Table 2 PCR-based results detecting fish pathogen species and their species-specific virulence genes in microbiome DNA samples from different habitats (fish tank, river, fish farm)
Standard PCR | Fish tank | River | Fish farm | |||
|---|---|---|---|---|---|---|
Detected | Samples | Detected | Samples | Detected | Samples | |
E. faecium/E. faecalis | + | 16/18 | + | 3/3 | + | 3/3 |
esp | + | 15/18 | + | 3/3 | + | 3/3 |
gelE | + | 12/18 | + | 3/3 | + | 3/3 |
efaA | + | 5/18 | + | 3/3 | + | 3/3 |
ace | + | 1/18 | − | 0/3 | − | 0/3 |
as | − | 0/18 | − | 0/3 | − | 0/3 |
A. hydrophila | + | 17/18 | + | 3/3 | + | 3/3 |
act | + | 5/18 | + | 3/3 | + | 3/3 |
alt | + | 16/18 | + | 3/3 | + | 3/3 |
ast | + | 10/18 | + | 3/3 | + | 3/3 |
aerA | + | 13/18 | + | 3/3 | + | 3/3 |
qPCR | Fish tank (n = 90) | River (n = 3) | Fish farm (n = 3) |
|---|---|---|---|
Copy numbers/16S rDNA | Copy numbers/16S rDNA | Copy numbers/16S rDNA | |
E. faecium/E. faecalis | 8.16E−04 ± 6.41E−04 | 3.52E−04 ± 3.43E−04 | 6.20E−02 ± 4.79E−05 |
A. hydrophila | 1.69E−01 ± 5.09E−02 | 5.52E−02 ± 5.93E−02 | 7.35E−03 ± 4.83E−03 |