae Megasphaera and Lachnospiraceae UCG_008, both of which were overrepresented in NAFLD as well as in PDAC. The genus Veillonella was associated with biliary obstruction.	The low incidence of PDAC and the high variability in microbiome both within and between the cohorts, harnessing microbial patterns for diagnostic purposes may only be practical if combined with additional biomarkers.	Yes, available. PRJNA575620
Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China. Ren, ZG et al.²⁶ 2017. China	PDAC (n=85) Healthy controls (n=57)	16S rRNA gene analysis performed V3-V5 hypervariable regions of the 16SrRNA gene. The amplified reads were processed by FLASH version 1.2.10 and sequences were detected with UCHIME version 4.2.40 with 16S “golden standard” database. Annotation of taxonomy sequences were performed using RDP classifier version 2.6.	In PDAC pathogens included were: Veillonella Klebsiella Selenomonas LPS-producing bacteria were enriched including: Prevotella Hallella Enterobacter	Whereas in the healthy controls: Coprococcu Clostridium IV Blautia Flavonifractor Anaerostipe	The gut microbial profile was unique in PDAC, providing a microbial marker for non-invasive PDAC diagnosis.	Yes, available. PRJEB13286.