Table 1.
Selected studies reporting on microbes associated with benign biliary disease and biliary tract cancer in human studies.
| Author | Country | Type of study | No. of patients | Disease site | Sample type | Method of analysis | Microbiota results |
|---|---|---|---|---|---|---|---|
| Helicobacter species | |||||||
| Murphy et al. [43] | Finland | Prospective | 410 |
Biliary tract carcinoma (BTC) (89) Hepatocellular carcinoma (HCC) (97) Age-matched controls (224) |
Serum | Helicobacter spp. Multiplex serology assay |
Helicobacter pylori (H. pylori) seropositivity in 100% gallbladder cancer, 97% of extra-hepatic bile duct cancer, 96% of intrahepatic bile duct cancer and 91% of ampulla of Vater cancer. OR 5.47 (95% CI 1.17–25.65) for H.pylori seropositivity and risk of developing BTC. |
| Segura-López et al. [41] | Mexico | Prospective | 194 |
Extra-hepatic cholangiocarcinoma (ECCA) (103) Control—benign biliary pathology (91) |
aBiliary brushing | Polymerase chain reaction (PCR) |
Helicobacter bilis (H. bilis) infection was significantly associated with ECCA (43% of cases) compared to benign biliary pathology (21% of cases) (p = 0.002). Helicobacter hepaticus (H. hepaticus) infection not significantly different between the two groups (p = 0.82). |
| Avilés-Jiménez et al. [42] | Mexico | Prospective | 200 |
Extra-hepatic cholangiocarcinoma (100) Control—benign biliary pathology (100) |
aBiliary brushing |
PCR (all samples) 16S ribosomal ribonucleic acid (rRNA) gene sequencing (20 samples) |
H. pylori significantly more abundant in ECCA than in control group (p = 0.035) Significant difference in microbiota composition between ECCA and benign biliary pathology group (p = 0.01). Methylophilaceae, Fusobacterium, Prevotella, Actinomyces, Novosphingobium and H. pylori increased in ECCA. |
| Zhou et al. [40] |
Japan Thailand India Pakistan Germany |
Meta-analysis |
10 studies (726 patients) |
Biliary tract cancer (190) Benign biliary pathology (434) Control—no biliary pathology (102) |
Serum Bile Tissue |
PCR Enzyme linked immunosorbent assay (ELISA) Culture Immunohistochemistry |
Infection rate of Helicobacter spp significantly higher in BTC group compared to: -benign biliary pathology group (OR 3.2, 95% CI 2.15–4.77, p = 0.0001) -control group (OR 6.5, 95% CI 3.14–13.63, p = 0.0001) Higher rate of H. pylori (49.5% vs 33.3%, p = 0.003) and H. bilis (52.2% vs 23.7%, p < 0.0001) in BTC group vs benign biliary pathology group. No significant difference in rate of H. hepaticus and Helicobacter ganmani between groups. |
| Xiao et al. [39] |
Sweden Germany Japan Thailand China |
Meta-analysis |
10 studies (418 patients) |
Cholangiocarcinoma (CCA) Control—without cholelithiasis |
Serum Bile Tissue |
PCR ELISA Culture Immunohistochemistry |
Significant association between Helicobacter spp and CCA (cumulative OR 8.88, 95% CI 3.67–21.49). Subgroup analysis based on geographic distribution: -Asia (OR 6.68, 95% CI 2.29–19.49) -Europe (OR 14.9, 95% CI 4.79–46.35) |
| Salmonella typhi | |||||||
| Author | Country | Type of study | No. of patients | Disease site | Sample type | Method of analysis | Microbiota results |
| Nagaraja et al. [44] |
UK India Chile USA China Japan Bolivia Mexico |
Meta-analysis | 17 studies | Gallbladder carcinoma (GBC) |
Serum Bile Tissue |
Antibody levels Culture PCR |
Subgroup analysis of studies from South-East Asia showed significant association between chronic Salmonella typhi (S. typhi) status and GBC (OR 4.13, 95% CI 2.87–5.94, p < 0.01). Chronic S. typhi carrier state significantly associated with GBC based on S. typhi antibody levels (OR 3.52, 95% CI: 2.48–5.00, p < 0.01) and culture (OR: 4.14, 95% CI 2.41–7.12, p < 0.01). |
| Koshiol et al. [45] |
Chile India USA Denmark China Japan Bolivia Mexico |
Meta-analysis | 16 studies | Gallbladder carcinoma |
Serum Bile Stool Tissue |
Antibody levels Culture PCR |
Elevated S. typhi Vi antibody seropositivity associated with GBC risk (RR 4.6, 95% CI 3.1–6.8). Positive S. typhi bile or stool culture associated with GBC risk (RR 5.0, 95% CI 2.7–9.3) |
| Other identified microbiota | |||||||
| Author | Country | Type of study | No. of patients | Disease site | Sample type | Method of analysis | Microbiota results |
| Lenz et al. [55] | Germany | Prospective | 58 |
Biliary tract carcinoma (24%) Chronic pancreatitis (14%) Choledocholithiasis (14%) Unclear stenosis of common bile duct (9%) Remaining 39% not specified |
aBile | 16S rRNA gene sequencing |
In all patients, the 9 most common bacterial phyla were Pseudomonadales (11.8%), Enterobacteriales (10.0 %), Sphingomonadales (8.3 %), Burkholderiales (8.1%), Lactobacillales (7.6%), Caulobacterales (6.7%), Alteromonadales (6.3%), Rhizobiales (6.0%) and Clostridiales (5.8%). No significant correlation between phyla and primary diagnosis (p = 0.803), CCA (p = 0.664) or malignant biliary stenosis (p = 0.529). |
| Tsuchiya et al. [48] 2018 |
Bolivia Chile |
Prospective | 37 |
Gallbladder carcinoma (7) Cholelithiasis (30) |
bBile | 16S rRNA gene sequencing |
Fusobacterium nucleatum, Escherichia coli (E. coli) and Enterobacter sp. were the predominant species in patients with GBC. E. coli, Enterococcus gallinarum and Salmonella sp. were the predominant species in patients with cholelithiasis. |
| Poudel et al. [49] | USA | Prospective | 10 |
Cholangiocarcinoma (3) Ampullary carcinoma (1) Pancreatic ductal adenocarcinoma (PDAC) (5) Gallstone pancreatitis (1) |
aBile | 16S rRNA gene sequencing |
Most reads were from phyla Firmicutes (57.9%) and Proteobacteria (14.9%). Benign specimen (pancreatitis) separated clearly from the rest showing 98.9% of reads from Clostridium sensu stricto (phylum Firmicutes). Beta-diversity analysis: a cluster including 3 samples (2 with CCA, 1 with PDAC) had higher abundance of phyla Fusobacteria (90.6%) and Verrucomicrobia (92.9%) |
| Jia et al. [50] | China | Prospective | 84 |
Intrahepatic cholangiocarcinoma (ICCA) (28) Hepatocellular carcinoma (28) Liver cirrhosis (16) Control—no biliary pathology (12) |
Faecal | 16S rRNA gene sequencing |
ICCA patients showed higher prevalence rates of Lactobacillus, Actinomyces, Peptostreptococcaceae, and Alloscardovia than the other groups The family Ruminococcaceae was more abundant in patients with ICCA with vascular invasion (compared to those without vascular invasion) |
| Chng et al. [51] |
Singapore Thailand Romania |
Retrospective | 60 |
Cholangiocarcinoma Opisthorchis.viverrini associated (28) Non O. viverrini associated (32) |
cTumour | 16S rRNA gene sequencing |
Dietziaceae, Pseudomonadaceae and Oxalobacteraceae were the major inhabitants of bile duct tissues in CCA patients. Bifidobacteriaceae, Enterobacteriaceae and Enterococcaceae enrichment in O. viverrini versus non - O. viverrini groups. Stenotrophomonas significantly enriched in tumour vs adjacent normal tissue in non - O. viverrini group (p = 0.039) |
| Lee et al. [57] | South Korea | Prospective | 155 |
Biliary tract cancer (24) Cholecystitis/cholangitis (43) Control—no biliary pathology (88) |
dPlasma | 16S rRNA gene sequencing | Compositional differences of Bifidobacteriaceae family and Oxalobacteraceae Ralstonia found to be a significant positive marker, and the Pseudomonadaceae family, Corynebacteriaceae Corynebacterium and Comamonadaceae Comamonas were significant negative markers to differentiate BTC patients from control group. |
| Chen et al. [52] | China | Prospective | 68 |
Distal cholangiocarcinoma (dCCA) (8) Common bile duct stones (44) Recurrent choledocholithiasis (16) |
aBile | 16S rRNA gene sequencing |
Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the most dominant phyla in the bile of patients with dCCA and common bile duct stones. Significant increase in the phyla Gemmatimonadetes, Nitrospirae, Chloroflexi, Latescibacteria, and Planctomycetes in dCCA patients compared to common bile duct stones. |
| Dangtakot et al. [53] | Thailand | Prospective | 60 |
Cholangiocarcinoma (30) Choledocholithiasis (CDL) (30) |
aBile | 16S rRNA gene sequencing |
Enterobacter, Stenotrophomonas and Pseudomonas significantly more abundant in CCA compared to CDL (p < 0.05). Cetobacterium, Pyramidobacter and Streptococcus species significantly less abundant in CCA compared to CDL (p < 0.05). |
| Katsuyuki et al. [56] | USA | Prospective |
95 bile (b) samples 58 faecal (f) samples |
Cholangiocarcinoma (11f, 26b) Primary sclerosing cholangitis (31f, 35b) PSC co-existing with CCA (16f, 17b) Control—cholelithiasis or choledocholithiasis (17b) |
eBile Faecal |
16S rRNA gene sequencing |
CCA bile samples had significant difference of alpha diversity compared to control group, with less Streptococcaceae and Desulfovibrionaceae. An increased abundance of Fusobacteria was found after biliary stent placement and increased with the number of stents in the bile duct. |
| Zhang et al. [54] | China | Prospective | 71 |
Cholangiocarcinoma (8) Hepatocellular carcinoma (10) Mixed-type liver cancer (6) Liver cirrhosis (24) Control—healthy (23) |
Faecal | 16S rRNA gene sequencing |
Enterobacter and Escherichia-Shigella most significantly represented in patients with primary liver cancer (CCA, HCC, mixed-type). Relative abundance of Enterobacter ludwigii highest in primary liver cancer group and 100× greater than liver cirrhosis and healthy controls. Significantly decreased Firmicutes/Bacteroidetes ratio in primary liver cancer group compared to healthy controls (p < 0.05). |
| Song et al. [58] | China | Prospective | 14 |
Gallbladder carcinoma (7) Chronic calculous cholecystitis (7) |
bTissue | Metagenomic sequencing | Peptostreptococcus stomatis, Fusobacterium mortiferum, Acinetobacter junii and Enterococcus faecium positively correlated and significantly contributed to GBC group. |
| Saab et al. [38] | Iran | Prospective | 75 |
Extra-hepatic cholangiocarcinoma (28) Control—benign biliary pathology (47) |
aBile | 16S rRNA gene sequencing |
The most abundant genera in ECCA group were Enterococcus, Streptococcus, Bacteroides, Klebsiella and Pyramidobacter. In a subgroup analysis of patients without comorbidities (19 ECCA and 37 controls), relative abundance of Bacteroides, Geobacillus, Meiothermus and Anoxybacillus significantly higher in ECCA compared with controls (p < 0.05). |
| Serra et al. [46] | Italy | Prospective | 53 |
Cholangiocarcinoma (20) Gallbladder carcinoma (2) Carcinoma of the head of the pancreas (31) |
bBile | Phoenix Automated Microbiology System |
E. coli and Pseudomonas spp were significant positive predictors for presence of CCA (p < 0.0001). Pseudomonas spp only significant positive predictor for presence of GBC (p = 0.0001). |
| Di Carlo et al. [47] 2019 | Italy | Retrospective | 152 |
Cholangiocarcinoma (42) Gallbladder carcinoma (5) Ampullary carcinoma (4) Carcinoma of the head of the pancreas (72) Cholelithiasis (27) Cholangitis (1) Chronic pancreatitis (1) |
cBile | Phoenix Automated Microbiology System or Vitek-2 System | E. coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were identified in the cancer population and their presence was associated with reduced survival time. |
aSamples obtained at time of scheduled endoscopic retrograde cholangiopancreatography (ERCP) or percutaneous transhepatic biliary drainage (PTBD).
bSamples obtained at time of surgery.
cArchived samples (previous biopsy or biliary tract procedure).
dBacteria-derived extracellular vesicles isolated in the plasma.
eTiming of sample collection not specified.