Fig 1.
Flow diagram showing the approaches used to obtain genome sequences from cultured and uncultured microbes.
Pink lines show the sequence of manipulations for frozen samples, and green lines for culture-based samples.
Table 1.
List of primers and conditions for PCR reactions used to amplify a particular target of bacteria regions.
Table 2.
Number of read sequences in bacteria at the genus-level in hamster liver and worm samples obtained by next generation sequencing (Illumina MiSeq platform) of V3-V4 hypervariable regions of prokaryotic 16S rDNA.
Fig 2.
Distribution and diversity of bacterial DNA at genus-level in hamster liver and worm samples.
(a) Normal, OV-infected and worm groups. (b) OV-infected group (cultured specimen vs. frozen liver). Genera accounting for less than 0.5% of sequences in all samples were classified into 'others'. Normal: Normal group, OV: O. viverrini-infected group, Worm: O. viverrini adult worms.
Fig 3.
Distribution and diversity of bacterial DNA at species-level in hamster livers and worm samples.
(a) Normal, OV-infected and worm groups. (b) OV-infected group (cultured specimen vs. frozen liver). Species accounting for less than 0.5% of sequences in all samples were classified into 'others'. Normal: Normal group, OV: O. viverrini-infected group, Worm: O. viverrini adult.
Fig 4.
Heat map of identified bacteria at genus (a) and certain species (b) levels in hamster livers and adult worms.
Rows indicate the abundance of sequences from each taxon among different samples, and columns indicate the abundance of sequences from each taxon within each sample. The tree at the left-hand side of each heat map clusters rows according their similarity and the tree above each heat map groups samples by their similarity. Normal. 15 m: Normal group (n = 7, pooled), OV.15m: O. viverrini-infected group at 15 months (n = 8, pooled), OV.8.12m: O. viverrini-infected groups at 8 and 12 months (n = 6, pooled), Worm 15 m: worms obtained from O. viverrini-infected hamsters 15 months p.i. (n = 2 pooled)
Fig 5.
Complexity of microbial diversity in hamster liver and worm samples in chronic opisthorchiasis.
(a) OTU rank abundance curve. (b) Rarefaction plot of alpha diversity (observed species indices).
Fig 6.
Venn diagram of identified bacterial species among different groups.
(a) Normal group and adult worm group. (b) Normal group and OV-infected group. (c) Worm group and OV-infected group. (d) Among three groups.
Fig 7.
Immunohistochemical localization of Helicobacter pylori infection in hamster liver infected with O. viverrini.
Immunostaining for H. pylori appears as brown color (arrow) within (a) hepatocytes, (b) sinusoid, (c) bile duct and (d) O. viverrini adult worm. Original magnification, x1000, Scale bar is 10μm.