Table 1.
Predicted tetracycline resistance genes
|
Dataset |
Size (nt) |
Efflux |
Ribosomal protection |
Enzymatic |
|||
|---|---|---|---|---|---|---|---|
|
Genes* |
Families (new/total)† |
Genes* |
Families (new/total)† |
Genes* |
Families (new/total)† |
||
|
Genomic | |||||||
|
NCBI RefSeq [77] |
2.78×1010 |
137 |
16/29 |
232 |
51/57 |
20 |
9/11 |
|
NCBI plasmids [77] |
1.07×109 |
54 |
2/13 |
35 |
3/7 |
3 |
0/1 |
|
NCBI nt [19] |
1.66×1011 |
289 |
30/45 |
563 |
77/87 |
76 |
14/20 |
|
NCBI environmental [19] |
1.09×1011 |
23 |
7/15 |
317 |
17/23 |
17 |
3/6 |
|
HMP genomic [41] |
6.83×109 |
20 |
2/8 |
105 |
7/12 |
4 |
1/3 |
|
Metagenomic | |||||||
|
Human gut [47] |
2.80×1011 |
3 |
0/2 |
13 |
0/5 |
2 |
0/2 |
|
HMP metagenome [45] |
3.51×1012 |
3 |
0/3 |
10 |
3/5 |
2 |
0/2 |
|
Pig gut [44] |
1.74×1012 |
9 |
0/7 |
13 |
6/10 |
1 |
0/1 |
|
WWTPs [42] |
4.82×1011 |
11 |
4/8 |
14 |
5/12 |
3 |
2/3 |
|
Pune river [43] |
3.93×1011 |
5 |
1/5 |
19 |
8/13 |
1 |
0/1 |
|
Polluted lake [50] |
6.76×109 |
0 |
0 |
0 |
0 |
0 |
0 |
|
Polluted river [46] |
2.86×1010 |
3 |
0/2 |
2 |
1/2 |
1 |
0/1 |
|
Oil spill [49] |
3.39×1011 |
0 |
0 |
0 |
0 |
0 |
0 |
|
Tara Ocean [48] |
4.89×1012 |
4 |
2/3 |
0 |
0 |
4 |
2/3 |
|
Well water [51] |
7.62×1010 |
0 |
0 |
0 |
0 |
0 |
0 |
|
Soil [51] |
5.05×1010 |
0 |
0 |
0 |
0 |
0 |
0 |
|
Total‡ |
1.21×1013 |
331 |
38/53 |
927 |
106/116 |
96 |
20/26 |
*Non-redundant genes.
†Amino acid sequence identity cut-off of 70 %.
‡Non redundant genes/gene families.