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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)

From: The impact of the anti-diabetic drug metformin on the intestinal microbiome of larval brown trout (Salmo trutta f. fario)

Standard PCRFish tankRiverFish farm
DetectedSamplesDetectedSamplesDetectedSamples
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+1/180/30/3
as0/180/30/3
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
qPCRFish tank (n = 90)River (n = 3)Fish farm (n = 3)
Copy numbers/16S rDNACopy numbers/16S rDNACopy numbers/16S rDNA
E. faecium/E. faecalis8.16E−04 ± 6.41E−043.52E−04 ± 3.43E−046.20E−02 ± 4.79E−05
A. hydrophila1.69E−01 ± 5.09E−025.52E−02 ± 5.93E−027.35E−03 ± 4.83E−03
  1. The number of investigated fish samples is given together with the target-specific positive tested fish samples. The fish pathogens in microbiome DNA extracts were also quantified by qPCR including standard deviation (bottom part of the table)