Table 1.
Baseline characteristics of the patients with primary biliary cholangitis.
Fig 1.
DNA library in control and PBC sera.
(A) The quality check of DNA library in E.coli (as a control) and PBC sera detected an amplification read peak at 200–300 bp. (B) The Reads peak histogram in PBC samples. The results of the library check ensured the quantity and quality of DNA required for metagenomic analysis.
Fig 2.
Laser capture microdissection (LMD) of paraffin-embedded liver tissues from PBC portal area and hepatocyte area.
(A) The PBC liver histology before and after selective LMD of the portal area. (B) The PBC liver histology before and after LMD of the hepatocyte area. Each area was selectively and reliably dissected. Scale bare = 50 μm.
Table 2.
The total areas of the dissected portal and hepatocyte regions after LMD.
Table 3.
The list of the most common bacterial genera detected by metagenomic analysis of PBC and healthy control sera (mean read counts).
Fig 3.
Validation study in serum samples.
Sphingomonas paucimobilis, the reference species of Sphingomonas, was used as a control for comparison in the validation PCR study. The gene sequences that could detect both S. panacis and S. paucimobilis reference species. S. panacis was detected in the 2 PBC sera samples (sample ID: S8 and S11) and the detection rate was 18%.
Table 4.
The detected bacterial genera by 16S rRNA metagenome analysis in PBC liver tissues (mean read counts).
Fig 4.
Validation study in liver tissues.
(A) A comparison of the concentration of the PCR-amplified product (280 bp) of DNA extracted from the portal and hepatocellular regions. The PCR band extracted from the portal region was detected in all the samples. The concentration of S. panacis band detected in the portal region was higher than that of the band detected in the hepatocyte region in all samples. (B) The concentration of the PCR-detected bands was standardized between the hepatocellular and portal areas of each LMD section, the PCR product extracted from the portal area was significantly more highly expressed than that from the hepatocellular area.