Table 2 Median read numbers and relative abundance (%) of the total read numbers of the most common bacterial genera for different sample groups in datasets 1 and 2: samples PCR positive for Staph. aureus and NAS/C. bovis, Strep. uberis, minor pathogens (= NAS and C. bovis), NAS only, C. bovis only, and samples from healthy quarters (PCR negative and NAGase value < 1)
From: Bovine milk microbiome: a more complex issue than expected
Genus | Dataset 1, groups by PCR result | Dataset 2, groups by PCR result | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 Staph. aureus Read no/% | 1 Strep. uberis Read no/% | 7 Minor Read no/% | 4 NAS Read no/% | 1 C. bovis Read no/% | 4 Neg. NAG < 1 Read no/% | 1 Staph. aureus Read no/% | 1 Strep. uberis Read no/% | 14 Minor Read no/% | 6 NAS Read no/% | 3 C. bovis Read no/% | 2 Neg. NAG < 1 Read no/% | |
Alicyclobacillus | 97/0.05 | 3/0.00 | 173/0.11 | 68/0.05 | 1434/0.87 | 2328/2.48 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 |
Alkaliphilus | 28/0.02 | 74/0.04 | 1155/0.70 | 391/0.30 | 2334/1.42 | 1691/1.80 | 163/0.04 | 43/0.44 | 201/0.23 | 251/0.37 | 334/0.12 | 160/0.06 |
Bacteroides | 122/0.07 | 318/0.17 | 1526/0.93 | 2053/1.55 | 757/0.46 | 2683/2.86 | 9/0.00 | 77/0.79 | 140/0.16 | 31/0.05 | 696/0.26 | 216/0.08 |
Blautia | 331/0.18 | 554/0.30 | 2809/1.71 | 3495/2.64 | 1023/0.62 | 4461/4.76 | 19/0.00 | 386/3.96 | 634/0.71 | 707/1.03 | 870/0.32 | 1034/0.39 |
Bradyrhizobium | 212/0.12 | 19/0.01 | 706/0.43 | 71/0.05 | 1996/1.22 | 2821/3.01 | 0/0 | 10/0.10 | 6/0.01 | 9/0.01 | 7/0.00 | 13/0.00 |
Clostridium | 208/0.12 | 295/0.16 | 1469/0.89 | 1594/1.20 | 1371/0.83 | 2039/2.18 | 259/0.07 | 6/0.06 | 318/0.36 | 309/0.45 | 801/0.30 | 496/0.19 |
Corynebacterium | 25/0.01 | 142/0.08 | 3383/2.06 | 173/0.13 | 86 420/52.63 | 1081/1.15 | 8154/2.11 | 261/2.68 | 2705/3.04 | 2493/3.65 | 83 936/31.10 | 1406/0.54 |
Fibrobacter | 62/0.03 | 301/0.16 | 941/0.57 | 1418/1.07 | 422/0.26 | 1352/1.44 | 0/0 | 2/0.02 | 0/0 | 0/0 | 17/0.01 | 32/0.01 |
C. Methylacidiphilum | 158/0.09 | 221/0.12 | 818/0.50 | 1737/1.31 | 430/0.26 | 1204/1.28 | 0/0 | 0/0 | 0/0 | 0/0 | 42/0.02 | 124/0.05 |
Methylobacterium | 18/0.01 | 13/0.01 | 104/0.06 | 35/0.03 | 686/0.42 | 502/0.54 | 2472/0.64 | 5840/59.92 | 43 264/48.57 | 46 816/68.48 | 124 470/46.12 | 245 445/93.49 |
Oscillospira | 82/0.05 | 157/0.08 | 644/0.39 | 678/0.51 | 497/0.30 | 1163/1.24 | 10/0.00 | 0/0 | 122/0.14 | 91/0.13 | 214/0.08 | 386/0.15 |
Paraprevotella | 83/0.05 | 147/0.08 | 521/0.32 | 1061/0.80 | 212/0.13 | 857/0.91 | 0/0 | 0/0 | 1/0.00 | 0/0 | 231/0.09 | 54/0.02 |
Pedobacter | 73/0.04 | 101/0.05 | 633/0.39 | 869/0.66 | 290/0.18 | 1045/1.12 | 2/0.00 | 3/0.03 | 34/0.04 | 9/0.01 | 300/0.11 | 148/0.06 |
Prevotella | 102/0.06 | 245/0.13 | 415/0.25 | 1368/1.03 | 366/0.22 | 1156/1.23 | 1/0.00 | 0/0 | 25/0.03 | 13/0.02 | 0/0 | 71/0.03 |
Ruminococcus | 59/0.03 | 117/0.06 | 907/0.55 | 939/0.71 | 488/0.30 | 1678/1.79 | 43/0.01 | 58/0.60 | 295/0.33 | 165/0.24 | 1299/0.48 | 626/0.24 |
Sphingobacterium | 195/0.12 | 519/0.28 | 2529/1.54 | 3123/2.36 | 932/0.57 | 3233/3.45 | 0/0 | 1/0.01 | 30/0.03 | 2/0.00 | 169/0.06 | 54/0.02 |
Staphylococcus | 175 062/97.3 | 378/0.20 | 9225/5.62 | 14 278/10.79 | 1311/0.80 | 869/0.93 | 370 539/95.88 | 12/0.12 | 664/0.75 | 785/1.15 | 233/0.09 | 397/0.15 |
Streptococcus | 353/0.20 | 179 331/96.1 | 2143/1.31 | 1510/1.14 | 38 249/23.29 | 3835/4.09 | 645/0.17 | 1037/10.64 | 3/0.00 | 1/0.00 | 91/0.03 | 68/0.03 |
Treponema | 234/0.13 | 415/0.22 | 2017/1.23 | 2825/2.13 | 674/0.41 | 1701/1.82 | 11/0.00 | 0/0 | 0/0 | 1/0.00 | 72/0.03 | 1/0.00 |
Reads total | 179 938 | 186 696 | 164 205 | 132 326 | 164 205 | 93 700 | 386 450 | 9746 | 89 072 | 68 364 | 269 890 | 262 526 |