Table 2 EGTs assigned to putative pathogenic bacterial species and corresponding genera and orders by means of CARMA3
Dataset | B55 | S55 | S65 | S70 | G5 | G30 | U1 | Average | Average [%] |
|---|---|---|---|---|---|---|---|---|---|
All reads | 248,775 | 303,493 | 309,589 | 315,387 | 265,256 | 274,138 | 1,347,644 | 437,755 | 100.00 |
All classified reads | 180,454 | 223,536 | 237,134 | 255,499 | 193,025 | 196,763 | 897,311 | 311,960 | 72.26 |
Clostridiales (order) | 21,479 | 53,756 | 62,570 | 43,940 | 33,353 | 26,989 | 23,482 | 37,939 | 8.67 |
Clostridium | 1,535 | 6,622 | 16,459 | 6,326 | 2,855 | 2,163 | 3,333 | 5,613 | 1.28 |
C. botulinum | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0.00 |
C. sordelii | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
C. butyricum | 5 | 2 | 0 | 0 | 0 | 0 | 0 | 1 | 0.00 |
C. difficile | 0 | 1 | 0 | 0 | 0 | 3 | 1 | 1 | 0.00 |
C. perfringens | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.00 |
C. tetani | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0.00 |
C. clostridioforme | 0 | 0 | 0 | 0 | 1 | 1 | 2 | 1 | 0.00 |
Enterobacteriales (order) | 26 | 25 | 24 | 12 | 57 | 41 | 39 | 32 | 0.01 |
Escherichia | 1 | 0 | 0 | 0 | 1 | 3 | 3 | 1 | 0.00 |
E. coli | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0.00 |
Salmonella | 1 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0.00 |
S. enterica | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
Shigella | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.00 |
S. boydii | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
S. dysenteriae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
S. flexneri | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
S. sonnei | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
Lactobacillales (order) | 227 | 344 | 385 | 318 | 744 | 654 | 683 | 479 | 0.11 |
Streptococcus | 19 | 30 | 30 | 12 | 149 | 100 | 193 | 76 | 0.02 |
S. agalactiae | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0.00 |
S. pyogenes | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
S. mitis | 0 | 2 | 0 | 0 | 2 | 0 | 0 | 1 | 0.00 |
S. pneumoniae | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0.00 |
S. infantarius | 0 | 0 | 0 | 0 | 2 | 1 | 5 | 1 | 0.00 |
Vibrionales (order) | 5 | 11 | 12 | 3 | 11 | 14 | 11 | 10 | 0.00 |
Vibrio | 1 | 3 | 2 | 0 | 2 | 4 | 15 | 3 | 0.00 |
V. cholerae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |
V. fischeri | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.00 |